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.hibernate.HibernateProxyHelper;
  47 import eu.etaxonomy.cdm.model.common.CdmBase;
  48 import eu.etaxonomy.cdm.model.common.DefinedTermBase;
  49 import eu.etaxonomy.cdm.model.common.ITreeNode;
  50 import eu.etaxonomy.cdm.model.common.MarkerType;
  51 import eu.etaxonomy.cdm.model.common.TreeIndex;
  52 import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
  53 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  54 import eu.etaxonomy.cdm.model.media.Media;
  55 import eu.etaxonomy.cdm.model.media.MediaRepresentation;
  56 import eu.etaxonomy.cdm.model.media.MediaUtils;
  57 import eu.etaxonomy.cdm.model.name.INonViralName;
  58 import eu.etaxonomy.cdm.model.name.Rank;
  59 import eu.etaxonomy.cdm.model.name.TaxonName;
  60 import eu.etaxonomy.cdm.model.reference.Reference;
  61 import eu.etaxonomy.cdm.model.taxon.Classification;
  62 import eu.etaxonomy.cdm.model.taxon.ITaxonNodeComparator;
  63 import eu.etaxonomy.cdm.model.taxon.ITaxonTreeNode;
  64 import eu.etaxonomy.cdm.model.taxon.Synonym;
  65 import eu.etaxonomy.cdm.model.taxon.Taxon;
  66 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  67 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
  68 import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
  69 import eu.etaxonomy.cdm.persistence.dao.common.IDefinedTermDao;
  70 import eu.etaxonomy.cdm.persistence.dao.initializer.IBeanInitializer;
  71 import eu.etaxonomy.cdm.persistence.dao.taxon.IClassificationDao;
  72 import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao;
  73 import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonNodeDao;
  74 import eu.etaxonomy.cdm.persistence.dto.ClassificationLookupDTO;
  75 import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDto;
  76 import eu.etaxonomy.cdm.persistence.dto.TaxonStatus;
  77 import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
  78 import eu.etaxonomy.cdm.persistence.query.OrderHint;
  79 import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
  80 import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
  81
  82 /**
  83  * @author n.hoffmann
  84  * @created Sep 21, 2009
  85  */
  86 @Service
  87 @Transactional(readOnly = true)
  88 public class ClassificationServiceImpl extends IdentifiableServiceBase<Classification, IClassificationDao>
  89     implements IClassificationService {
  90     private static final Logger logger = Logger.getLogger(ClassificationServiceImpl.class);
  91
  92     @Autowired
  93     private ITaxonNodeDao taxonNodeDao;
  94
  95     @Autowired
  96     private ITaxonDao taxonDao;
  97
  98     @Autowired
  99     private ITaxonNodeService taxonNodeService;
 100
 101     @Autowired
 102     private IDefinedTermDao termDao;
 103
 104     @Autowired
 105     private IBeanInitializer defaultBeanInitializer;
 106
 107     @Override
 108     @Autowired
 109     protected void setDao(IClassificationDao dao) {
 110         this.dao = dao;
 111     }
 112
 113     private Comparator<? super TaxonNode> taxonNodeComparator;
 114
 115     @Autowired
 116     public void setTaxonNodeComparator(ITaxonNodeComparator<? super TaxonNode> taxonNodeComparator){
 117         this.taxonNodeComparator = (Comparator<? super TaxonNode>) taxonNodeComparator;
 118     }
 119
 120     @Override
 121     public TaxonNode loadTaxonNodeByTaxon(Taxon taxon, UUID classificationUuid, List<String> propertyPaths){
 122         Classification tree = dao.load(classificationUuid);
 123         TaxonNode node = tree.getNode(taxon);
 124
 125         return loadTaxonNode(node.getUuid(), propertyPaths);
 126     }
 127
 128     @Override
 129     @Deprecated // use loadTaxonNode(UUID, List<String>) instead
 130     public TaxonNode loadTaxonNode(TaxonNode taxonNode, List<String> propertyPaths){
 131         return taxonNodeDao.load(taxonNode.getUuid(), propertyPaths);
 132     }
 133
 134     public TaxonNode loadTaxonNode(UUID taxonNodeUuid, List<String> propertyPaths){
 135         return taxonNodeDao.load(taxonNodeUuid, propertyPaths);
 136     }
 137
 138     @Override
 139     @Transactional(readOnly = false)
 140     public UpdateResult cloneClassification(UUID classificationUuid,
 141                 String name, Reference sec, TaxonRelationshipType relationshipType) {
