cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/OccurrenceServiceImpl.java

   1 // $Id$
   2 /**
   3  * Copyright (C) 2007 EDIT
   4  * European Distributed Institute of Taxonomy
   5  * http://www.e-taxonomy.eu
   6  *
   7  * The contents of this file are subject to the Mozilla Public License Version 1.1
   8  * See LICENSE.TXT at the top of this package for the full license terms.
   9  */
  10
  11 package eu.etaxonomy.cdm.api.service;
  12
  13 import java.io.IOException;
  14 import java.net.URI;
  15 import java.net.URISyntaxException;
  16 import java.util.ArrayList;
  17 import java.util.Arrays;
  18 import java.util.Collection;
  19 import java.util.Collections;
  20 import java.util.HashMap;
  21 import java.util.HashSet;
  22 import java.util.List;
  23 import java.util.Map;
  24 import java.util.Map.Entry;
  25 import java.util.Set;
  26 import java.util.UUID;
  27
  28 import org.apache.log4j.Logger;
  29 import org.apache.lucene.index.CorruptIndexException;
  30 import org.apache.lucene.queryParser.ParseException;
  31 import org.apache.lucene.search.BooleanClause.Occur;
  32 import org.apache.lucene.search.BooleanQuery;
  33 import org.apache.lucene.search.SortField;
  34 import org.hibernate.TransientObjectException;
  35 import org.hibernate.search.spatial.impl.Rectangle;
  36 import org.joda.time.Partial;
  37 import org.springframework.beans.factory.annotation.Autowired;
  38 import org.springframework.dao.DataRetrievalFailureException;
  39 import org.springframework.stereotype.Service;
  40 import org.springframework.transaction.annotation.Transactional;
  41
  42 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
  43 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeConfigurator;
  44 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeNotSupportedException;
  45 import eu.etaxonomy.cdm.api.service.UpdateResult.Status;
  46 import eu.etaxonomy.cdm.api.service.config.DeleteConfiguratorBase;
  47 import eu.etaxonomy.cdm.api.service.config.FindOccurrencesConfigurator;
  48 import eu.etaxonomy.cdm.api.service.config.IIdentifiableEntityServiceConfigurator;
  49 import eu.etaxonomy.cdm.api.service.config.SpecimenDeleteConfigurator;
  50 import eu.etaxonomy.cdm.api.service.dto.DerivateDTO;
  51 import eu.etaxonomy.cdm.api.service.dto.DerivateDataDTO;
  52 import eu.etaxonomy.cdm.api.service.dto.DerivateDataDTO.ContigFile;
  53 import eu.etaxonomy.cdm.api.service.dto.DerivateDataDTO.MolecularData;
  54 import eu.etaxonomy.cdm.api.service.dto.FieldUnitDTO;
  55 import eu.etaxonomy.cdm.api.service.dto.PreservedSpecimenDTO;
  56 import eu.etaxonomy.cdm.api.service.exception.ReferencedObjectUndeletableException;
  57 import eu.etaxonomy.cdm.api.service.molecular.ISequenceService;
  58 import eu.etaxonomy.cdm.api.service.pager.Pager;
  59 import eu.etaxonomy.cdm.api.service.pager.impl.DefaultPagerImpl;
  60 import eu.etaxonomy.cdm.api.service.search.ILuceneIndexToolProvider;
  61 import eu.etaxonomy.cdm.api.service.search.ISearchResultBuilder;
  62 import eu.etaxonomy.cdm.api.service.search.LuceneSearch;
  63 import eu.etaxonomy.cdm.api.service.search.LuceneSearch.TopGroupsWithMaxScore;
  64 import eu.etaxonomy.cdm.api.service.search.QueryFactory;
  65 import eu.etaxonomy.cdm.api.service.search.SearchResult;
  66 import eu.etaxonomy.cdm.api.service.search.SearchResultBuilder;
  67 import eu.etaxonomy.cdm.api.service.util.TaxonRelationshipEdge;
  68 import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
  69 import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
  70 import eu.etaxonomy.cdm.model.CdmBaseType;
  71 import eu.etaxonomy.cdm.model.agent.AgentBase;
  72 import eu.etaxonomy.cdm.model.common.CdmBase;
  73 import eu.etaxonomy.cdm.model.common.DefinedTerm;
  74 import eu.etaxonomy.cdm.model.common.DefinedTermBase;
  75 import eu.etaxonomy.cdm.model.common.ICdmBase;
  76 import eu.etaxonomy.cdm.model.common.Language;
  77 import eu.etaxonomy.cdm.model.common.UuidAndTitleCache;
  78 import eu.etaxonomy.cdm.model.description.CategoricalData;
  79 import eu.etaxonomy.cdm.model.description.DescriptionBase;
  80 import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
  81 import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
  82 import eu.etaxonomy.cdm.model.description.QuantitativeData;
  83 import eu.etaxonomy.cdm.model.description.SpecimenDescription;
  84 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  85 import eu.etaxonomy.cdm.model.location.Country;
  86 import eu.etaxonomy.cdm.model.location.NamedArea;
  87 import eu.etaxonomy.cdm.model.media.Media;
  88 import eu.etaxonomy.cdm.model.media.MediaRepresentation;
  89 import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;
  90 import eu.etaxonomy.cdm.model.media.MediaUtils;
  91 import eu.etaxonomy.cdm.model.molecular.AmplificationResult;
  92 import eu.etaxonomy.cdm.model.molecular.DnaSample;
  93 import eu.etaxonomy.cdm.model.molecular.Sequence;
  94 import eu.etaxonomy.cdm.model.molecular.SingleRead;
  95 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
  96 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  97 import eu.etaxonomy.cdm.model.name.TypeDesignationStatusBase;
  98 import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
  99 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
 100 import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
 101 import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
 102 import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
 103 import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen;
 104 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
 105 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
 106 import eu.etaxonomy.cdm.model.taxon.Taxon;
 107 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
 108 import eu.etaxonomy.cdm.persistence.dao.common.IDefinedTermDao;
 109 import eu.etaxonomy.cdm.persistence.dao.initializer.AbstractBeanInitializer;
 110 import eu.etaxonomy.cdm.persistence.dao.occurrence.IOccurrenceDao;
 111 import eu.etaxonomy.cdm.persistence.query.OrderHint;
 112 import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
 113
 114 /**
 115  * @author a.babadshanjan
 116  * @created 01.09.2008
 117  */
 118 @Service
 119 @Transactional(readOnly = true)
 120 public class OccurrenceServiceImpl extends IdentifiableServiceBase<SpecimenOrObservationBase, IOccurrenceDao> implements IOccurrenceService {
 121
 122     static private final Logger logger = Logger.getLogger(OccurrenceServiceImpl.class);
 123
 124     @Autowired
 125     private IDefinedTermDao definedTermDao;
 126
 127     @Autowired
 128     private IDescriptionService descriptionService;
 129
 130     @Autowired
 131     private ITaxonService taxonService;
 132
 133     @Autowired
 134     private ISequenceService sequenceService;
 135
 136     @Autowired
 137     private AbstractBeanInitializer beanInitializer;
 138
 139     @Autowired
 140     private ILuceneIndexToolProvider luceneIndexToolProvider;
 141
 142     private static final String SEPARATOR_STRING = ", ";
 143
 144     public OccurrenceServiceImpl() {
 145         logger.debug("Load OccurrenceService Bean");
 146     }
 147
 148
 149     /* (non-Javadoc)
 150      * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#updateTitleCache(java.lang.Integer, eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy)
 151      */
 152     @Override
 153     @Transactional(readOnly = false)
 154     public void updateTitleCache(Class<? extends SpecimenOrObservationBase> clazz, Integer stepSize, IIdentifiableEntityCacheStrategy<SpecimenOrObservationBase> cacheStrategy, IProgressMonitor monitor) {
 155         if (clazz == null) {
 156             clazz = SpecimenOrObservationBase.class;
 157         }
 158         super.updateTitleCacheImpl(clazz, stepSize, cacheStrategy, monitor);
