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.SubtreeCloneConfigurator;
  38 import eu.etaxonomy.cdm.api.service.config.TaxonDeletionConfigurator;
  39 import eu.etaxonomy.cdm.api.service.dto.EntityDTO;
  40 import eu.etaxonomy.cdm.api.service.dto.GroupedTaxonDTO;
  41 import eu.etaxonomy.cdm.api.service.dto.MarkedEntityDTO;
  42 import eu.etaxonomy.cdm.api.service.dto.TaxonInContextDTO;
  43 import eu.etaxonomy.cdm.api.service.pager.Pager;
  44 import eu.etaxonomy.cdm.api.service.pager.PagerUtils;
  45 import eu.etaxonomy.cdm.api.service.pager.impl.AbstractPagerImpl;
  46 import eu.etaxonomy.cdm.api.service.pager.impl.DefaultPagerImpl;
  47 import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
  48 import eu.etaxonomy.cdm.exception.FilterException;
  49 import eu.etaxonomy.cdm.exception.UnpublishedException;
  50 import eu.etaxonomy.cdm.hibernate.HHH_9751_Util;
  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.reference.Reference;
  64 import eu.etaxonomy.cdm.model.taxon.Classification;
  65 import eu.etaxonomy.cdm.model.taxon.ITaxonNodeComparator;
  66 import eu.etaxonomy.cdm.model.taxon.ITaxonTreeNode;
  67 import eu.etaxonomy.cdm.model.taxon.Synonym;
  68 import eu.etaxonomy.cdm.model.taxon.Taxon;
  69 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  70 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
  71 import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
  72 import eu.etaxonomy.cdm.model.term.DefinedTermBase;
  73 import eu.etaxonomy.cdm.persistence.dao.initializer.IBeanInitializer;
  74 import eu.etaxonomy.cdm.persistence.dao.reference.IReferenceDao;
  75 import eu.etaxonomy.cdm.persistence.dao.taxon.IClassificationDao;
  76 import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao;
  77 import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonNodeDao;
  78 import eu.etaxonomy.cdm.persistence.dao.term.IDefinedTermDao;
  79 import eu.etaxonomy.cdm.persistence.dto.ClassificationLookupDTO;
  80 import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDto;
  81 import eu.etaxonomy.cdm.persistence.dto.TaxonStatus;
  82 import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
  83 import eu.etaxonomy.cdm.persistence.query.OrderHint;
  84 import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
  85 import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
  86
  87 /**
  88  * @author n.hoffmann
  89  * @since Sep 21, 2009
  90  */
  91 @Service
  92 @Transactional(readOnly = true)
  93 public class ClassificationServiceImpl
  94              extends IdentifiableServiceBase<Classification, IClassificationDao>
  95              implements IClassificationService {
  96
  97     private static final Logger logger = Logger.getLogger(ClassificationServiceImpl.class);
  98
  99     @Autowired
 100     private ITaxonNodeDao taxonNodeDao;
 101
 102     @Autowired
 103     private ITaxonDao taxonDao;
 104
 105     @Autowired
 106     private ITaxonNodeService taxonNodeService;
 107
 108     @Autowired
 109     private IReferenceDao referenceDao;
 110
 111     @Autowired
 112     private IDefinedTermDao termDao;
 113
 114     @Autowired
 115     private IBeanInitializer defaultBeanInitializer;
 116
 117     @Override
 118     @Autowired
 119     protected void setDao(IClassificationDao dao) {
 120         this.dao = dao;
 121     }
 122
 123     private Comparator<? super TaxonNode> taxonNodeComparator;
 124
 125     @Autowired
 126     public void setTaxonNodeComparator(ITaxonNodeComparator<? super TaxonNode> taxonNodeComparator){
 127         this.taxonNodeComparator = (Comparator<? super TaxonNode>) taxonNodeComparator;
 128     }
 129
 130     @Override
 131     public TaxonNode loadTaxonNodeByTaxon(Taxon taxon, UUID classificationUuid, List<String> propertyPaths){
 132         Classification tree = dao.load(classificationUuid);
 133         TaxonNode node = tree.getNode(taxon);
 134
 135         return loadTaxonNode(node.getUuid(), propertyPaths);
 136     }
 137
 138     public TaxonNode loadTaxonNode(UUID taxonNodeUuid, List<String> propertyPaths){
 139         return taxonNodeDao.load(taxonNodeUuid, propertyPaths);
 140     }
 141
 142     @Override
 143     @Transactional(readOnly = false)
 144     public UpdateResult cloneClassification(SubtreeCloneConfigurator config) {
 145         UpdateResult result = new UpdateResult();
 146
 147         if (config.getSubTreeUuids().isEmpty()){
 148             return result;
 149         }
 150
 151         //TODO error handling
 152         Reference taxonSecundum = config.isReuseTaxa() || config.isReuseTaxonSecundum() || config.getTaxonSecundumUuid() == null ?
 153                 null : referenceDao.findByUuid(config.getTaxonSecundumUuid());
 154         config.setTaxonSecundum(taxonSecundum);
 155
 156         Reference parentChildReference = config.isReuseParentChildReference() || config.getParentChildReferenceUuid() == null ?
 157                 null : referenceDao.findByUuid(config.getParentChildReferenceUuid());
 158         config.setParentChildReference(parentChildReference);