 142         UpdateResult result = new UpdateResult();
 143         Classification classification = load(classificationUuid);
 144         Classification clone = Classification.NewInstance(name);
 145         clone.setReference(sec);
 146
 147         //clone taxa and taxon nodes
 148         List<TaxonNode> childNodes = classification.getRootNode().getChildNodes();
 149         for (TaxonNode taxonNode : childNodes) {
 150                 addChildTaxa(taxonNode, null, clone, relationshipType);
 151         }
 152         dao.saveOrUpdate(clone);
 153         result.setCdmEntity(clone);
 154         return result;
 155     }
 156
 157     private void addChildTaxa(TaxonNode originalParentNode, TaxonNode cloneParentNode, Classification classification, TaxonRelationshipType relationshipType){
 158         Reference reference = classification.getReference();
 159         Taxon cloneTaxon = (Taxon) HibernateProxyHelper.deproxy(originalParentNode.getTaxon(), Taxon.class).clone();
 160         cloneTaxon.setSec(reference);
 161                 String microReference = null;
 162                 List<TaxonNode> originalChildNodes = originalParentNode.getChildNodes();
 163
 164                 //add relation between taxa
 165                 if (relationshipType != null){
 166                     cloneTaxon.addTaxonRelation(originalParentNode.getTaxon(), relationshipType, reference, microReference);
 167                 }
 168
 169                 TaxonNode cloneChildNode = null;
 170         //add taxon node to either parent node or classification (no parent node)
 171         if(cloneParentNode==null){
 172                 cloneChildNode = classification.addChildTaxon(cloneTaxon, reference, microReference);
 173         }
 174         else{
 175                 cloneChildNode = cloneParentNode.addChildTaxon(cloneTaxon, reference, microReference);
 176         }
 177         taxonNodeDao.saveOrUpdate(cloneChildNode);
 178         //add children
 179                 for (TaxonNode originalChildNode : originalChildNodes) {
 180                 addChildTaxa(originalChildNode, cloneChildNode, classification, relationshipType);
 181         }
 182     }
 183
 184     @Override
 185     public List<TaxonNode> listRankSpecificRootNodes(Classification classification, Rank rank, Integer pageSize,
 186             Integer pageIndex, List<String> propertyPaths) {
 187         return pageRankSpecificRootNodes(classification, rank, pageSize, pageIndex, propertyPaths).getRecords();
 188     }
 189
 190     @Override
 191     public Pager<TaxonNode> pageRankSpecificRootNodes(Classification classification, Rank rank, Integer pageSize,
 192             Integer pageIndex, List<String> propertyPaths) {
 193         long[] numberOfResults = dao.countRankSpecificRootNodes(classification, rank);
 194         long totalNumberOfResults = numberOfResults[0] + (numberOfResults.length > 1 ? numberOfResults[1] : 0);
 195
 196         List<TaxonNode> results = new ArrayList<TaxonNode>();
 197
 198         if (AbstractPagerImpl.hasResultsInRange(totalNumberOfResults, pageIndex, pageSize)) { // no point checking again
 199             Integer limit = PagerUtils.limitFor(pageSize);
 200             Integer start = PagerUtils.startFor(pageSize, pageIndex);
 201
 202             Integer remainingLimit = limit;
 203             int[] queryIndexes = rank == null ? new int[]{0} : new int[]{0,1};
 204
 205             for(int queryIndex: queryIndexes) {
 206                 if(start != null && start > numberOfResults[queryIndex]) {
 207                     // start in next query with new start value
 208                     start = start - (int)numberOfResults[queryIndex];
 209                     continue;
 210                 }
 211
 212                 List<TaxonNode> perQueryResults = dao.listRankSpecificRootNodes(classification, rank, remainingLimit, start, propertyPaths, queryIndex);
 213                 results.addAll(perQueryResults);
 214                 if(remainingLimit != null ){
 215                     remainingLimit = remainingLimit - results.size();
 216                     if(remainingLimit <= 0) {
 217                         // no need to run further queries if first query returned enough items!