 159     }
 160
 161     /**
 162      * FIXME Candidate for harmonization
 163      * move to termService
 164      */
 165     @Override
 166     public Country getCountryByIso(String iso639) {
 167         return this.definedTermDao.getCountryByIso(iso639);
 168
 169     }
 170
 171     /**
 172      * FIXME Candidate for harmonization
 173      * move to termService
 174      */
 175     @Override
 176     public List<Country> getCountryByName(String name) {
 177         List<? extends DefinedTermBase> terms = this.definedTermDao.findByTitle(Country.class, name, null, null, null, null, null, null);
 178         List<Country> countries = new ArrayList<Country>();
 179         for (int i = 0; i < terms.size(); i++) {
 180             countries.add((Country) terms.get(i));
 181         }
 182         return countries;
 183     }
 184
 185     @Override
 186     @Autowired
 187     protected void setDao(IOccurrenceDao dao) {
 188         this.dao = dao;
 189     }
 190
 191     @Override
 192     public Pager<DerivationEvent> getDerivationEvents(SpecimenOrObservationBase occurence, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
 193         Integer numberOfResults = dao.countDerivationEvents(occurence);
 194
 195         List<DerivationEvent> results = new ArrayList<DerivationEvent>();
 196         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 197             results = dao.getDerivationEvents(occurence, pageSize, pageNumber, propertyPaths);
 198         }
 199
 200         return new DefaultPagerImpl<DerivationEvent>(pageNumber, numberOfResults, pageSize, results);
 201     }
 202
 203     /* (non-Javadoc)
 204      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#countDeterminations(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase, eu.etaxonomy.cdm.model.taxon.TaxonBase)
 205      */
 206     @Override
 207     public int countDeterminations(SpecimenOrObservationBase occurence, TaxonBase taxonbase) {
 208         return dao.countDeterminations(occurence, taxonbase);
 209     }
 210
 211     @Override
 212     public Pager<DeterminationEvent> getDeterminations(SpecimenOrObservationBase occurrence, TaxonBase taxonBase, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
 213         Integer numberOfResults = dao.countDeterminations(occurrence, taxonBase);
 214
 215         List<DeterminationEvent> results = new ArrayList<DeterminationEvent>();
 216         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 217             results = dao.getDeterminations(occurrence, taxonBase, pageSize, pageNumber, propertyPaths);
 218         }
 219
 220         return new DefaultPagerImpl<DeterminationEvent>(pageNumber, numberOfResults, pageSize, results);
 221     }
 222
 223     @Override
 224     public Pager<Media> getMedia(SpecimenOrObservationBase occurence, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
 225         Integer numberOfResults = dao.countMedia(occurence);
 226
 227         List<Media> results = new ArrayList<Media>();
 228         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 229             results = dao.getMedia(occurence, pageSize, pageNumber, propertyPaths);
 230         }
 231
 232         return new DefaultPagerImpl<Media>(pageNumber, numberOfResults, pageSize, results);
 233     }
 234
 235     /* (non-Javadoc)
 236      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#list(java.lang.Class, eu.etaxonomy.cdm.model.taxon.TaxonBase, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
 237      */
 238     @Override
 239     public Pager<SpecimenOrObservationBase> list(Class<? extends SpecimenOrObservationBase> type, TaxonBase determinedAs, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 240         Integer numberOfResults = dao.count(type, determinedAs);
 241         List<SpecimenOrObservationBase> results = new ArrayList<SpecimenOrObservationBase>();
 242         pageNumber = pageNumber == null ? 0 : pageNumber;
 243         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 244             Integer start = pageSize == null ? 0 : pageSize * pageNumber;
 245             results = dao.list(type, determinedAs, pageSize, start, orderHints, propertyPaths);
 246         }
 247         return new DefaultPagerImpl<SpecimenOrObservationBase>(pageNumber, numberOfResults, pageSize, results);
 248     }
 249
 250     @Override
 251     public List<UuidAndTitleCache<DerivedUnit>> getDerivedUnitUuidAndTitleCache() {
 252         return dao.getDerivedUnitUuidAndTitleCache();
 253     }
 254
 255     @Override
 256     public List<UuidAndTitleCache<FieldUnit>> getFieldUnitUuidAndTitleCache() {
 257         return dao.getFieldUnitUuidAndTitleCache();
 258     }
 259
 260     /* (non-Javadoc)
 261      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getDerivedUnitFacade(eu.etaxonomy.cdm.model.occurrence.DerivedUnit)
 262      */
 263     @Override
 264     public DerivedUnitFacade getDerivedUnitFacade(DerivedUnit derivedUnit, List<String> propertyPaths) throws DerivedUnitFacadeNotSupportedException {
 265         derivedUnit = (DerivedUnit) dao.load(derivedUnit.getUuid(), null);
 266         DerivedUnitFacadeConfigurator config = DerivedUnitFacadeConfigurator.NewInstance();
 267         config.setThrowExceptionForNonSpecimenPreservationMethodRequest(false);
 268         DerivedUnitFacade derivedUnitFacade = DerivedUnitFacade.NewInstance(derivedUnit, config);
 269         beanInitializer.initialize(derivedUnitFacade, propertyPaths);
 270         return derivedUnitFacade;
 271     }
 272
 273     /* (non-Javadoc)
 274      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#listDerivedUnitFacades(eu.etaxonomy.cdm.model.description.DescriptionBase, java.util.List)
 275      */
 276     @Override
 277     public List<DerivedUnitFacade> listDerivedUnitFacades(
 278             DescriptionBase description, List<String> propertyPaths) {
 279
 280         List<DerivedUnitFacade> derivedUnitFacadeList = new ArrayList<DerivedUnitFacade>();
 281         IndividualsAssociation tempIndividualsAssociation;
 282         SpecimenOrObservationBase tempSpecimenOrObservationBase;
 283         List<DescriptionElementBase> elements = descriptionService.listDescriptionElements(description, null, IndividualsAssociation.class, null, 0, Arrays.asList(new String []{"associatedSpecimenOrObservation"}));
 284         for (DescriptionElementBase element : elements) {
 285             if (element.isInstanceOf(IndividualsAssociation.class)) {
 286                 tempIndividualsAssociation = HibernateProxyHelper.deproxy(element, IndividualsAssociation.class);
 287                 if (tempIndividualsAssociation.getAssociatedSpecimenOrObservation() != null) {
 288                     tempSpecimenOrObservationBase = HibernateProxyHelper.deproxy(tempIndividualsAssociation.getAssociatedSpecimenOrObservation(), SpecimenOrObservationBase.class);
 289                     if (tempSpecimenOrObservationBase.isInstanceOf(DerivedUnit.class)) {
 290                         try {
 291                             derivedUnitFacadeList.add(DerivedUnitFacade.NewInstance(HibernateProxyHelper.deproxy(tempSpecimenOrObservationBase, DerivedUnit.class)));
 292                         } catch (DerivedUnitFacadeNotSupportedException e) {
 293                             logger.warn(tempIndividualsAssociation.getAssociatedSpecimenOrObservation().getTitleCache() + " : " + e.getMessage());
 294                         }
 295                     }
 296                 }
 297
 298             }
 299         }
 300
 301         beanInitializer.initializeAll(derivedUnitFacadeList, propertyPaths);
 302
 303         return derivedUnitFacadeList;
 304     }
 305
 306
 307     /* (non-Javadoc)