 159
 160         Reference taxonRelationshipReference = config.getRelationTypeToOldTaxon() == null ?
 161                 null : referenceDao.findByUuid(config.getRelationshipReferenceUuid());
 162         config.setRelationshipReference(taxonRelationshipReference);
 163
 164         Classification classificationClone = Classification.NewInstance(config.getClassificationName());
 165
 166         if (config.isReuseClassificationReference()){
 167             TaxonNode anyNode = taxonNodeDao.findByUuid(config.getSubTreeUuids().iterator().next());
 168             if (anyNode != null){
 169                 Reference oldClassificationRef = anyNode.getClassification().getReference();
 170                 classificationClone.setReference(oldClassificationRef);
 171             }
 172         }else if (config.getClassificationReferenceUuid() != null) {
 173             Reference classificationReference = referenceDao.findByUuid(config.getClassificationReferenceUuid());
 174             classificationClone.setReference(classificationReference);
 175         }
 176
 177         //clone taxa and taxon nodes
 178 //      List<Integer> childNodeIds = taxonNodeService.idList(taxonNodeFilter);
 179 //      List<TaxonNode> childNodes = taxonNodeService.loadByIds(childNodeIds, null);
 180         List<TaxonNode> rootNodes = taxonNodeService.find(config.getSubTreeUuids());
 181         for (TaxonNode taxonNode : rootNodes) {
 182             addChildTaxaToClone(taxonNode, classificationClone.getRootNode(), config);
 183         }
 184         dao.saveOrUpdate(classificationClone);
 185         result.setCdmEntity(classificationClone);
 186         return result;
 187     }
 188
 189     private void addChildTaxaToClone(TaxonNode originalParentNode, TaxonNode parentNodeClone,
 190             SubtreeCloneConfigurator config){
 191
 192         Taxon originalTaxon = CdmBase.deproxy(originalParentNode.getTaxon());
 193         if (originalTaxon == null){
 194             for (TaxonNode originalChildChildNode : originalParentNode.getChildNodes()) {
 195                 addChildTaxaToClone(originalChildChildNode, parentNodeClone, config);
 196             }
 197         }else{
 198             TaxonNode childNodeClone;
 199             String microReference = null;
 200             if (config.isReuseTaxa()){
 201                 childNodeClone = parentNodeClone.addChildTaxon(originalTaxon, config.getParentChildReference(), microReference);
 202             }else{
 203                 Taxon cloneTaxon = originalTaxon.clone(config.isCloneSynonyms(), config.isCloneTaxonRelationships(),
 204                         config.isCloneDescriptiveData(), config.isCloneMedia());
 205 //                xxx KonzeptClone MAN, ppSyns;
 206                 if (!config.isReuseTaxonSecundum()){
 207                     cloneTaxon.setSec(config.getTaxonSecundum());
 208                 }
 209
 210                 //add relation between taxa
 211                 if (config.getRelationTypeToOldTaxon() != null){
 212                     TaxonRelationship rel = cloneTaxon.addTaxonRelation(originalParentNode.getTaxon(), config.getRelationTypeToOldTaxon(),
 213                             config.getRelationshipReference(), microReference);
 214                     rel.setDoubtful(config.isRelationDoubtful());
 215                 }
 216                 childNodeClone = parentNodeClone.addChildTaxon(cloneTaxon, config.getParentChildReference(), microReference);
 217             }
 218
 219             //TODO necessary?
 220             taxonNodeDao.saveOrUpdate(childNodeClone);
 221             //add children
 222             List<TaxonNode> originalChildNodes = originalParentNode.getChildNodes();
 223             HHH_9751_Util.removeAllNull(originalChildNodes);
 224
 225             for (TaxonNode originalChildNode : originalChildNodes) {
 226                 addChildTaxaToClone(originalChildNode, childNodeClone, config);
 227             }
 228         }
 229     }
 230
 231     @Override
 232     public List<TaxonNode> listRankSpecificRootNodes(Classification classification,
 233             TaxonNode subtree, Rank rank,
 234             boolean includeUnpublished, Integer pageSize, Integer pageIndex, List<String> propertyPaths) {
 235         return pageRankSpecificRootNodes(classification, subtree, rank, includeUnpublished, pageSize, pageIndex, propertyPaths).getRecords();
 236     }
 237
 238     @Override
 239     public List<TaxonNodeDto> listRankSpecificRootNodeDtos(Classification classification, TaxonNode subtree,
 240             Rank rank, boolean includeUnpublished, Integer pageSize, Integer pageIndex, TaxonNodeDtoSortMode sortMode,
 241             List<String> propertyPaths) {
 242         List<TaxonNode> list = listRankSpecificRootNodes(classification, subtree, rank, includeUnpublished, pageSize, pageIndex, propertyPaths);
 243         return list.stream().filter(e ->  e != null).map(e -> new TaxonNodeDto(e)).sorted(sortMode.newComparator()).collect(Collectors.toList());
 244     }
 245
 246     @Override
 247     public Pager<TaxonNode> pageRankSpecificRootNodes(Classification classification, Rank rank,
 248             boolean includeUnpublished, Integer pageSize, Integer pageIndex, List<String> propertyPaths) {
 249         return pageRankSpecificRootNodes(classification, null, rank, includeUnpublished, pageSize, pageIndex, propertyPaths);
 250     }
 251
 252     @Override
 253     public Pager<TaxonNode> pageRankSpecificRootNodes(Classification classification, TaxonNode subtree, Rank rank,
 254             boolean includeUnpublished, Integer pageSize, Integer pageIndex, List<String> propertyPaths) {
 255         long[] numberOfResults = dao.countRankSpecificRootNodes(classification, subtree, includeUnpublished, rank);
 256         long totalNumberOfResults = numberOfResults[0] + (numberOfResults.length > 1 ? numberOfResults[1] : 0);
 257
 258         List<TaxonNode> results = new ArrayList<>();
 259
 260         if (AbstractPagerImpl.hasResultsInRange(totalNumberOfResults, pageIndex, pageSize)) { // no point checking again
 261             Integer limit = PagerUtils.limitFor(pageSize);
 262             Integer start = PagerUtils.startFor(pageSize, pageIndex);
 263
 264             Integer remainingLimit = limit;
 265             int[] queryIndexes = rank == null ? new int[]{0} : new int[]{0,1};
 266
 267             for(int queryIndex: queryIndexes) {
 268                 if(start != null && start > numberOfResults[queryIndex]) {
 269                     // start in next query with new start value
 270                     start = start - (int)numberOfResults[queryIndex];
 271                     continue;
 272                 }
 273
 274                 List<TaxonNode> perQueryResults = dao.listRankSpecificRootNodes(classification,
 275                         subtree, rank, includeUnpublished, remainingLimit,
 276                         start, propertyPaths, queryIndex);
 277                 results.addAll(perQueryResults);
 278                 if(remainingLimit != null ){
 279                     remainingLimit = remainingLimit - results.size();
 280                     if(remainingLimit <= 0) {
 281                         // no need to run further queries if first query returned enough items!
 282                         break;
 283                     }
 284                     // start at with fist item of next query to fetch the remaining items
 285                     start = 0;
 286                 }
 287             }
 288         }
 289 //        long start_t = System.currentTimeMillis();
 290         Collections.sort(results, taxonNodeComparator); // TODO is ordering during the hibernate query in the dao possible?