 218                         break;
 219                     }
 220                     // start at with fist item of next query to fetch the remaining items
 221                     start = 0;
 222                 }
 223             }
 224         }
 225 //        long start_t = System.currentTimeMillis();
 226         Collections.sort(results, taxonNodeComparator); // TODO is ordering during the hibernate query in the dao possible?
 227 //        System.err.println("service.pageRankSpecificRootNodes() - Collections.sort(results,  taxonNodeComparator) " + (System.currentTimeMillis() - start_t));
 228         return new DefaultPagerImpl<TaxonNode>(pageIndex, (int) totalNumberOfResults, pageSize, results);
 229
 230     }
 231
 232     /**
 233      * @implements {@link IClassificationService#loadTreeBranch(TaxonNode, Rank, List)
 234      * @see eu.etaxonomy.cdm.api.service.ITaxonService#loadTreeBranchTo(eu.etaxonomy.cdm.model.taxon.TaxonNode, eu.etaxonomy.cdm.model.name.Rank, java.util.List)
 235      * FIXME Candidate for harmonization
 236      * move to classification service
 237      */
 238     @Override
 239     public List<TaxonNode> loadTreeBranch(TaxonNode taxonNode, Rank baseRank, List<String> propertyPaths){
 240
 241         TaxonNode thisNode = taxonNodeDao.load(taxonNode.getUuid(), propertyPaths);
 242         List<TaxonNode> pathToRoot = new ArrayList<TaxonNode>();
 243         pathToRoot.add(thisNode);
 244
 245         while(!thisNode.isTopmostNode()){
 246             //TODO why do we need to deproxy here?
 247             //     without this thisNode.getParent() will return NULL in
 248             //     some cases (environment dependend?) even if the parent exits
 249             TaxonNode parentNode = CdmBase.deproxy(thisNode, TaxonNode.class).getParent();
 250
 251             if(parentNode == null){
 252                 throw new NullPointerException("taxonNode " + thisNode + " must have a parent since it is not top most");
 253             }
 254             if(parentNode.getTaxon() == null){
 255                 throw new NullPointerException("The taxon associated with taxonNode " + parentNode + " is NULL");
 256             }
 257             if(parentNode.getTaxon().getName() == null){
 258                 throw new NullPointerException("The name of the taxon associated with taxonNode " + parentNode + " is NULL");
 259             }
 260
 261             Rank parentNodeRank = parentNode.getTaxon().getName() == null ? null : parentNode.getTaxon().getName().getRank();
 262             // stop if the next parent is higher than the baseRank
 263             if(baseRank != null && parentNodeRank != null && baseRank.isLower(parentNodeRank)){
 264                 break;
 265             }
 266
 267             pathToRoot.add(parentNode);
 268             thisNode = parentNode;
 269         }
 270
 271         // initialize and invert order of nodes in list
 272         defaultBeanInitializer.initializeAll(pathToRoot, propertyPaths);
 273         Collections.reverse(pathToRoot);
 274
 275         return pathToRoot;
 276     }
 277
 278     @Override
 279     public List<TaxonNode> loadTreeBranchToTaxon(Taxon taxon, Classification classification, Rank baseRank, List<String> propertyPaths){
 280         Classification tree = dao.load(classification.getUuid());
 281         taxon = (Taxon) taxonDao.load(taxon.getUuid());
 282         TaxonNode node = tree.getNode(taxon);
 283         if(node == null){
 284             logger.warn("The specified taxon is not found in the given tree.");
 285             return null;
 286         }
 287         return loadTreeBranch(node, baseRank, propertyPaths);
 288     }
 289
 290
 291     @Override
 292     public List<TaxonNode> loadChildNodesOfTaxonNode(TaxonNode taxonNode,
 293             List<String> propertyPaths) {
 294         taxonNode = taxonNodeDao.load(taxonNode.getUuid());
 295         List<TaxonNode> childNodes = new ArrayList<TaxonNode>(taxonNode.getChildNodes());
 296         defaultBeanInitializer.initializeAll(childNodes, propertyPaths);
 297         Collections.sort(childNodes, taxonNodeComparator);
 298         return childNodes;
 299     }
 300
 301     @Override
 302     public List<TaxonNode> listChildNodesOfTaxon(UUID taxonUuid, UUID classificationUuid, Integer pageSize,
 303             Integer pageIndex, List<String> propertyPaths){
 304
 305         Classification classification = dao.load(classificationUuid);
 306         Taxon taxon = (Taxon) taxonDao.load(taxonUuid);
 307
 308         List<TaxonNode> results = dao.listChildrenOf(taxon, classification, pageSize, pageIndex, propertyPaths);
 309         Collections.sort(results, taxonNodeComparator); // FIXME this is only a HACK, order during the hibernate query in the dao