 308      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#listByAnyAssociation(java.lang.Class, java.util.Set, eu.etaxonomy.cdm.model.taxon.Taxon, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
 309      */
 310     @Override
 311     public <T extends SpecimenOrObservationBase> List<T> listByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
 312             Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 313
 314         return pageByAssociatedTaxon(type, includeRelationships, associatedTaxon, maxDepth, pageSize, pageNumber, orderHints, propertyPaths).getRecords();
 315     }
 316
 317     /* (non-Javadoc)
 318      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#listByAnyAssociation(java.lang.Class, java.util.Set, eu.etaxonomy.cdm.model.taxon.Taxon, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
 319      */
 320     @Override
 321     public Collection<SpecimenOrObservationBase> listFieldUnitsByAssociatedTaxon(Taxon associatedTaxon, List<OrderHint> orderHints, List<String> propertyPaths) {
 322         return pageFieldUnitsByAssociatedTaxon(null, associatedTaxon, null, null, null, null, propertyPaths).getRecords();
 323     }
 324
 325     /* (non-Javadoc)
 326      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#pageFieldUnitsByAssociatedTaxon(java.util.Set, eu.etaxonomy.cdm.model.taxon.Taxon, java.lang.Integer, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
 327      */
 328     @Override
 329     public Pager<SpecimenOrObservationBase> pageFieldUnitsByAssociatedTaxon(Set<TaxonRelationshipEdge> includeRelationships,
 330             Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
 331             List<String> propertyPaths) {
 332
 333         if (!getSession().contains(associatedTaxon)) {
 334             associatedTaxon = (Taxon) taxonService.load(associatedTaxon.getUuid());
 335         }
 336
 337         // gather the IDs of all relevant field units
 338         Set<Integer> fieldUnitIds = new HashSet<Integer>();
 339         List<SpecimenOrObservationBase> records = listByAssociatedTaxon(null, includeRelationships, associatedTaxon, maxDepth, null, null, orderHints, propertyPaths);
 340         for (SpecimenOrObservationBase<?> specimen : records) {
 341             for (FieldUnit fieldUnit : getFieldUnits(specimen.getUuid())) {
 342                 fieldUnitIds.add(fieldUnit.getId());
 343             }
 344         }
 345         //dao.listByIds() does the paging of the field units. Passing the field units directly to the Pager would not work
 346         List<SpecimenOrObservationBase> fieldUnits = dao.listByIds(fieldUnitIds, pageSize, pageNumber, orderHints, propertyPaths);
 347         return new DefaultPagerImpl<SpecimenOrObservationBase>(pageNumber, fieldUnitIds.size(), pageSize, fieldUnits);
 348     }
 349
 350     @Override
 351     public FieldUnitDTO assembleFieldUnitDTO(FieldUnit fieldUnit, UUID associatedTaxonUuid) {
 352
 353         if (!getSession().contains(fieldUnit)) {
 354             fieldUnit = (FieldUnit) load(fieldUnit.getUuid());
 355         }
 356         TaxonBase associatedTaxon = taxonService.load(associatedTaxonUuid);
 357
 358         FieldUnitDTO fieldUnitDTO = new FieldUnitDTO();
 359
 360         if (fieldUnit.getGatheringEvent() != null) {
 361             GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
 362             // Country
 363             NamedArea country = gatheringEvent.getCountry();
 364             fieldUnitDTO.setCountry(country != null ? country.getDescription() : null);
 365             // Collection
 366             AgentBase collector = gatheringEvent.getCollector();
 367             String fieldNumber = fieldUnit.getFieldNumber();
 368             String collectionString = "";
 369             if (collector != null || fieldNumber != null) {
 370                 collectionString += collector != null ? collector : "";
 371                 if (!collectionString.isEmpty()) {
 372                     collectionString += " ";
 373                 }
 374                 collectionString += (fieldNumber != null ? fieldNumber : "");
 375                 collectionString.trim();
 376             }
 377             fieldUnitDTO.setCollection(collectionString);
 378             // Date
 379             Partial gatheringDate = gatheringEvent.getGatheringDate();
 380             String dateString = null;
 381             if (gatheringDate != null) {
 382                 gatheringDate.toString();
 383             }
 384             else if(gatheringEvent.getTimeperiod()!=null && gatheringEvent.getTimeperiod().getFreeText()!=null){
 385                 dateString = gatheringEvent.getTimeperiod().getFreeText();
 386             }
 387             fieldUnitDTO.setDate(dateString);
 388         }
 389
 390         // Taxon Name
 391         fieldUnitDTO.setTaxonName(associatedTaxon.getName().getTitleCache());
 392
 393         // Herbaria map
 394         Map<eu.etaxonomy.cdm.model.occurrence.Collection, Integer> collectionToCountMap = new HashMap<eu.etaxonomy.cdm.model.occurrence.Collection, Integer>();
 395         // List of accession numbers for citation
 396         List<String> preservedSpecimenAccessionNumbers = new ArrayList<String>();
 397
 398         // assemble preserved specimen DTOs
 399         Set<DerivationEvent> derivationEvents = fieldUnit.getDerivationEvents();
 400         for (DerivationEvent derivationEvent : derivationEvents) {
 401             Set<DerivedUnit> derivatives = derivationEvent.getDerivatives();
 402             for (DerivedUnit derivedUnit : derivatives) {
 403                 // collect accession numbers for citation
 404                 String mostSignificantIdentifier = getMostSignificantIdentifier(derivedUnit);
 405                 if (mostSignificantIdentifier != null) {
 406                     preservedSpecimenAccessionNumbers.add(mostSignificantIdentifier);
 407                 }
 408                 // collect collections for herbaria column
 409                 if (derivedUnit.getCollection() != null) {
 410                     Integer herbariumCount = collectionToCountMap.get(derivedUnit.getCollection());
 411                     if (herbariumCount == null) {
 412                         herbariumCount = 0;
 413                     }
 414                     collectionToCountMap.put(derivedUnit.getCollection(), herbariumCount + 1);
 415                 }
 416                 if (derivedUnit.getRecordBasis().equals(SpecimenOrObservationType.PreservedSpecimen)) {
 417                     PreservedSpecimenDTO preservedSpecimenDTO = assemblePreservedSpecimenDTO(derivedUnit, fieldUnitDTO);
 418                     fieldUnitDTO.addPreservedSpecimenDTO(preservedSpecimenDTO);
 419                     fieldUnitDTO.setHasCharacterData(fieldUnitDTO.isHasCharacterData() || preservedSpecimenDTO.isHasCharacterData());
 420                     fieldUnitDTO.setHasDetailImage(fieldUnitDTO.isHasDetailImage() || preservedSpecimenDTO.isHasDetailImage());
 421                     fieldUnitDTO.setHasDna(fieldUnitDTO.isHasDna() || preservedSpecimenDTO.isHasDna());
 422                     fieldUnitDTO.setHasSpecimenScan(fieldUnitDTO.isHasSpecimenScan() || preservedSpecimenDTO.isHasSpecimenScan());
 423                 }
 424             }
 425         }
 426         // assemble derivate data DTO
 427         assembleDerivateDataDTO(fieldUnitDTO, fieldUnit);
 428
 429         // assemble citation
 430         String citation = fieldUnit.getTitleCache();
 431         if (!preservedSpecimenAccessionNumbers.isEmpty()) {
 432             citation += " (";
 433             for (String accessionNumber : preservedSpecimenAccessionNumbers) {
 434                 if (!accessionNumber.isEmpty()) {
 435                     citation += accessionNumber + SEPARATOR_STRING;
 436                 }
 437             }