 291 //        System.err.println("service.pageRankSpecificRootNodes() - Collections.sort(results,  taxonNodeComparator) " + (System.currentTimeMillis() - start_t));
 292         return new DefaultPagerImpl<>(pageIndex, totalNumberOfResults, pageSize, results);
 293
 294     }
 295
 296     @Override
 297     public List<TaxonNode> loadTreeBranch(TaxonNode taxonNode, Rank baseRank,
 298             boolean includeUnpublished, List<String> propertyPaths) throws UnpublishedException{
 299         return loadTreeBranch(taxonNode, null, baseRank, includeUnpublished, propertyPaths);
 300     }
 301
 302     @Override
 303     public List<TaxonNode> loadTreeBranch(TaxonNode taxonNode, TaxonNode subtree, Rank baseRank,
 304             boolean includeUnpublished, List<String> propertyPaths) throws UnpublishedException{
 305
 306         TaxonNode thisNode = taxonNodeDao.load(taxonNode.getUuid(), propertyPaths);
 307         if(baseRank != null){
 308             baseRank = (Rank) termDao.load(baseRank.getUuid());
 309         }
 310         if (!includeUnpublished && thisNode.getTaxon() != null && !thisNode.getTaxon().isPublish()){
 311             throw new UnpublishedException("Final taxon in tree branch is unpublished.");
 312         }
 313
 314         List<TaxonNode> pathToRoot = new ArrayList<>();
 315         pathToRoot.add(thisNode);
 316
 317         while(!thisNode.isTopmostNode()){
 318             //TODO why do we need to deproxy here?
 319             //     without this thisNode.getParent() will return NULL in
 320             //     some cases (environment dependend?) even if the parent exits
 321             TaxonNode parentNode = CdmBase.deproxy(thisNode).getParent();
 322
 323             if(parentNode == null){
 324                 throw new NullPointerException("Taxon node " + thisNode + " must have a parent since it is not top most");
 325             }
 326             if(parentNode.getTaxon() == null){
 327                 throw new NullPointerException("The taxon associated with taxon node " + parentNode + " is NULL");
 328             }
 329             if(!includeUnpublished && !parentNode.getTaxon().isPublish()){
 330                 throw new UnpublishedException("Some taxon in tree branch is unpublished.");
 331             }
 332             if(parentNode.getTaxon().getName() == null){
 333                 throw new NullPointerException("The name of the taxon associated with taxonNode " + parentNode + " is NULL");
 334             }
 335
 336             Rank parentNodeRank = (parentNode.getTaxon().getName() == null) ? null : parentNode.getTaxon().getName().getRank();
 337             // stop if the next parent is higher than the baseRank
 338             if(baseRank != null && parentNodeRank != null && baseRank.isLower(parentNodeRank)){
 339                 break;
 340             }
 341             if((subtree!= null && !subtree.isAncestor(parentNode) )){
 342                 break;
 343             }
 344
 345             pathToRoot.add(parentNode);
 346             thisNode = parentNode;
 347         }
 348
 349         // initialize and invert order of nodes in list
 350         defaultBeanInitializer.initializeAll(pathToRoot, propertyPaths);
 351         Collections.reverse(pathToRoot);
 352
 353         return pathToRoot;
 354     }
 355
 356     @Override
 357     public List<TaxonNode> loadTreeBranchToTaxon(Taxon taxon, Classification classification, Rank baseRank,
 358             boolean includeUnpublished, List<String> propertyPaths) throws UnpublishedException{
 359         return loadTreeBranchToTaxon(taxon, classification, null, baseRank, includeUnpublished, propertyPaths);
 360     }
 361
 362     @Override
 363     public List<TaxonNodeDto> loadTreeBranchDTOsToTaxon(Taxon taxon, Classification classification,
 364             TaxonNode subtree, Rank baseRank,
 365             boolean includeUnpublished, List<String> propertyPaths) throws UnpublishedException {
 366         List<TaxonNode> list = loadTreeBranchToTaxon(taxon, classification, subtree, baseRank, includeUnpublished, propertyPaths);
 367         return list.stream().map(e -> new TaxonNodeDto(e)).collect(Collectors.toList());
 368     }
 369
 370     @Override
 371     public List<TaxonNode> loadTreeBranchToTaxon(Taxon taxon, Classification classification,
 372             TaxonNode subtree, Rank baseRank,
 373             boolean includeUnpublished, List<String> propertyPaths) throws UnpublishedException{
 374
 375         UUID nodeUuid = getTaxonNodeUuidByTaxonUuid(classification.getUuid(), taxon.getUuid());
 376         TaxonNode node = taxonNodeService.find(nodeUuid);
 377         if(node == null){
 378             logger.warn("The specified taxon is not found in the given tree.");
 379             return null;
 380         }else if (subtree != null && !node.isDescendant(subtree)){
 381             //TODO handle as exception? E.g. FilterException, AccessDeniedException?
 382             logger.warn("The specified taxon is not found for the given subtree.");
 383             return null;
 384         }
 385
 386         return loadTreeBranch(node, subtree, baseRank, includeUnpublished, propertyPaths);
 387     }
 388
 389
 390     @Override
 391     public List<TaxonNode> loadChildNodesOfTaxonNode(TaxonNode taxonNode,
 392             List<String> propertyPaths) {
 393         taxonNode = taxonNodeDao.load(taxonNode.getUuid());
 394         List<TaxonNode> childNodes = new ArrayList<TaxonNode>(taxonNode.getChildNodes());
 395         defaultBeanInitializer.initializeAll(childNodes, propertyPaths);
 396         Collections.sort(childNodes, taxonNodeComparator);
 397         return childNodes;
 398     }
 399
 400     @Override
 401     public List<TaxonNode> listChildNodesOfTaxon(UUID taxonUuid, UUID classificationUuid,
 402             boolean includeUnpublished, Integer pageSize, Integer pageIndex, List<String> propertyPaths){
 403         try {
 404             return listChildNodesOfTaxon(taxonUuid, classificationUuid, null, includeUnpublished, pageSize, pageIndex, propertyPaths);
 405         } catch (FilterException e) {
 406             throw new RuntimeException(e);  //this should not happen as filter is null
 407         }
 408     }
 409
 410     @Override
 411     public List<TaxonNode> listChildNodesOfTaxon(UUID taxonUuid, UUID classificationUuid, UUID subtreeUuid,
 412             boolean includeUnpublished, Integer pageSize, Integer pageIndex, List<String> propertyPaths) throws FilterException{
 413
 414         Classification classification = dao.load(classificationUuid);
 415         Taxon taxon = (Taxon) taxonDao.load(taxonUuid);
 416         TaxonNode subtree = taxonNodeDao.load(subtreeUuid);
 417         if (subtreeUuid != null && subtree == null){
 418             throw new FilterException("Taxon node for subtree filter can not be found in database", true);
 419         }
 420
 421         List<TaxonNode> results = dao.listChildrenOf(
 422                 taxon, classification, subtree, includeUnpublished, pageSize, pageIndex, propertyPaths);
 423         Collections.sort(results, taxonNodeComparator); // FIXME this is only a HACK, order during the hibernate query in the dao
 424         return results;
 425     }
 426
 427     @Override
 428     public List<TaxonNodeDto> listChildNodeDtosOfTaxon(UUID taxonUuid, UUID classificationUuid, UUID subtreeUuid, boolean includeUnpublished,
 429             Integer pageSize, Integer pageIndex, TaxonNodeDtoSortMode sortMode, List<String> propertyPaths) throws FilterException{
 430         Classification classification = dao.load(classificationUuid);
 431         Taxon taxon = (Taxon) taxonDao.load(taxonUuid);
 432         TaxonNode subtree = taxonNodeDao.load(subtreeUuid);
 433         if (subtreeUuid != null && subtree == null){
 434             throw new FilterException("Taxon node for subtree filter can not be found in database", true);
 435         }
 436
 437         List<TaxonNode> results = dao.listChildrenOf(
 438                 taxon, classification, subtree, includeUnpublished, pageSize, pageIndex, propertyPaths);
 439         Comparator<TaxonNodeDto> comparator = sortMode.newComparator();
 440         // TODO order during the hibernate query in the dao?