 310         return results;
 311     }
 312
 313     @Override
 314     public Pager<TaxonNode> pageSiblingsOfTaxon(UUID taxonUuid, UUID classificationUuid, Integer pageSize,
 315             Integer pageIndex, List<String> propertyPaths){
 316
 317         Classification classification = dao.load(classificationUuid);
 318         Taxon taxon = (Taxon) taxonDao.load(taxonUuid);
 319
 320         long numberOfResults = dao.countSiblingsOf(taxon, classification);
 321
 322         List<TaxonNode> results;
 323         if(PagerUtils.hasResultsInRange(numberOfResults, pageIndex, pageSize)) {
 324             results = dao.listSiblingsOf(taxon, classification, pageSize, pageIndex, propertyPaths);
 325             Collections.sort(results, taxonNodeComparator); // FIXME this is only a HACK, order during the hibernate query in the dao
 326         } else {
 327             results = new ArrayList<>();
 328         }
 329
 330         return new DefaultPagerImpl<TaxonNode>(pageIndex, numberOfResults, pageSize, results);
 331     }
 332
 333     @Override
 334     public List<TaxonNode> listSiblingsOfTaxon(UUID taxonUuid, UUID classificationUuid, Integer pageSize,
 335             Integer pageIndex, List<String> propertyPaths){
 336
 337         Pager<TaxonNode> pager = pageSiblingsOfTaxon(taxonUuid, classificationUuid, pageSize, pageIndex, propertyPaths);
 338         return pager.getRecords();
 339     }
 340
 341     @Override
 342     public TaxonNode getTaxonNodeByUuid(UUID uuid) {
 343         return taxonNodeDao.findByUuid(uuid);
 344     }
 345
 346     @Override
 347     public ITaxonTreeNode getTreeNodeByUuid(UUID uuid){
 348         ITaxonTreeNode treeNode = taxonNodeDao.findByUuid(uuid);
 349         if(treeNode == null){
 350             treeNode = dao.findByUuid(uuid);
 351         }
 352
 353         return treeNode;
 354     }
 355
 356     @Override
 357     public TaxonNode getRootNode(UUID classificationUuid){
 358         return dao.getRootNode(classificationUuid);
 359     }
 360
 361     @Override
 362     public List<Classification> listClassifications(Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
 363         return dao.list(limit, start, orderHints, propertyPaths);
 364     }
 365
 366     @Override
 367     public UUID removeTaxonNode(TaxonNode taxonNode) {
 368         return taxonNodeDao.delete(taxonNode);
 369     }
 370     @Override
 371     public UUID removeTreeNode(ITaxonTreeNode treeNode) {
 372         if(treeNode instanceof Classification){
 373             return dao.delete((Classification) treeNode);
 374         }else if(treeNode instanceof TaxonNode){
 375             return taxonNodeDao.delete((TaxonNode)treeNode);
 376         }
 377         return null;
 378     }
 379     @Override
 380     public UUID saveTaxonNode(TaxonNode taxonNode) {
 381         return taxonNodeDao.save(taxonNode).getUuid();
 382     }
 383
 384     @Override
 385     public Map<UUID, TaxonNode> saveTaxonNodeAll(
 386             Collection<TaxonNode> taxonNodeCollection) {
 387         return taxonNodeDao.saveAll(taxonNodeCollection);
 388     }
 389
 390     @Override
 391     public UUID saveClassification(Classification classification) {
 392
 393        taxonNodeDao.saveOrUpdateAll(classification.getAllNodes());
 394        UUID result =dao.saveOrUpdate(classification);
 395        return result;
 396     }
 397
 398     @Override
 399     public UUID saveTreeNode(ITaxonTreeNode treeNode) {
 400         if(treeNode instanceof Classification){
 401             return dao.save((Classification) treeNode).getUuid();
 402         }else if(treeNode instanceof TaxonNode){
 403             return taxonNodeDao.save((TaxonNode)treeNode).getUuid();
 404         }
 405         return null;
 406     }
 407
 408     @Override
 409     public List<TaxonNode> getAllNodes(){
 410         return taxonNodeDao.list(null,null);
 411     }
 412
 413     @Override
 414     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(UUID classificationUuid, Integer limit, String pattern) {
 415         return taxonDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(dao.load(classificationUuid),  limit, pattern);
 416     }
 417
 418     @Override
 419     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification,  Integer limit, String pattern) {
 420         return taxonDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification,  limit, pattern);
 421     }
 422
 423     @Override
 424     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(UUID classificationUuid ) {
 425         return taxonDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(dao.load(classificationUuid), null, null);
 426     }
 427
 428     @Override