 438             citation = removeTail(citation, SEPARATOR_STRING);
 439             citation += ")";
 440         }
 441         fieldUnitDTO.setCitation(citation);
 442
 443         // assemble herbaria string
 444         String herbariaString = "";
 445         for (Entry<eu.etaxonomy.cdm.model.occurrence.Collection, Integer> e : collectionToCountMap.entrySet()) {
 446             eu.etaxonomy.cdm.model.occurrence.Collection collection = e.getKey();
 447             if (collection.getCode() != null) {
 448                 herbariaString += collection.getCode();
 449             }
 450             if (e.getValue() > 1) {
 451                 herbariaString += "(" + e.getValue() + ")";
 452             }
 453             herbariaString += SEPARATOR_STRING;
 454         }
 455         herbariaString = removeTail(herbariaString, SEPARATOR_STRING);
 456         fieldUnitDTO.setHerbarium(herbariaString);
 457
 458         return fieldUnitDTO;
 459     }
 460
 461     @Override
 462     public PreservedSpecimenDTO assemblePreservedSpecimenDTO(DerivedUnit derivedUnit) {
 463         return assemblePreservedSpecimenDTO(derivedUnit, null);
 464     }
 465
 466     @Override
 467     public String getMostSignificantIdentifier(DerivedUnit derivedUnit) {
 468         if (derivedUnit.getAccessionNumber() != null && !derivedUnit.getAccessionNumber().isEmpty()) {
 469             return derivedUnit.getAccessionNumber();
 470         }
 471         else if(derivedUnit.getBarcode()!=null && !derivedUnit.getBarcode().isEmpty()){
 472             return derivedUnit.getBarcode();
 473         }
 474         else if(derivedUnit.getCatalogNumber()!=null && !derivedUnit.getCatalogNumber().isEmpty()){
 475             return derivedUnit.getCatalogNumber();
 476         }
 477         return null;
 478     }
 479
 480     public PreservedSpecimenDTO assemblePreservedSpecimenDTO(DerivedUnit derivedUnit, FieldUnitDTO fieldUnitDTO) {
 481         if (!getSession().contains(derivedUnit)) {
 482             derivedUnit = (DerivedUnit) load(derivedUnit.getUuid());
 483         }
 484         PreservedSpecimenDTO preservedSpecimenDTO = new PreservedSpecimenDTO();
 485
 486         // check identifiers in priority order accNo>barCode>catalogNumber
 487         if (derivedUnit.getAccessionNumber() != null && !derivedUnit.getAccessionNumber().isEmpty()) {
 488             preservedSpecimenDTO.setAccessionNumber(derivedUnit.getAccessionNumber());
 489         }
 490         else if(derivedUnit.getBarcode()!=null && !derivedUnit.getBarcode().isEmpty()){
 491             preservedSpecimenDTO.setAccessionNumber(derivedUnit.getBarcode());
 492         }
 493         else if(derivedUnit.getCatalogNumber()!=null && !derivedUnit.getCatalogNumber().isEmpty()){
 494             preservedSpecimenDTO.setAccessionNumber(derivedUnit.getCatalogNumber());
 495         }
 496         preservedSpecimenDTO.setUuid(derivedUnit.getUuid().toString());
 497
 498         // citation
 499         Collection<FieldUnit> fieldUnits = getFieldUnits(derivedUnit);
 500         if (fieldUnits.size() == 1) {
 501             preservedSpecimenDTO.setCitation(fieldUnits.iterator().next().getTitleCache());
 502         }
 503         else{
 504             preservedSpecimenDTO.setCitation("No Citation available. This specimen either has no or multiple field units.");
 505         }
 506
 507         // character state data
 508         Collection<DescriptionElementBase> characterDataForSpecimen = getCharacterDataForSpecimen(derivedUnit);
 509         if (!characterDataForSpecimen.isEmpty()) {
 510             if (fieldUnitDTO != null) {
 511                 fieldUnitDTO.setHasCharacterData(true);
 512             }
 513         }
 514         for (DescriptionElementBase descriptionElementBase : characterDataForSpecimen) {
 515             String character = descriptionElementBase.getFeature().getLabel();
 516             ArrayList<Language> languages = new ArrayList<Language>(Collections.singleton(Language.DEFAULT()));
 517             if (descriptionElementBase instanceof QuantitativeData) {
 518                 QuantitativeData quantitativeData = (QuantitativeData) descriptionElementBase;
 519                 DefaultQuantitativeDescriptionBuilder builder = new DefaultQuantitativeDescriptionBuilder();
 520                 String state = builder.build(quantitativeData, languages).getText(Language.DEFAULT());
 521                 preservedSpecimenDTO.addCharacterData(character, state);
 522             }
 523             else if(descriptionElementBase instanceof CategoricalData){
 524                 CategoricalData categoricalData = (CategoricalData) descriptionElementBase;
 525                 DefaultCategoricalDescriptionBuilder builder = new DefaultCategoricalDescriptionBuilder();
 526                 String state = builder.build(categoricalData, languages).getText(Language.DEFAULT());
 527                 preservedSpecimenDTO.addCharacterData(character, state);
 528             }
 529         }
 530         // check type designations
 531         Collection<SpecimenTypeDesignation> specimenTypeDesignations = listTypeDesignations(derivedUnit, null, null, null, null);
 532         for (SpecimenTypeDesignation specimenTypeDesignation : specimenTypeDesignations) {
 533             if (fieldUnitDTO != null) {
 534                 fieldUnitDTO.setHasType(true);
 535             }
 536             TypeDesignationStatusBase<?> typeStatus = specimenTypeDesignation.getTypeStatus();
 537             if (typeStatus != null) {
 538                 List<String> typedTaxaNames = new ArrayList<String>();
 539                 String label = typeStatus.getLabel();
 540                 Set<TaxonNameBase> typifiedNames = specimenTypeDesignation.getTypifiedNames();
 541                 for (TaxonNameBase taxonNameBase : typifiedNames) {
 542                     typedTaxaNames.add(taxonNameBase.getFullTitleCache());
 543                 }
 544                 preservedSpecimenDTO.addTypes(label, typedTaxaNames);
 545             }
 546         }
 547
 548         // individuals associations
 549         Collection<IndividualsAssociation> individualsAssociations = listIndividualsAssociations(derivedUnit, null, null, null, null);
 550         for (IndividualsAssociation individualsAssociation : individualsAssociations) {
 551             if (individualsAssociation.getInDescription() != null) {
 552                 if (individualsAssociation.getInDescription().isInstanceOf(TaxonDescription.class)) {
 553                     TaxonDescription taxonDescription = HibernateProxyHelper.deproxy(individualsAssociation.getInDescription(), TaxonDescription.class);
 554                     Taxon taxon = taxonDescription.getTaxon();
 555                     if (taxon != null && taxon.getName() != null) {
 556                         preservedSpecimenDTO.addAssociatedTaxon(taxon.getName().getTitleCache());
 557                     }
 558                 }
 559             }
 560         }
 561         // assemble sub derivates
 562         preservedSpecimenDTO.setDerivateDataDTO(assembleDerivateDataDTO(preservedSpecimenDTO, derivedUnit));
 563         return preservedSpecimenDTO;
 564     }
 565
 566     /**
 567      * @param derivedUnit
 568      * @param derivateDataDTO
 569      * @return
 570      */
 571     private DerivateDataDTO assembleDerivateDataDTO(DerivateDTO derivateDTO, SpecimenOrObservationBase<?> specimenOrObservation) {
 572         DerivateDataDTO derivateDataDTO = new DerivateDataDTO();
 573         Collection<DerivedUnit> childDerivates = getDerivedUnitsFor(specimenOrObservation);
 574         for (DerivedUnit childDerivate : childDerivates) {
 575             // assemble molecular data
 576             //pattern: DNAMarker [contig1, primer1_1, primer1_2, ...][contig2, primer2_1, ...]...
