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