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