 577             if (childDerivate.isInstanceOf(DnaSample.class)) {
 578                 if (childDerivate.getRecordBasis() == SpecimenOrObservationType.TissueSample) {
 579                     // TODO implement TissueSample assembly for web service
 580                 }
 581                 if (childDerivate.getRecordBasis() == SpecimenOrObservationType.DnaSample) {
 582
 583                     DnaSample dna = HibernateProxyHelper.deproxy(childDerivate, DnaSample.class);
 584                     if (!dna.getSequences().isEmpty()) {
 585                         derivateDTO.setHasDna(true);
 586                     }
 587                     for (Sequence sequence : dna.getSequences()) {
 588                         URI boldUri = null;
 589                         try {
 590                             boldUri = sequence.getBoldUri();
 591                         } catch (URISyntaxException e1) {
 592                             logger.error("Could not create BOLD URI", e1);
 593                         }
 594                         final DefinedTerm dnaMarker = sequence.getDnaMarker();
 595                         MolecularData molecularData = derivateDataDTO.addProviderLink(boldUri != null ? boldUri : null, dnaMarker != null ? dnaMarker.getLabel() : "[no marker]");
 596
 597                         //contig file
 598                         ContigFile contigFile = null;
 599                         if (sequence.getContigFile() != null) {
 600                             MediaRepresentationPart contigMediaRepresentationPart = MediaUtils.getFirstMediaRepresentationPart(sequence.getContigFile());
 601                             if (contigMediaRepresentationPart != null) {
 602                                 contigFile = molecularData.addContigFile(contigMediaRepresentationPart.getUri(), "contig");
 603                             }
 604                         }
 605                         if(contigFile==null){
 606                             contigFile = molecularData.addContigFile(null, "[no contig]");
 607                         }
 608                         // primer files
 609                         if (sequence.getSingleReads() != null) {
 610                             int readCount = 1;
 611                             for (SingleRead singleRead : sequence.getSingleReads()) {
 612                                 MediaRepresentationPart pherogramMediaRepresentationPart = MediaUtils.getFirstMediaRepresentationPart(singleRead.getPherogram());
 613                                 if (pherogramMediaRepresentationPart != null) {
 614                                     contigFile.addPrimerLink(pherogramMediaRepresentationPart.getUri(), "read"+readCount++);
 615                                 }
 616                             }
 617                         }
 618                     }
 619                 }
 620             }
 621             // assemble media data
 622             else if (childDerivate.isInstanceOf(MediaSpecimen.class)) {
 623                 MediaSpecimen media = HibernateProxyHelper.deproxy(childDerivate, MediaSpecimen.class);
 624
 625                 String mediaUriString = getMediaUriString(media);
 626                 if (media.getKindOfUnit() != null) {
 627                     // specimen scan
 628                     if (media.getKindOfUnit().getUuid().equals(UUID.fromString("acda15be-c0e2-4ea8-8783-b9b0c4ad7f03"))) {
 629                         derivateDataDTO.addSpecimenScanUuid(media.getMediaSpecimen().getUuid());
 630                         derivateDTO.setHasSpecimenScan(true);
 631                         String imageLinkText = "scan";
 632                         if (derivateDTO instanceof PreservedSpecimenDTO && ((PreservedSpecimenDTO) derivateDTO).getAccessionNumber() != null) {
 633                             imageLinkText = ((PreservedSpecimenDTO) derivateDTO).getAccessionNumber();
 634                         }
 635                         derivateDataDTO.addSpecimenScan(mediaUriString == null ? "" : mediaUriString, imageLinkText);
 636                     }
 637                     // detail image
 638                     else if (media.getKindOfUnit().getUuid().equals(UUID.fromString("31eb8d02-bf5d-437c-bcc6-87a626445f34"))) {
 639                         derivateDataDTO.addDetailImageUuid(media.getMediaSpecimen().getUuid());
 640                         derivateDTO.setHasDetailImage(true);
 641                         String motif = "";
 642                         if (media.getMediaSpecimen() != null && media.getMediaSpecimen().getTitle() != null) {
 643                             motif = media.getMediaSpecimen().getTitle().getText();
 644                         }
 645                         derivateDataDTO.addDetailImage(mediaUriString == null ? "" : mediaUriString, motif != null ? motif : "[no motif]");
 646                     }
 647                 }
 648             }
 649         }
 650         return derivateDataDTO;
 651     }
 652
 653     /**
 654      * @param string
 655      * @param tail
 656      * @return
 657      */
 658     private String removeTail(String string, final String tail) {
 659         if (string.endsWith(tail)) {
 660             string = string.substring(0, string.length() - tail.length());
 661         }
 662         return string;
 663     }
 664
 665     private String getMediaUriString(MediaSpecimen mediaSpecimen) {
 666         String mediaUri = null;
 667         Collection<MediaRepresentation> mediaRepresentations = mediaSpecimen.getMediaSpecimen().getRepresentations();
 668         if (mediaRepresentations != null && !mediaRepresentations.isEmpty()) {
 669             Collection<MediaRepresentationPart> mediaRepresentationParts = mediaRepresentations.iterator().next().getParts();
 670             if (mediaRepresentationParts != null && !mediaRepresentationParts.isEmpty()) {
 671                 MediaRepresentationPart part = mediaRepresentationParts.iterator().next();
 672                 if (part.getUri() != null) {
 673                     mediaUri = part.getUri().toASCIIString();
 674                 }
 675             }
 676         }
 677         return mediaUri;
 678     }
 679
 680     private Collection<DerivedUnit> getDerivedUnitsFor(SpecimenOrObservationBase<?> specimen) {
 681         Collection<DerivedUnit> derivedUnits = new ArrayList<DerivedUnit>();
 682         for (DerivationEvent derivationEvent : specimen.getDerivationEvents()) {
 683             for (DerivedUnit derivative : derivationEvent.getDerivatives()) {
 684                 derivedUnits.add(derivative);
 685                 derivedUnits.addAll(getDerivedUnitsFor(derivative));
 686             }
 687         }
 688         return derivedUnits;
 689     }
 690
 691
 692     /* (non-Javadoc)
 693      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#pageByAssociatedTaxon(java.lang.Class, java.util.Set, eu.etaxonomy.cdm.model.taxon.Taxon, java.lang.Integer, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
 694      */
 695     @SuppressWarnings("unchecked")
 696     @Override
 697     public <T extends SpecimenOrObservationBase> Pager<T> pageByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
 698             Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 699
 700         Set<Taxon> taxa = new HashSet<Taxon>();
 701         Set<Integer> occurrenceIds = new HashSet<Integer>();
 702         List<T> occurrences = new ArrayList<T>();
 703
 704         // Integer limit = PagerUtils.limitFor(pageSize);
 705         // Integer start = PagerUtils.startFor(pageSize, pageNumber);
 706
 707         if (!getSession().contains(associatedTaxon)) {
 708             associatedTaxon = (Taxon) taxonService.load(associatedTaxon.getUuid());
 709         }
 710
 711         if (includeRelationships != null) {
 712             taxa = taxonService.listRelatedTaxa(associatedTaxon, includeRelationships, maxDepth, null, null, propertyPaths);
 713         }
 714
 715         taxa.add(associatedTaxon);
 716
 717         for (Taxon taxon : taxa) {
 718             List<T> perTaxonOccurrences = dao.listByAssociatedTaxon(type, taxon, null, null, orderHints, propertyPaths);
 719             for (SpecimenOrObservationBase o : perTaxonOccurrences) {
 720                 occurrenceIds.add(o.getId());
 721             }
 722         }
 723         occurrences = (List<T>) dao.listByIds(occurrenceIds, pageSize, pageNumber, orderHints, propertyPaths);
 724
 725         return new DefaultPagerImpl<T>(pageNumber, occurrenceIds.size(), pageSize, occurrences);
 726
 727     }
 728
 729     @Override
 730     public <T extends SpecimenOrObservationBase> Pager<T> pageByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
 731             String taxonUUID, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 732
 733         UUID uuid = UUID.fromString(taxonUUID);
 734         Taxon tax = (Taxon) taxonService.load(uuid);
 735         // TODO REMOVE NULL STATEMENT
 736         type = null;
 737         return pageByAssociatedTaxon(type, includeRelationships, tax, maxDepth, pageSize, pageNumber, orderHints, propertyPaths);
 738
 739     }
 740
 741     @Override
 742     public Pager<SearchResult<SpecimenOrObservationBase>> findByFullText(
 743             Class<? extends SpecimenOrObservationBase> clazz, String queryString, Rectangle boundingBox, List<Language> languages,
 744             boolean highlightFragments, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
 745             List<String> propertyPaths) throws CorruptIndexException, IOException, ParseException {
 746
 747         LuceneSearch luceneSearch = prepareByFullTextSearch(clazz, queryString, boundingBox, languages, highlightFragments);
 748
 749         // --- execute search
 750         TopGroupsWithMaxScore topDocsResultSet = luceneSearch.executeSearch(pageSize, pageNumber);
 751
 752         Map<CdmBaseType, String> idFieldMap = new HashMap<CdmBaseType, String>();
 753         idFieldMap.put(CdmBaseType.SPECIMEN_OR_OBSERVATIONBASE, "id");
 754
 755         // --- initialize taxa, highlight matches ....