 441         List<TaxonNodeDto> dtos = results.stream().map(e -> new TaxonNodeDto(e)).sorted(comparator).collect(Collectors.toList());
 442         return dtos;
 443     }
 444
 445     @Override
 446     public Pager<TaxonNode> pageSiblingsOfTaxon(UUID taxonUuid, UUID classificationUuid, boolean includeUnpublished,
 447             Integer pageSize, Integer pageIndex, List<String> propertyPaths){
 448
 449         Classification classification = dao.load(classificationUuid);
 450         Taxon taxon = (Taxon) taxonDao.load(taxonUuid);
 451
 452         long numberOfResults = dao.countSiblingsOf(taxon, classification, includeUnpublished);
 453
 454         List<TaxonNode> results;
 455         if(PagerUtils.hasResultsInRange(numberOfResults, pageIndex, pageSize)) {
 456             results = dao.listSiblingsOf(taxon, classification, includeUnpublished, pageSize, pageIndex, propertyPaths);
 457             Collections.sort(results, taxonNodeComparator); // FIXME this is only a HACK, order during the hibernate query in the dao
 458         } else {
 459             results = new ArrayList<>();
 460         }
 461
 462         return new DefaultPagerImpl<>(pageIndex, numberOfResults, pageSize, results);
 463     }
 464
 465     @Override
 466     public List<TaxonNode> listSiblingsOfTaxon(UUID taxonUuid, UUID classificationUuid, boolean includeUnpublished,
 467             Integer pageSize, Integer pageIndex, List<String> propertyPaths){
 468
 469         Pager<TaxonNode> pager = pageSiblingsOfTaxon(taxonUuid, classificationUuid, includeUnpublished, pageSize, pageIndex, propertyPaths);
 470         return pager.getRecords();
 471     }
 472
 473     @Override
 474     public ITaxonTreeNode getTreeNodeByUuid(UUID uuid){
 475         ITaxonTreeNode treeNode = taxonNodeDao.findByUuid(uuid);
 476         if(treeNode == null){
 477             treeNode = dao.findByUuid(uuid);
 478         }
 479
 480         return treeNode;
 481     }
 482
 483     @Override
 484     public TaxonNode getRootNode(UUID classificationUuid){
 485         return dao.getRootNode(classificationUuid);
 486     }
 487
 488     @Override
 489     public List<Classification> listClassifications(Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
 490         return dao.list(limit, start, orderHints, propertyPaths);
 491     }
 492
 493     @Override
 494     public UUID removeTaxonNode(TaxonNode taxonNode) {
 495         return taxonNodeDao.delete(taxonNode);
 496     }
 497     @Override
 498     public UUID removeTreeNode(ITaxonTreeNode treeNode) {
 499         if(treeNode instanceof Classification){
 500             return dao.delete((Classification) treeNode);
 501         }else if(treeNode instanceof TaxonNode){
 502             return taxonNodeDao.delete((TaxonNode)treeNode);
 503         }
 504         return null;
 505     }
 506     @Override
 507     public UUID saveTaxonNode(TaxonNode taxonNode) {
 508         return taxonNodeDao.save(taxonNode).getUuid();
 509     }
 510
 511     @Override
 512     public Map<UUID, TaxonNode> saveTaxonNodeAll(
 513             Collection<TaxonNode> taxonNodeCollection) {
 514         return taxonNodeDao.saveAll(taxonNodeCollection);
 515     }
 516
 517     @Override
 518     public UUID saveClassification(Classification classification) {
 519
 520        taxonNodeDao.saveOrUpdateAll(classification.getAllNodes());
 521        UUID result =dao.saveOrUpdate(classification);
 522        return result;
 523     }
 524
 525     @Override
 526     public UUID saveTreeNode(ITaxonTreeNode treeNode) {
 527         if(treeNode instanceof Classification){
 528             return dao.save((Classification) treeNode).getUuid();
 529         }else if(treeNode instanceof TaxonNode){
 530             return taxonNodeDao.save((TaxonNode)treeNode).getUuid();
 531         }
 532         return null;
 533     }
 534
 535     @Override
 536     public List<TaxonNode> getAllNodes(){
 537         return taxonNodeDao.list(null,null);
 538     }
 539
 540     @Override
 541     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(UUID classificationUuid, Integer limit, String pattern, boolean searchForClassifications, boolean includeDoubtful) {
 542         return taxonNodeDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(dao.load(classificationUuid),  limit, pattern, searchForClassifications, includeDoubtful);
 543     }
 544
 545     @Override
 546     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification,  Integer limit, String pattern, boolean searchForClassifications) {
 547         return taxonNodeDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification,  limit, pattern, searchForClassifications);
 548     }
 549
 550     @Override
 551     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(UUID classificationUuid, boolean searchForClassifications ) {
 552         return taxonNodeDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(dao.load(classificationUuid), null, null, searchForClassifications);
 553     }
 554
 555     @Override
 556     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification, boolean searchForClassifications ) {
 557         return taxonNodeDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification, null, null, searchForClassifications);
 558     }
 559
 560     @Override
 561     public List<UuidAndTitleCache<Classification>> getUuidAndTitleCache(Integer limit, String pattern) {
 562         return dao.getUuidAndTitleCache(limit, pattern);
 563     }
 564
 565     @Override
 566     public Map<UUID, List<MediaRepresentation>> getAllMediaForChildNodes(
 567             TaxonNode taxonNode, List<String> propertyPaths, int size,
 568             int height, int widthOrDuration, String[] mimeTypes) {
 569
 570         TreeMap<UUID, List<MediaRepresentation>> result = new TreeMap<>();
 571         List<MediaRepresentation> mediaRepresentations = new ArrayList<>();
 572
 573         //add all media of the children to the result map
 574         if (taxonNode != null){
 575
 576             List<TaxonNode> nodes = new ArrayList<>();
 577
 578             nodes.add(loadTaxonNode(taxonNode.getUuid(), propertyPaths));
 579             nodes.addAll(loadChildNodesOfTaxonNode(taxonNode, propertyPaths));
 580
 581             for(TaxonNode node : nodes){
 582                 Taxon taxon = node.getTaxon();
 583                 for (TaxonDescription taxonDescription: taxon.getDescriptions()){
 584                     for (DescriptionElementBase descriptionElement: taxonDescription.getElements()){
 585                         for(Media media : descriptionElement.getMedia()){
 586                             //find the best matching representation
 587                             mediaRepresentations.add(MediaUtils.findBestMatchingRepresentation(media,null, size, height, widthOrDuration, mimeTypes, MediaUtils.MissingValueStrategy.MAX));