 429     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification ) {
 430         return taxonDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification, null, null);
 431     }
 432
 433     @Override
 434     public List<UuidAndTitleCache<Classification>> getUuidAndTitleCache(Integer limit, String pattern) {
 435         return dao.getUuidAndTitleCache(limit, pattern);
 436     }
 437
 438     @Override
 439     public Map<UUID, List<MediaRepresentation>> getAllMediaForChildNodes(
 440             TaxonNode taxonNode, List<String> propertyPaths, int size,
 441             int height, int widthOrDuration, String[] mimeTypes) {
 442
 443         TreeMap<UUID, List<MediaRepresentation>> result = new TreeMap<UUID, List<MediaRepresentation>>();
 444         List<Media> taxonMedia = new ArrayList<Media>();
 445         List<MediaRepresentation> mediaRepresentations = new ArrayList<MediaRepresentation>();
 446
 447         //add all media of the children to the result map
 448         if (taxonNode != null){
 449
 450             List<TaxonNode> nodes = new ArrayList<TaxonNode>();
 451
 452             nodes.add(loadTaxonNode(taxonNode, propertyPaths));
 453             nodes.addAll(loadChildNodesOfTaxonNode(taxonNode, propertyPaths));
 454
 455             if (nodes != null){
 456                 for(TaxonNode node : nodes){
 457                     Taxon taxon = node.getTaxon();
 458                     for (TaxonDescription taxonDescription: taxon.getDescriptions()){
 459                         for (DescriptionElementBase descriptionElement: taxonDescription.getElements()){
 460                             for(Media media : descriptionElement.getMedia()){
 461                                 taxonMedia.add(media);
 462
 463                                 //find the best matching representation
 464                                 mediaRepresentations.add(MediaUtils.findBestMatchingRepresentation(media,null, size, height, widthOrDuration, mimeTypes));
 465
 466                             }
 467                         }
 468                     }
 469                     result.put(taxon.getUuid(), mediaRepresentations);
 470
 471                 }
 472             }
 473
 474         }
 475
 476         return result;
 477
 478     }
 479
 480     @Override
 481     public Map<UUID, List<MediaRepresentation>> getAllMediaForChildNodes(Taxon taxon, Classification taxTree, List<String> propertyPaths, int size, int height, int widthOrDuration, String[] mimeTypes){
 482         TaxonNode node = taxTree.getNode(taxon);
 483
 484         return getAllMediaForChildNodes(node, propertyPaths, size, height, widthOrDuration, mimeTypes);
 485     }
 486
 487     @Override
 488     @Transactional(readOnly = false)
 489     public void updateTitleCache(Class<? extends Classification> clazz, Integer stepSize, IIdentifiableEntityCacheStrategy<Classification> cacheStrategy, IProgressMonitor monitor) {
 490         if (clazz == null){
 491             clazz = Classification.class;
 492         }
 493         super.updateTitleCacheImpl(clazz, stepSize, cacheStrategy, monitor);
 494     }
 495
 496     /**
 497      *
 498      * @param allNodesOfClassification
 499      * @return null - if  allNodesOfClassification is empty <br>
 500      */
 501
 502     private Map<String, List<TaxonNode>> getSortedGenusList(Collection<TaxonNode> allNodesOfClassification){
 503
 504         if(allNodesOfClassification == null || allNodesOfClassification.isEmpty()){
 505                 return null;
 506         }
 507         Map<String, List<TaxonNode>> sortedGenusMap = new HashMap<>();
 508         for(TaxonNode node:allNodesOfClassification){
 509                 final TaxonNode tn = node;
 510                 Taxon taxon = node.getTaxon();
 511                 INonViralName name = taxon.getName();
 512                 String genusOrUninomial = name.getGenusOrUninomial();
 513                 //if rank unknown split string and take first word
 514                 if(genusOrUninomial == null){
 515                         String titleCache = taxon.getTitleCache();
 516                         String[] split = titleCache.split("\\s+");
 517                         for(String s:split){
 518                                 genusOrUninomial = s;
 519                                 break;
 520                         }
 521                 }
 522                 //if node has children
 523
 524                 //retrieve list from map if not create List
 525                 if(sortedGenusMap.containsKey(genusOrUninomial)){
 526                         List<TaxonNode> list = sortedGenusMap.get(genusOrUninomial);
 527                         list.add(node);
 528                         sortedGenusMap.put(genusOrUninomial, list);