 756         ISearchResultBuilder searchResultBuilder = new SearchResultBuilder(luceneSearch, luceneSearch.getQuery());
 757         @SuppressWarnings("rawtypes")
 758         List<SearchResult<SpecimenOrObservationBase>> searchResults = searchResultBuilder.createResultSet(
 759                 topDocsResultSet, luceneSearch.getHighlightFields(), dao, idFieldMap, propertyPaths);
 760
 761         int totalHits = topDocsResultSet != null ? topDocsResultSet.topGroups.totalGroupCount : 0;
 762
 763         return new DefaultPagerImpl<SearchResult<SpecimenOrObservationBase>>(pageNumber, totalHits, pageSize,
 764                 searchResults);
 765
 766     }
 767
 768     /**
 769      * @param clazz
 770      * @param queryString
 771      * @param languages
 772      * @param highlightFragments
 773      * @return
 774      */
 775     private LuceneSearch prepareByFullTextSearch(Class<? extends SpecimenOrObservationBase> clazz, String queryString, Rectangle bbox,
 776             List<Language> languages, boolean highlightFragments) {
 777
 778         BooleanQuery finalQuery = new BooleanQuery();
 779         BooleanQuery textQuery = new BooleanQuery();
 780
 781         LuceneSearch luceneSearch = new LuceneSearch(luceneIndexToolProvider, FieldUnit.class);
 782         QueryFactory queryFactory = luceneIndexToolProvider.newQueryFactoryFor(FieldUnit.class);
 783
 784         // --- criteria
 785         luceneSearch.setCdmTypRestriction(clazz);
 786         if (queryString != null) {
 787             textQuery.add(queryFactory.newTermQuery("titleCache", queryString), Occur.SHOULD);
 788             finalQuery.add(textQuery, Occur.MUST);
 789         }
 790
 791         // --- spacial query
 792         if (bbox != null) {
 793             finalQuery.add(QueryFactory.buildSpatialQueryByRange(bbox, "gatheringEvent.exactLocation.point"), Occur.MUST);
 794         }
 795
 796         luceneSearch.setQuery(finalQuery);
 797
 798         // --- sorting
 799         SortField[] sortFields = new SortField[] { SortField.FIELD_SCORE, new SortField("titleCache__sort", SortField.STRING, false) };
 800         luceneSearch.setSortFields(sortFields);
 801
 802         if (highlightFragments) {
 803             luceneSearch.setHighlightFields(queryFactory.getTextFieldNamesAsArray());
 804         }
 805         return luceneSearch;
 806     }
 807
 808
 809     /* (non-Javadoc)
 810      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getFieldUnits(eu.etaxonomy.cdm.model.occurrence.DerivedUnit)
 811      */
 812     @Override
 813     public Collection<FieldUnit> getFieldUnits(UUID derivedUnitUuid) {
 814         //It will search recursively over all {@link DerivationEvent}s and get the "originals" ({@link SpecimenOrObservationBase})
 815         //from which this DerivedUnit was derived until all FieldUnits are found.
 816
 817         // FIXME: use HQL queries to increase performance
 818         SpecimenOrObservationBase<?> specimen = load(derivedUnitUuid);
 819 //        specimen = HibernateProxyHelper.deproxy(specimen, SpecimenOrObservationBase.class);
 820         Collection<FieldUnit> fieldUnits = new ArrayList<FieldUnit>();
 821
 822         if (specimen.isInstanceOf(FieldUnit.class)) {
 823             fieldUnits.add(HibernateProxyHelper.deproxy(specimen, FieldUnit.class));
 824         }
 825         else if(specimen.isInstanceOf(DerivedUnit.class)){
 826             fieldUnits.addAll(getFieldUnits(HibernateProxyHelper.deproxy(specimen, DerivedUnit.class)));
 827         }
 828         return fieldUnits;
 829     }
 830
 831     /**
 832      * @param original
 833      * @param fieldUnits
 834      */
 835     private Collection<FieldUnit> getFieldUnits(DerivedUnit derivedUnit) {
 836         Collection<FieldUnit> fieldUnits = new HashSet<FieldUnit>();
 837         Set<SpecimenOrObservationBase> originals = derivedUnit.getOriginals();
 838         if (originals != null && !originals.isEmpty()) {
 839             for (SpecimenOrObservationBase<?> original : originals) {
 840                 if (original.isInstanceOf(FieldUnit.class)) {
 841                     fieldUnits.add(HibernateProxyHelper.deproxy(original, FieldUnit.class));
 842                 }
 843                 else if(original.isInstanceOf(DerivedUnit.class)){
 844                     fieldUnits.addAll(getFieldUnits(HibernateProxyHelper.deproxy(original, DerivedUnit.class)));
 845                 }
 846             }
 847         }
 848         return fieldUnits;
 849     }
 850
 851     /* (non-Javadoc)
 852      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#moveSequence(eu.etaxonomy.cdm.model.molecular.DnaSample, eu.etaxonomy.cdm.model.molecular.DnaSample, eu.etaxonomy.cdm.model.molecular.Sequence)
 853      */
 854     @Override
 855     public boolean moveSequence(DnaSample from, DnaSample to, Sequence sequence) {
 856         // reload specimens to avoid session conflicts
 857         from = (DnaSample) load(from.getUuid());
 858         to = (DnaSample) load(to.getUuid());
 859         sequence = sequenceService.load(sequence.getUuid());
 860
 861         if (from == null || to == null || sequence == null) {
 862             throw new TransientObjectException("One of the CDM entities has not been saved to the data base yet. Moving only works for persisted/saved CDM entities.\n" +
 863                     "Operation was move "+sequence+ " from "+from+" to "+to);
 864         }
 865         from.removeSequence(sequence);
 866         saveOrUpdate(from);
 867         to.addSequence(sequence);
 868         saveOrUpdate(to);
 869         return true;
 870     }
 871
 872     /* (non-Javadoc)
 873      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#moveDerivate(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase, eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase, eu.etaxonomy.cdm.model.occurrence.DerivedUnit)
 874      */
 875     @Override
 876     public boolean moveDerivate(SpecimenOrObservationBase<?> from, SpecimenOrObservationBase<?> to, DerivedUnit derivate) {
 877         // reload specimens to avoid session conflicts
 878         from = load(from.getUuid());
 879         to = load(to.getUuid());
 880         derivate = (DerivedUnit) load(derivate.getUuid());
 881
 882         if (from == null || to == null || derivate == null) {
 883             throw new TransientObjectException("One of the CDM entities has not been saved to the data base yet. Moving only works for persisted/saved CDM entities.\n" +
 884                         "Operation was move "+derivate+ " from "+from+" to "+to);
 885         }
 886
 887         SpecimenOrObservationType derivateType = derivate.getRecordBasis();
 888         SpecimenOrObservationType toType = to.getRecordBasis();
 889         // check if type is a sub derivate type
 890         if(toType==SpecimenOrObservationType.FieldUnit //moving to FieldUnit always works
 891                 || derivateType==SpecimenOrObservationType.Media //moving media always works
 892                 || (derivateType.isKindOf(toType) && toType!=derivateType)){ //moving only to parent derivate type