 588                         }
 589                     }
 590                 }
 591                 result.put(taxon.getUuid(), mediaRepresentations);
 592             }
 593         }
 594
 595         return result;
 596     }
 597
 598     @Override
 599     @Transactional(readOnly = false)
 600     public UpdateResult updateCaches(Class<? extends Classification> clazz, Integer stepSize, IIdentifiableEntityCacheStrategy<Classification> cacheStrategy, IProgressMonitor monitor) {
 601         if (clazz == null){
 602             clazz = Classification.class;
 603         }
 604         return super.updateCachesImpl(clazz, stepSize, cacheStrategy, monitor);
 605     }
 606
 607     /**
 608      *
 609      * @param allNodesOfClassification
 610      * @return null - if  allNodesOfClassification is empty <br>
 611      */
 612
 613     private Map<String, List<TaxonNode>> getSortedGenusList(Collection<TaxonNode> allNodesOfClassification){
 614
 615         if(allNodesOfClassification == null || allNodesOfClassification.isEmpty()){
 616                 return null;
 617         }
 618         Map<String, List<TaxonNode>> sortedGenusMap = new HashMap<>();
 619         for(TaxonNode node:allNodesOfClassification){
 620                 Taxon taxon = node.getTaxon();
 621                 INonViralName name = taxon.getName();
 622                 String genusOrUninomial = name.getGenusOrUninomial();
 623                 //if rank unknown split string and take first word
 624                 if(genusOrUninomial == null){
 625                         String titleCache = taxon.getTitleCache();
 626                         String[] split = titleCache.split("\\s+");
 627                         for(String s:split){
 628                                 genusOrUninomial = s;
 629                                 break;
 630                         }
 631                 }
 632                 //if node has children
 633
 634                 //retrieve list from map if not create List
 635                 if(sortedGenusMap.containsKey(genusOrUninomial)){
 636                         List<TaxonNode> list = sortedGenusMap.get(genusOrUninomial);
 637                         list.add(node);
 638                         sortedGenusMap.put(genusOrUninomial, list);
 639                 }else{
 640                         //create List for genus
 641                         List<TaxonNode> list = new ArrayList<>();
 642                         list.add(node);
 643                         sortedGenusMap.put(genusOrUninomial, list);
 644                 }
 645         }
 646         return sortedGenusMap;
 647     }
 648
 649     /**
 650      *
 651      * creates new Classification and parent TaxonNodes at genus level
 652      *
 653      *
 654      * @param map GenusMap which holds a name (Genus) and all the same Taxa as a list
 655      * @param classification you want to improve the hierarchy (will not be modified)
 656      * @param configurator to change certain settings, if null then standard settings will be taken
 657      * @return new classification with parentNodes for each entry in the map
 658      */
 659     @SuppressWarnings({ "unchecked" })
 660         @Transactional(readOnly = false)
 661         @Override
 662     public UpdateResult createHierarchyInClassification(Classification classification, CreateHierarchyForClassificationConfigurator configurator){
 663         UpdateResult result = new UpdateResult();
 664         classification = dao.findByUuid(classification.getUuid());
 665         Map<String, List<TaxonNode>> map = getSortedGenusList(classification.getAllNodes());
 666
 667         final String APPENDIX = "repaired";
 668         String titleCache = StringUtils.isBlank(classification.getTitleCache()) ? " " : classification.getTitleCache() ;
 669         //TODO classification clone???
 670         Classification newClassification = Classification.NewInstance(titleCache +" "+ APPENDIX);
 671         newClassification.setReference(classification.getReference());
 672
 673         for(Map.Entry<String, List<TaxonNode>> entry:map.entrySet()){
 674                 String genus = entry.getKey();
 675                 List<TaxonNode> listOfTaxonNodes = entry.getValue();
 676                 TaxonNode parentNode = null;
 677                 //Search for genus in list
 678                 for(TaxonNode tNode:listOfTaxonNodes){
 679                         //take that taxonNode as parent and remove from list with all it possible children
 680                         //FIXME NPE for name
 681                         TaxonName name = tNode.getTaxon().getName();
 682                         if(name.getNameCache().equalsIgnoreCase(genus)){
 683                                 TaxonNode clone = tNode.clone();
 684                                 if(!tNode.hasChildNodes()){
 685                                         //FIXME remove classification
 686 //                                      parentNode = newClassification.addChildNode(clone, 0, classification.getCitation(), classification.getMicroReference());
 687                                         parentNode = newClassification.addChildNode(clone, 0, clone.getReference(), clone.getMicroReference());
 688                                         //remove taxonNode from list because just added to classification
 689                                         result.addUpdatedObject(tNode);
 690                                         listOfTaxonNodes.remove(tNode);
 691                                 }else{
 692                                         //get all childNodes
 693                                         //save prior Hierarchy and remove them from the list
 694                                         List<TaxonNode> copyAllChildrenToTaxonNode = copyAllChildrenToTaxonNode(tNode, clone, result);
 695 //                                      parentNode = newClassification.addChildNode(clone, 0, classification.getCitation(), classification.getMicroReference());
 696                                         //FIXME remove classification
 697                                         parentNode = newClassification.addChildNode(clone, 0, clone.getReference(), clone.getMicroReference());
 698                                         //remove taxonNode from list because just added to classification
 699                                         result.addUpdatedObject(tNode);
 700                                         listOfTaxonNodes.remove(tNode);
 701                                         if(copyAllChildrenToTaxonNode != null){
 702                                                 listOfTaxonNodes = (List<TaxonNode>) CollectionUtils.removeAll(listOfTaxonNodes, copyAllChildrenToTaxonNode);
 703                                         }
 704                                 }
 705                                 break;
 706                         }