 529                 }else{
 530                         //create List for genus
 531                         List<TaxonNode> list = new ArrayList<TaxonNode>();
 532                         list.add(node);
 533                         sortedGenusMap.put(genusOrUninomial, list);
 534                 }
 535         }
 536         return sortedGenusMap;
 537     }
 538
 539     /**
 540      *
 541      * creates new Classification and parent TaxonNodes at genus level
 542      *
 543      *
 544      * @param map GenusMap which holds a name (Genus) and all the same Taxa as a list
 545      * @param classification you want to improve the hierarchy (will not be modified)
 546      * @param configurator to change certain settings, if null then standard settings will be taken
 547      * @return new classification with parentNodes for each entry in the map
 548      */
 549     @SuppressWarnings({ "rawtypes", "unchecked" })
 550         @Transactional(readOnly = false)
 551         @Override
 552     public UpdateResult createHierarchyInClassification(Classification classification, CreateHierarchyForClassificationConfigurator configurator){
 553         UpdateResult result = new UpdateResult();
 554         classification = dao.findByUuid(classification.getUuid());
 555         Map<String, List<TaxonNode>> map = getSortedGenusList(classification.getAllNodes());
 556
 557         final String APPENDIX = "repaired";
 558         String titleCache = org.apache.commons.lang.StringUtils.isBlank(classification.getTitleCache()) ? " " : classification.getTitleCache() ;
 559         //TODO classification clone???
 560         Classification newClassification = Classification.NewInstance(titleCache +" "+ APPENDIX);
 561         newClassification.setReference(classification.getReference());
 562
 563         for(Map.Entry<String, List<TaxonNode>> entry:map.entrySet()){
 564                 String genus = entry.getKey();
 565                 List<TaxonNode> listOfTaxonNodes = entry.getValue();
 566                 TaxonNode parentNode = null;
 567                 //Search for genus in list
 568                 for(TaxonNode tNode:listOfTaxonNodes){
 569                         //take that taxonNode as parent and remove from list with all it possible children
 570                         //FIXME NPE for name
 571                         TaxonName name = tNode.getTaxon().getName();
 572                         if(name.getNameCache().equalsIgnoreCase(genus)){
 573                                 TaxonNode clone = (TaxonNode) tNode.clone();
 574                                 if(!tNode.hasChildNodes()){
 575                                         //FIXME remove classification
 576 //                                      parentNode = newClassification.addChildNode(clone, 0, classification.getCitation(), classification.getMicroReference());
 577                                         parentNode = newClassification.addChildNode(clone, 0, clone.getReference(), clone.getMicroReference());
 578                                         //remove taxonNode from list because just added to classification
 579                                         result.addUpdatedObject(tNode);
 580                                         listOfTaxonNodes.remove(tNode);
 581                                 }else{
 582                                         //get all childNodes
 583                                         //save prior Hierarchy and remove them from the list
 584                                         List<TaxonNode> copyAllChildrenToTaxonNode = copyAllChildrenToTaxonNode(tNode, clone, result);
 585 //                                      parentNode = newClassification.addChildNode(clone, 0, classification.getCitation(), classification.getMicroReference());
 586                                         //FIXME remove classification
 587                                         parentNode = newClassification.addChildNode(clone, 0, clone.getReference(), clone.getMicroReference());
 588                                         //remove taxonNode from list because just added to classification
 589                                         result.addUpdatedObject(tNode);
 590                                         listOfTaxonNodes.remove(tNode);
 591                                         if(copyAllChildrenToTaxonNode != null){
 592                                                 listOfTaxonNodes = (List<TaxonNode>) CollectionUtils.removeAll(listOfTaxonNodes, copyAllChildrenToTaxonNode);
 593                                         }
 594                                 }
 595                                 break;
 596                         }
 597                 }