 893             // remove derivation event from parent specimen of dragged object
 894             DerivationEvent eventToRemove = null;
 895             for (DerivationEvent event : from.getDerivationEvents()) {
 896                 if (event.getDerivatives().contains(derivate)) {
 897                     eventToRemove = event;
 898                     break;
 899                 }
 900             }
 901             from.removeDerivationEvent(eventToRemove);
 902             saveOrUpdate(from);
 903             // add new derivation event to target
 904             DerivationEvent derivedFromNewOriginalEvent = DerivationEvent.NewSimpleInstance(to, derivate, eventToRemove == null ? null : eventToRemove.getType());
 905             to.addDerivationEvent(derivedFromNewOriginalEvent);
 906             derivate.setDerivedFrom(derivedFromNewOriginalEvent);
 907             saveOrUpdate(to);
 908             return true;
 909         }
 910         return false;
 911     }
 912
 913     @Override
 914     public Collection<ICdmBase> getNonCascadedAssociatedElements(SpecimenOrObservationBase<?> specimen) {
 915         // potential fields that are not persisted cascadingly
 916         /*
 917          * SOOB
 918         -DescriptionBase
 919         -determinations
 920         --modifier TERM
 921         -kindOfUnit TERM
 922         -lifeStage TERM
 923         -sex TERM
 924
 925         FieldUnit
 926         -GatheringEvent
 927         --Country TERM
 928         --CollectingAreas TERM
 929
 930         DerivedUnit
 931         -collection
 932         --institute
 933         ---types TERM
 934         -preservationMethod
 935         --medium TERM
 936         -storedUnder CDM TaxonNameBase
 937          */
 938
 939         Collection<ICdmBase> nonCascadedCdmEntities = new HashSet<ICdmBase>();
 940
 941         //Choose the correct entry point to traverse the graph (FieldUnit or DerivedUnit)
 942
 943         // FieldUnit
 944         if (specimen.isInstanceOf(FieldUnit.class)) {
 945             nonCascadedCdmEntities.addAll(getFieldUnitNonCascadedAssociatedElements(HibernateProxyHelper.deproxy(specimen, FieldUnit.class)));
 946         }
 947         // DerivedUnit
 948         else if (specimen.isInstanceOf(DerivedUnit.class)) {
 949             DerivedUnit derivedUnit = HibernateProxyHelper.deproxy(specimen, DerivedUnit.class);
 950             if (derivedUnit.getDerivedFrom() != null) {
 951                 Collection<FieldUnit> fieldUnits = getFieldUnits(derivedUnit);
 952                 for (FieldUnit fieldUnit : fieldUnits) {
 953                     nonCascadedCdmEntities.addAll(getFieldUnitNonCascadedAssociatedElements(fieldUnit));
 954                 }
 955             }
 956         }
 957         return nonCascadedCdmEntities;
 958     }
 959
 960     private Collection<ICdmBase> getFieldUnitNonCascadedAssociatedElements(FieldUnit fieldUnit) {
 961         // get non cascaded element on SpecimenOrObservationBase level
 962         Collection<ICdmBase> nonCascadedCdmEntities = getSpecimenOrObservationNonCascadedAssociatedElements(fieldUnit);
 963
 964         // get FieldUnit specific elements
 965         GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
 966         if (gatheringEvent != null) {
 967             // country
 968             if (gatheringEvent.getCountry() != null) {
 969                 nonCascadedCdmEntities.add(gatheringEvent.getCountry());
 970             }
 971             // collecting areas
 972             for (NamedArea namedArea : gatheringEvent.getCollectingAreas()) {
 973                 nonCascadedCdmEntities.add(namedArea);
 974             }
 975         }
 976         for (DerivationEvent derivationEvent : fieldUnit.getDerivationEvents()) {
 977             for (DerivedUnit derivedUnit : derivationEvent.getDerivatives()) {
 978                 nonCascadedCdmEntities.addAll(getDerivedUnitNonCascadedAssociatedElements(derivedUnit));
 979             }
 980         }
 981         return nonCascadedCdmEntities;
 982     }
 983
 984     private Collection<ICdmBase> getDerivedUnitNonCascadedAssociatedElements(DerivedUnit derivedUnit) {
 985         // get non cascaded element on SpecimenOrObservationBase level
 986         Collection<ICdmBase> nonCascadedCdmEntities = getSpecimenOrObservationNonCascadedAssociatedElements(derivedUnit);
 987
 988         // get DerivedUnit specific elements
 989         if (derivedUnit.getCollection() != null && derivedUnit.getCollection().getInstitute() != null) {
 990             for (DefinedTerm type : derivedUnit.getCollection().getInstitute().getTypes()) {
 991                 nonCascadedCdmEntities.add(type);
 992             }
 993         }
 994         if (derivedUnit.getPreservation() != null && derivedUnit.getPreservation().getMedium() != null) {
 995             nonCascadedCdmEntities.add(derivedUnit.getPreservation().getMedium());
 996         }
 997         if (derivedUnit.getStoredUnder() != null) {
 998             nonCascadedCdmEntities.add(derivedUnit.getStoredUnder());
 999         }
1000         return nonCascadedCdmEntities;
1001     }
1002
1003     /**
1004      * @param specimen
1005      * @return
1006      */
1007     private Collection<ICdmBase> getSpecimenOrObservationNonCascadedAssociatedElements(
1008             SpecimenOrObservationBase<?> specimen) {
1009         Collection<ICdmBase> nonCascadedCdmEntities = new HashSet<ICdmBase>();
1010         // scan SpecimenOrObservationBase
1011         for (DeterminationEvent determinationEvent : specimen.getDeterminations()) {
1012             // modifier
1013             if (determinationEvent.getModifier() != null) {
1014                 nonCascadedCdmEntities.add(determinationEvent.getModifier());
1015             }
1016         }
1017         // kindOfUnit
1018         if (specimen.getKindOfUnit() != null) {
1019             nonCascadedCdmEntities.add(specimen.getKindOfUnit());
1020         }
1021         // lifeStage
1022         if (specimen.getLifeStage() != null) {
1023             nonCascadedCdmEntities.add(specimen.getLifeStage());
1024         }
1025         // sex
1026         if (specimen.getSex() != null) {
1027             nonCascadedCdmEntities.add(specimen.getSex());
1028         }
1029         return nonCascadedCdmEntities;
1030     }
1031
1032     /* (non-Javadoc)
1033      * @see eu.etaxonomy.cdm.api.service.VersionableServiceBase#isDeletable(eu.etaxonomy.cdm.model.common.VersionableEntity, eu.etaxonomy.cdm.api.service.config.DeleteConfiguratorBase)
1034      */
1035     @Override
1036     public DeleteResult isDeletable(SpecimenOrObservationBase specimen, DeleteConfiguratorBase config) {
1037         DeleteResult deleteResult = new DeleteResult();
1038         SpecimenDeleteConfigurator specimenDeleteConfigurator = (SpecimenDeleteConfigurator) config;
1039
1040         // check elements found by super method
1041         Set<CdmBase> relatedObjects = super.isDeletable(specimen, config).getRelatedObjects();
1042         for (CdmBase cdmBase : relatedObjects) {
1043             // check for type designation