 707                 }
 708                 if(parentNode == null){
 709                         //if no match found in list, create parentNode
 710                         NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance();
 711                         TaxonName TaxonName = (TaxonName)parser.parseFullName(genus);
 712                         //TODO Sec via configurator
 713                         Taxon taxon = Taxon.NewInstance(TaxonName, null);
 714                         parentNode = newClassification.addChildTaxon(taxon, 0, null, null);
 715                         result.addUpdatedObject(parentNode);
 716                 }
 717                 //iterate over the rest of the list
 718                 for(TaxonNode tn : listOfTaxonNodes){
 719                         //if TaxonNode has a parent and this is not the classification then skip it
 720                         //and add to new classification via the parentNode as children of it
 721                         //this should assures to keep the already existing hierarchy
 722                         //FIXME: Assert is not rootnode --> entrypoint is not classification in future but rather rootNode
 723
 724                         if(!tn.isTopmostNode()){
 725                                 continue; //skip to next taxonNode
 726                         }
 727
 728                         TaxonNode clone = tn.clone();
 729                         //FIXME: citation from node
 730                         //TODO: addchildNode without citation and references
 731 //                      TaxonNode taxonNode = parentNode.addChildNode(clone, classification.getCitation(), classification.getMicroReference());
 732                         TaxonNode taxonNode = parentNode.addChildNode(clone, clone.getReference(), clone.getMicroReference());
 733                         result.addUnChangedObject(clone);
 734                         if(tn.hasChildNodes()){
 735                                 //save hierarchy in new classification
 736                                 List<TaxonNode> copyAllChildrenToTaxonNode = copyAllChildrenToTaxonNode(tn, taxonNode, result);
 737                                 if(copyAllChildrenToTaxonNode != null){
 738                                         listOfTaxonNodes = (List<TaxonNode>) CollectionUtils.removeAll(listOfTaxonNodes, copyAllChildrenToTaxonNode);
 739                                 }
 740                         }
 741                 }
 742         }
 743         dao.saveOrUpdate(newClassification);
 744         result.setCdmEntity(newClassification);
 745         return result;
 746     }
 747
 748     /**
 749      *
 750      * recursive method to get all childnodes of taxonNode in classification.
 751      *
 752      * @param classification just for References and Citation, can be null
 753      * @param copyFromNode TaxonNode with Children
 754      * @param copyToNode TaxonNode which will receive the children
 755      * @return List of ChildNode which has been added. If node has no children returns null
 756      */
 757    private List<TaxonNode> copyAllChildrenToTaxonNode(TaxonNode copyFromNode, TaxonNode copyToNode, UpdateResult result) {
 758                 List<TaxonNode> childNodes;
 759                 if(!copyFromNode.hasChildNodes()){
 760                         return null;
 761                 }else{
 762                         childNodes = copyFromNode.getChildNodes();
 763                 }
 764                 for(TaxonNode childNode:childNodes){
 765                         TaxonNode clone = childNode.clone();
 766                         result.addUnChangedObject(clone);
 767                         if(childNode.hasChildNodes()){
 768                                 copyAllChildrenToTaxonNode(childNode, clone, result);
 769                         }
 770                         //FIXME: citation from node instead of classification
 771 //                      copyToNode.addChildNode(clone,classification.getCitation(), classification.getMicroReference());
 772                         copyToNode.addChildNode(clone, clone.getReference(), clone.getMicroReference());
 773                 }
 774                 return childNodes;
 775         }
 776
 777     @Override
 778     public ClassificationLookupDTO classificationLookup(Classification classification) {
 779         return dao.classificationLookup(classification);
 780     }
 781
 782     @Override
 783     @Transactional
 784     public DeleteResult delete(UUID classificationUuid, TaxonDeletionConfigurator config){
 785         DeleteResult result = new DeleteResult();
 786         Classification classification = dao.findByUuid(classificationUuid);
 787         if (classification == null){
 788             result.addException(new IllegalArgumentException("The classification does not exist in database."));
 789             result.setAbort();
 790             return result;
 791         }
 792         if (!classification.hasChildNodes()){
 793             dao.delete(classification);
 794             result.addDeletedObject(classification);
 795             return result;
 796         }
 797         if (config.getTaxonNodeConfig().getChildHandling().equals(ChildHandling.DELETE)){
 798 //            TaxonNode root = classification.getRootNode();
 799 //            result.includeResult(taxonNodeService.deleteTaxonNode(HibernateProxyHelper.deproxy(root), config));
 800 //            result.addDeletedObject(classification);
 801             dao.delete(classification);
 802             result.addDeletedObject(classification);
 803             return result;
 804         }
 805
 806
 807         return result;
 808     }
 809
 810     @Override
 811     public List<GroupedTaxonDTO> groupTaxaByHigherTaxon(List<UUID> originalTaxonUuids, UUID classificationUuid, Rank minRank, Rank maxRank){
 812         List<GroupedTaxonDTO> result = new ArrayList<>();
 813
 814         //get treeindex for each taxonUUID
 815         Map<UUID, TreeIndex> taxonIdTreeIndexMap = dao.treeIndexForTaxonUuids(classificationUuid, originalTaxonUuids);
 816
 817         //build treeindex list (or tree)
 818         //TODO make it work with TreeIndex or move there
 819         List<String> treeIndexClosureStr = new ArrayList<>();
 820         for (TreeIndex treeIndex : taxonIdTreeIndexMap.values()){
 821             String[] splits = treeIndex.toString().substring(1).split(ITreeNode.separator);
 822             String currentIndex = ITreeNode.separator;
 823             for (String split : splits){
 824                 if (split.equals("")){
 825                     continue;
 826                 }
 827                 currentIndex += split + ITreeNode.separator;
 828                 if (!treeIndexClosureStr.contains(currentIndex) && !split.startsWith(ITreeNode.treePrefix)){
 829                     treeIndexClosureStr.add(currentIndex);