 598                 if(parentNode == null){
 599                         //if no match found in list, create parentNode
 600                         NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance();
 601                         TaxonName<?,?> TaxonName = (TaxonName<?,?>)parser.parseFullName(genus);
 602                         //TODO Sec via configurator
 603                         Taxon taxon = Taxon.NewInstance(TaxonName, null);
 604                         parentNode = newClassification.addChildTaxon(taxon, 0, null, null);
 605                         result.addUpdatedObject(parentNode);
 606                 }
 607                 //iterate over the rest of the list
 608                 for(TaxonNode tn : listOfTaxonNodes){
 609                         //if TaxonNode has a parent and this is not the classification then skip it
 610                         //and add to new classification via the parentNode as children of it
 611                         //this should assures to keep the already existing hierarchy
 612                         //FIXME: Assert is not rootnode --> entrypoint is not classification in future but rather rootNode
 613
 614                         if(!tn.isTopmostNode()){
 615                                 continue; //skip to next taxonNode
 616                         }
 617
 618                         TaxonNode clone = (TaxonNode) tn.clone();
 619                         //FIXME: citation from node
 620                         //TODO: addchildNode without citation and references
 621 //                      TaxonNode taxonNode = parentNode.addChildNode(clone, classification.getCitation(), classification.getMicroReference());
 622                         TaxonNode taxonNode = parentNode.addChildNode(clone, clone.getReference(), clone.getMicroReference());
 623                         result.addUnChangedObject(clone);
 624                         if(tn.hasChildNodes()){
 625                                 //save hierarchy in new classification
 626                                 List<TaxonNode> copyAllChildrenToTaxonNode = copyAllChildrenToTaxonNode(tn, taxonNode, result);
 627                                 if(copyAllChildrenToTaxonNode != null){
 628                                         listOfTaxonNodes = (List<TaxonNode>) CollectionUtils.removeAll(listOfTaxonNodes, copyAllChildrenToTaxonNode);
 629                                 }
 630                         }
 631                 }
 632         }
 633         dao.saveOrUpdate(newClassification);
 634         result.setCdmEntity(newClassification);
 635         return result;
 636     }
 637
 638     /**
 639      *
 640      * recursive method to get all childnodes of taxonNode in classification.
 641      *
 642      * @param classification just for References and Citation, can be null
 643      * @param copyFromNode TaxonNode with Children
 644      * @param copyToNode TaxonNode which will receive the children
 645      * @return List of ChildNode which has been added. If node has no children returns null
 646      */
 647    private List<TaxonNode> copyAllChildrenToTaxonNode(TaxonNode copyFromNode, TaxonNode copyToNode, UpdateResult result) {
 648                 List<TaxonNode> childNodes;
 649                 if(!copyFromNode.hasChildNodes()){
 650                         return null;
 651                 }else{
 652                         childNodes = copyFromNode.getChildNodes();
 653                 }
 654                 for(TaxonNode childNode:childNodes){
 655                         TaxonNode clone = (TaxonNode) childNode.clone();
 656                         result.addUnChangedObject(clone);
 657                         if(childNode.hasChildNodes()){
 658                                 copyAllChildrenToTaxonNode(childNode, clone, result);
 659                         }
 660                         //FIXME: citation from node instead of classification
 661 //                      copyToNode.addChildNode(clone,classification.getCitation(), classification.getMicroReference());
 662                         copyToNode.addChildNode(clone, clone.getReference(), clone.getMicroReference());
 663                 }
 664                 return childNodes;
 665         }
 666
 667     /**
 668      * {@inheritDoc}
 669      */
 670     @Override
 671     public ClassificationLookupDTO classificationLookup(Classification classification) {
 672         return dao.classificationLookup(classification);
 673     }
 674
 675
 676     @Override
 677     public DeleteResult delete(UUID classificationUuid, TaxonDeletionConfigurator config){
 678         DeleteResult result = new DeleteResult();
 679         Classification classification = dao.findByUuid(classificationUuid);
 680         if (classification == null){