 830                 }
 831             }
 832         }
 833
 834         //get rank sortindex for all parent taxa with sortindex <= minRank and sortIndex >= maxRank (if available)
 835         Integer minRankOrderIndex = minRank == null ? null : minRank.getOrderIndex();
 836         Integer maxRankOrderIndex = maxRank == null ? null : maxRank.getOrderIndex();
 837         List<TreeIndex> treeIndexClosure = TreeIndex.NewListInstance(treeIndexClosureStr);
 838
 839         Map<TreeIndex, Integer> treeIndexSortIndexMapTmp = taxonNodeDao.rankOrderIndexForTreeIndex(treeIndexClosure, minRankOrderIndex, maxRankOrderIndex);
 840
 841         //remove all treeindex with "exists child in above map(and child.sortindex > xxx)
 842         List<TreeIndex> treeIndexList = TreeIndex.sort(treeIndexSortIndexMapTmp.keySet());
 843
 844         Map<TreeIndex, Integer> treeIndexSortIndexMap = new HashMap<>();
 845         TreeIndex lastTreeIndex = null;
 846         for (TreeIndex treeIndex : treeIndexList){
 847             if (lastTreeIndex != null && lastTreeIndex.hasChild(treeIndex)){
 848                 treeIndexSortIndexMap.remove(lastTreeIndex);
 849             }
 850             treeIndexSortIndexMap.put(treeIndex, treeIndexSortIndexMapTmp.get(treeIndex));
 851             lastTreeIndex = treeIndex;
 852         }
 853
 854         //get taxonID for treeIndexes
 855         Map<TreeIndex, UuidAndTitleCache<?>> treeIndexTaxonIdMap = taxonNodeDao.taxonUuidsForTreeIndexes(treeIndexSortIndexMap.keySet());
 856
 857         //fill result list
 858         for (UUID originalTaxonUuid : originalTaxonUuids){
 859             GroupedTaxonDTO item = new GroupedTaxonDTO();
 860             result.add(item);
 861             item.setTaxonUuid(originalTaxonUuid);
 862             TreeIndex groupTreeIndex = taxonIdTreeIndexMap.get(originalTaxonUuid);
 863             String groupIndexX = TreeIndex.toString(groupTreeIndex);
 864             while (groupTreeIndex != null){
 865                 if (treeIndexTaxonIdMap.get(groupTreeIndex) != null){
 866                     UuidAndTitleCache<?> uuidAndLabel = treeIndexTaxonIdMap.get(groupTreeIndex);
 867                     item.setGroupTaxonUuid(uuidAndLabel.getUuid());
 868                     item.setGroupTaxonName(uuidAndLabel.getTitleCache());
 869                     break;
 870                 }else{
 871                     groupTreeIndex = groupTreeIndex.parent();
 872 //                    int index = groupIndex.substring(0, groupIndex.length()-1).lastIndexOf(ITreeNode.separator);
 873 //                    groupIndex = index < 0 ? null : groupIndex.substring(0, index+1);
 874                 }
 875             }
 876         }
 877
 878         return result;
 879     }
 880
 881     @Override
 882     public List<GroupedTaxonDTO> groupTaxaByMarkedParents(List<UUID> originalTaxonUuids, UUID classificationUuid,
 883             MarkerType markerType, Boolean flag) {
 884
 885         List<GroupedTaxonDTO> result = new ArrayList<>();
 886
 887         //get treeindex for each taxonUUID
 888         Map<UUID, TreeIndex> taxonIdTreeIndexMap = dao.treeIndexForTaxonUuids(classificationUuid, originalTaxonUuids);
 889
 890         //get all marked tree indexes
 891         Set<TreeIndex> markedTreeIndexes = dao.getMarkedTreeIndexes(markerType, flag);
 892
 893         Map<TreeIndex, TreeIndex> groupedMap = TreeIndex.group(markedTreeIndexes, taxonIdTreeIndexMap.values());
 894         Set<TreeIndex> notNullGroups = new HashSet<>(groupedMap.values());
 895         notNullGroups.remove(null);
 896
 897         //get taxonInfo for treeIndexes
 898         Map<TreeIndex, UuidAndTitleCache<?>> treeIndexTaxonIdMap = taxonNodeDao.taxonUuidsForTreeIndexes(notNullGroups);
 899
 900         //fill result list
 901         for (UUID originalTaxonUuid : originalTaxonUuids){
 902             GroupedTaxonDTO item = new GroupedTaxonDTO();
 903             result.add(item);
 904             item.setTaxonUuid(originalTaxonUuid);
 905
 906             TreeIndex toBeGroupedTreeIndex = taxonIdTreeIndexMap.get(originalTaxonUuid);
 907             TreeIndex groupTreeIndex = groupedMap.get(toBeGroupedTreeIndex);
 908             UuidAndTitleCache<?> uuidAndLabel = treeIndexTaxonIdMap.get(groupTreeIndex);
 909             if (uuidAndLabel != null){
 910                 item.setGroupTaxonUuid(uuidAndLabel.getUuid());
 911                 item.setGroupTaxonName(uuidAndLabel.getTitleCache());
 912             }
 913         }
 914
 915         return result;
 916     }
 917
 918     @Override
 919     public UUID getTaxonNodeUuidByTaxonUuid(UUID classificationUuid, UUID taxonUuid) {
 920         Map<UUID, UUID> map = dao.getTaxonNodeUuidByTaxonUuid(classificationUuid, Arrays.asList(taxonUuid));
 921         UUID taxonNodeUuid = map.get(taxonUuid);
 922         return taxonNodeUuid;
 923     }
 924
 925     @Override
 926     public TaxonInContextDTO getTaxonInContext(UUID classificationUuid, UUID taxonBaseUuid,
 927             Boolean doChildren, Boolean doSynonyms, boolean includeUnpublished, List<UUID> ancestorMarkers,
 928             TaxonNodeSortMode sortMode) {
 929
 930         TaxonInContextDTO result = new TaxonInContextDTO();
 931
 932         TaxonBase<?> taxonBase = taxonDao.load(taxonBaseUuid);
 933         if (taxonBase == null){
 934             throw new EntityNotFoundException("Taxon with uuid " + taxonBaseUuid + " not found in datasource");
 935         }
 936         boolean isSynonym = false;
 937         Taxon acceptedTaxon;
 938         if (taxonBase.isInstanceOf(Synonym.class)){
 939             isSynonym = true;
 940             Synonym synonym = CdmBase.deproxy(taxonBase, Synonym.class);
 941             acceptedTaxon = synonym.getAcceptedTaxon();
 942             if (acceptedTaxon == null) {
 943                 throw new EntityNotFoundException("Accepted taxon not found for synonym"  );
 944             }
 945             TaxonStatus taxonStatus = TaxonStatus.Synonym;
 946             if (synonym.getName()!= null && acceptedTaxon.getName() != null
 947                     && synonym.getName().getHomotypicalGroup().equals(acceptedTaxon.getName().getHomotypicalGroup())){
 948                 taxonStatus = TaxonStatus.SynonymObjective;
 949             }
 950             result.setTaxonStatus(taxonStatus);
 951
 952         }else{
 953             acceptedTaxon = CdmBase.deproxy(taxonBase, Taxon.class);
 954             result.setTaxonStatus(TaxonStatus.Accepted);
 955         }
 956         UUID acceptedTaxonUuid = acceptedTaxon.getUuid();
 957
 958         UUID taxonNodeUuid = getTaxonNodeUuidByTaxonUuid(classificationUuid, acceptedTaxonUuid);
 959         if (taxonNodeUuid == null) {
 960             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 );
 961         }
 962         result.setTaxonNodeUuid(taxonNodeUuid);
 963
 964         //TODO make it a dao call
 965         Taxon parentTaxon = getParentTaxon(classificationUuid, acceptedTaxon);
 966         if (parentTaxon != null){
 967             result.setParentTaxonUuid(parentTaxon.getUuid());
 968             result.setParentTaxonLabel(parentTaxon.getTitleCache());
 969             if (parentTaxon.getName() != null){
 970                 result.setParentNameLabel(parentTaxon.getName().getTitleCache());
 971             }
 972         }
 973
 974         result.setTaxonUuid(taxonBaseUuid);
 975         result.setClassificationUuid(classificationUuid);
 976         if (taxonBase.getSec() != null){
 977             result.setSecundumUuid(taxonBase.getSec().getUuid());
 978             result.setSecundumLabel(taxonBase.getSec().getTitleCache());
 979         }
 980         result.setTaxonLabel(taxonBase.getTitleCache());
 981
 982         TaxonName name = taxonBase.getName();
 983         result.setNameUuid(name.getUuid());
 984         result.setNameLabel(name.getTitleCache());
 985         result.setNameWithoutAuthor(name.getNameCache());
 986         result.setGenusOrUninomial(name.getGenusOrUninomial());
 987         result.setInfraGenericEpithet(name.getInfraGenericEpithet());
 988         result.setSpeciesEpithet(name.getSpecificEpithet());
 989         result.setInfraSpecificEpithet(name.getInfraSpecificEpithet());
 990
 991         result.setAuthorship(name.getAuthorshipCache());
 992
 993         Rank rank = name.getRank();
 994         if (rank != null){
 995             result.setRankUuid(rank.getUuid());
 996             String rankLabel = rank.getAbbreviation();
 997             if (StringUtils.isBlank(rankLabel)){
 998                 rankLabel = rank.getLabel();
 999             }
1000             result.setRankLabel(rankLabel);
1001         }
1002
1003         boolean recursive = false;
1004         Integer pageSize = null;
1005         Integer pageIndex = null;
1006         Pager<TaxonNodeDto> children = taxonNodeService.pageChildNodesDTOs(taxonNodeUuid, recursive, includeUnpublished, doSynonyms,
1007                 sortMode, pageSize, pageIndex);
1008
1009         //children
1010         if(! isSynonym) {
1011             for (TaxonNodeDto childDto : children.getRecords()){
1012                 if (doChildren && childDto.getTaxonStatus().equals(TaxonStatus.Accepted)){
1013                     EntityDTO<Taxon> child = new EntityDTO<Taxon>(childDto.getTaxonUuid(), childDto.getTitleCache());
1014                     result.addChild(child);
1015                 }else if (doSynonyms && childDto.getTaxonStatus().isSynonym()){
1016                     EntityDTO<Synonym> child = new EntityDTO<>(childDto.getTaxonUuid(), childDto.getTitleCache());
1017                     result.addSynonym(child);
1018                 }
1019             }
1020         }else{
1021             result.setAcceptedTaxonUuid(acceptedTaxonUuid);
1022             String nameTitel = acceptedTaxon.getName() == null ? null : acceptedTaxon.getName().getTitleCache();
1023             result.setAcceptedTaxonLabel(acceptedTaxon.getTitleCache());
1024             result.setAcceptedNameLabel(nameTitel);
1025         }
1026
1027         //marked ancestors
1028         if (ancestorMarkers != null && !ancestorMarkers.isEmpty()){
1029             @SuppressWarnings("rawtypes")
1030             List<DefinedTermBase> markerTypesTerms = termDao.list(ancestorMarkers, pageSize, null, null, null);
1031             List<MarkerType> markerTypes = new ArrayList<>();
1032             for (DefinedTermBase<?> term : markerTypesTerms){
1033                 if (term.isInstanceOf(MarkerType.class)){
1034                     markerTypes.add(CdmBase.deproxy(term, MarkerType.class));
1035                 }
1036             }
1037             if (! markerTypes.isEmpty()){
1038                 TaxonNode node = taxonNodeDao.findByUuid(taxonNodeUuid);
1039                 handleAncestorsForMarkersRecursive(result, markerTypes, node);
1040             }
1041         }
1042
1043         return result;
1044     }
1045
1046     private Taxon getParentTaxon(UUID classificationUuid, Taxon acceptedTaxon) {
1047         if (classificationUuid == null){
1048             return null;
1049         }
1050         TaxonNode parent = null;
1051         for (TaxonNode node : acceptedTaxon.getTaxonNodes()){
1052             if (classificationUuid.equals(node.getClassification().getUuid())){
1053                 parent = node.getParent();
1054             }
1055         }
1056         if (parent != null){
1057             return parent.getTaxon();
1058         }
1059         return null;
1060     }
1061
1062     private void handleAncestorsForMarkersRecursive(TaxonInContextDTO result, List<MarkerType> markerTypes, TaxonNode node) {
1063        for (MarkerType type : markerTypes){
1064             Taxon taxon = node.getTaxon();
1065             if (taxon != null && taxon.hasMarker(type, true)){
1066                 String label =  taxon.getName() == null? taxon.getTitleCache() : taxon.getName().getTitleCache();
1067                 MarkedEntityDTO<Taxon> dto = new MarkedEntityDTO<>(type, true, taxon.getUuid(), label);
1068                 result.addMarkedAncestor(dto);
1069             }
1070         }
1071         TaxonNode parentNode = node.getParent();
1072         if (parentNode != null){
1073             handleAncestorsForMarkersRecursive(result, markerTypes, parentNode);
1074         }
1075     }
1076
1077     @Override
1078     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
1079             Classification classification) {
1080         return getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification, false);
1081     }
1082
1083     @Override
1084     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
1085             UUID classificationUuid) {
1086         return getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classificationUuid, false);
1087     }
1088
1089     @Override
1090     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
1091             UUID classificationUuid, Integer limit, String pattern) {
1092         return  getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classificationUuid,  limit, pattern, false);
1093     }
1094
1095     @Override
1096     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
1097             Classification classification, Integer limit, String pattern) {
1098         return getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification, limit, pattern, false);
1099     }
1100
1101     @Override
1102     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
1103             UUID classificationUuid, Integer limit, String pattern, boolean searchForClassifications) {
1104         return getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
1105                 classificationUuid, limit, pattern, searchForClassifications, false);
1106     }
1107 }