 681             result.addException(new IllegalArgumentException("The classification does not exist in database."));
 682             result.setAbort();
 683             return result;
 684         }
 685         if (!classification.hasChildNodes()){
 686             dao.delete(classification);
 687         }
 688         if (config.getTaxonNodeConfig().getChildHandling().equals(ChildHandling.DELETE) ){
 689             TaxonNode root = classification.getRootNode();
 690             taxonNodeDao.delete(root, true);
 691             dao.delete(classification);
 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, 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
 872         result.setTaxonUuid(taxonBaseUuid);
 873         result.setClassificationUuid(classificationUuid);
 874         if (taxonBase.getSec() != null){
 875             result.setSecundumUuid(taxonBase.getSec().getUuid());
 876             result.setSecundumLabel(taxonBase.getSec().getTitleCache());
 877         }
 878         result.setTaxonLabel(taxonBase.getTitleCache());
 879
 880         TaxonName<?,?> name = taxonBase.getName();
 881         result.setNameUuid(name.getUuid());
 882         result.setNameLabel(name.getTitleCache());
 883         result.setNameWithoutAuthor(name.getNameCache());
 884         result.setGenusOrUninomial(name.getGenusOrUninomial());
 885         result.setInfraGenericEpithet(name.getInfraGenericEpithet());
 886         result.setSpeciesEpithet(name.getSpecificEpithet());
 887         result.setInfraSpecificEpithet(name.getInfraSpecificEpithet());
 888
 889         result.setAuthorship(name.getAuthorshipCache());
 890
 891         Rank rank = name.getRank();
 892         if (rank != null){
 893             result.setRankUuid(rank.getUuid());
 894             String rankLabel = rank.getAbbreviation();
 895             if (StringUtils.isBlank(rankLabel)){
 896                 rankLabel = rank.getLabel();
 897             }
 898             result.setRankLabel(rankLabel);
 899         }
 900
 901         boolean recursive = false;
 902         Integer pageSize = null;
 903         Integer pageIndex = null;
 904         Pager<TaxonNodeDto> children = taxonNodeService.pageChildNodesDTOs(taxonNodeUuid, recursive, doSynonyms, 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<Synonym>(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             List<DefinedTermBase> markerTypesTerms = termDao.list(ancestorMarkers, pageSize, null, null, null);
 927             List<MarkerType> markerTypes = new ArrayList<>();
 928             for (DefinedTermBase<?> term : markerTypesTerms){
 929                 if (term.isInstanceOf(MarkerType.class)){
 930                     markerTypes.add(CdmBase.deproxy(term, MarkerType.class));
 931                 }
 932             }
 933             if (! markerTypes.isEmpty()){
 934                 TaxonNode node = taxonNodeDao.findByUuid(taxonNodeUuid);
 935                 handleAncestorsForMarkersRecursive(result, markerTypes, node);
 936             }
 937         }
 938
 939         return result;
 940     }
 941
 942     /**
 943      * @param classificationUuid
 944      * @param acceptedTaxon
 945      * @return
 946      */
 947     private Taxon getParentTaxon(UUID classificationUuid, Taxon acceptedTaxon) {
 948         if (classificationUuid == null){
 949             return null;
 950         }
 951         TaxonNode parent = null;
 952         for (TaxonNode node : acceptedTaxon.getTaxonNodes()){
 953             if (classificationUuid.equals(node.getClassification().getUuid())){
 954                 parent = node.getParent();
 955             }
 956         }
 957         if (parent != null){
 958             return parent.getTaxon();
 959         }
 960         return null;
 961     }
 962
 963     /**
 964      * @param result
 965      * @param markerTypes
 966      * @param node
 967      */
 968     private void handleAncestorsForMarkersRecursive(TaxonInContextDTO result, List<MarkerType> markerTypes, TaxonNode node) {
 969        for (MarkerType type : markerTypes){
 970             Taxon taxon = node.getTaxon();
 971             if (taxon != null && taxon.hasMarker(type, true)){
 972                 String label =  taxon.getName() == null? taxon.getTitleCache() : taxon.getName().getTitleCache();
 973                 MarkedEntityDTO<Taxon> dto = new MarkedEntityDTO<>(type, true, taxon.getUuid(), label);
 974                 result.addMarkedAncestor(dto);
 975             }
 976         }
 977         TaxonNode parentNode = node.getParent();
 978         if (parentNode != null){
 979             handleAncestorsForMarkersRecursive(result, markerTypes, parentNode);
 980         }
 981     }
 982
 983
 984 }