1044             if (cdmBase.isInstanceOf(SpecimenTypeDesignation.class) && !specimenDeleteConfigurator.isDeleteFromTypeDesignation()) {
1045                 deleteResult.setAbort();
1046                 deleteResult.addException(new ReferencedObjectUndeletableException("Specimen is a type specimen."));
1047                 deleteResult.addRelatedObject(cdmBase);
1048                 break;
1049             }
1050             // check for IndividualsAssociations
1051             else if (cdmBase.isInstanceOf(IndividualsAssociation.class) && !specimenDeleteConfigurator.isDeleteFromIndividualsAssociation()) {
1052                 deleteResult.setAbort();
1053                 deleteResult.addException(new ReferencedObjectUndeletableException("Specimen is still associated via IndividualsAssociations"));
1054                 deleteResult.addRelatedObject(cdmBase);
1055                 break;
1056             }
1057             // check for specimen/taxon description
1058             else if((cdmBase.isInstanceOf(SpecimenDescription.class) || cdmBase.isInstanceOf(TaxonDescription.class))
1059                     && !specimenDeleteConfigurator.isDeleteFromDescription()){
1060                 deleteResult.setAbort();
1061                 deleteResult.addException(new ReferencedObjectUndeletableException("Specimen is still used in a Description."));
1062                 deleteResult.addRelatedObject(cdmBase);
1063                 break;
1064             }
1065             // check for children and parents (derivation events)
1066             else if (cdmBase.isInstanceOf(DerivationEvent.class)) {
1067                 DerivationEvent derivationEvent = HibernateProxyHelper.deproxy(cdmBase, DerivationEvent.class);
1068                 // check if derivation event is empty
1069                 if (!derivationEvent.getDerivatives().isEmpty()) {
1070                     if (derivationEvent.getDerivatives().size() == 1 && derivationEvent.getDerivatives().contains(specimen)) {
1071                         //if it is the parent event with only one derivate then the specimen is still deletable
1072                         continue;
1073                     }
1074                     else if(!specimenDeleteConfigurator.isDeleteChildren()){
1075                         //if not and children should not be deleted then it is undeletable
1076                         deleteResult.setAbort();
1077                         deleteResult.addException(new ReferencedObjectUndeletableException("Derivative still has child derivatives."));
1078                         deleteResult.addRelatedObject(cdmBase);
1079                         break;
1080                     }
1081                     else{
1082                         // check all children if they can be deleted
1083                         Set<DerivedUnit> derivatives = derivationEvent.getDerivatives();
1084                         DeleteResult childResult = new DeleteResult();
1085                         for (DerivedUnit derivedUnit : derivatives) {
1086                             childResult.includeResult(isDeletable(derivedUnit, specimenDeleteConfigurator));
1087                         }
1088                         if (!childResult.isOk()) {
1089                             deleteResult.setAbort();
1090                             deleteResult.includeResult(childResult);
1091                             deleteResult.addRelatedObject(cdmBase);
1092                             break;
1093                         }
1094                     }
1095                 }
1096             }
1097             // check for amplification
1098             else if (cdmBase.isInstanceOf(AmplificationResult.class) && !specimenDeleteConfigurator.isDeleteMolecularData()) {
1099                 deleteResult.setAbort();
1100                 deleteResult.addException(new ReferencedObjectUndeletableException("DnaSample is used in amplification results."));
1101                 deleteResult.addRelatedObject(cdmBase);
1102                 break;
1103             }
1104             // check for sequence
1105             else if (cdmBase.isInstanceOf(Sequence.class) && !specimenDeleteConfigurator.isDeleteMolecularData()) {
1106                 deleteResult.setAbort();
1107                 deleteResult.addException(new ReferencedObjectUndeletableException("DnaSample is used in sequences."));
1108                 deleteResult.addRelatedObject(cdmBase);
1109                 break;
1110             }
1111         }
1112         if (deleteResult.isOk()) {
1113             //add all related object if deletion is OK so they can be handled by the delete() method
1114             deleteResult.addRelatedObjects(relatedObjects);
1115         }
1116         return deleteResult;
1117     }
1118
1119     /* (non-Javadoc)
1120      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#delete(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase, eu.etaxonomy.cdm.api.service.config.SpecimenDeleteConfigurator)
1121      */
1122     @Override
1123     public DeleteResult delete(SpecimenOrObservationBase<?> specimen, SpecimenDeleteConfigurator config) {
1124         specimen = HibernateProxyHelper.deproxy(specimen, SpecimenOrObservationBase.class);
1125
1126         if (config.isDeleteChildren()) {
1127             Set<DerivationEvent> derivationEvents = specimen.getDerivationEvents();
1128             for (DerivationEvent derivationEvent : derivationEvents) {
1129                 Set<DerivedUnit> derivatives = derivationEvent.getDerivatives();
1130                 for (DerivedUnit derivedUnit : derivatives) {
1131                     delete(derivedUnit, config);
1132                 }
1133             }
1134         }
1135
1136         DeleteResult deleteResult = isDeletable(specimen, config);
1137         if (!deleteResult.isOk()) {
1138             return deleteResult;
1139         }
1140
1141         // check related objects
1142         Set<CdmBase> relatedObjects = deleteResult.getRelatedObjects();
1143
1144         for (CdmBase relatedObject : relatedObjects) {
1145             // check for TypeDesignations
1146             if (relatedObject.isInstanceOf(SpecimenTypeDesignation.class)) {
1147                 SpecimenTypeDesignation designation = HibernateProxyHelper.deproxy(relatedObject, SpecimenTypeDesignation.class);
1148                 designation.setTypeSpecimen(null);
1149                 Set<TaxonNameBase> typifiedNames = designation.getTypifiedNames();
1150                 for (TaxonNameBase taxonNameBase : typifiedNames) {
1151                     taxonNameBase.removeTypeDesignation(designation);
1152                 }
1153             }
1154             // delete IndividualsAssociation
1155             if (relatedObject.isInstanceOf(IndividualsAssociation.class)) {
1156                 IndividualsAssociation assciation = HibernateProxyHelper.deproxy(relatedObject, IndividualsAssociation.class);
1157                 assciation.setAssociatedSpecimenOrObservation(null);
1158                 assciation.getInDescription().removeElement(assciation);
1159             }
1160             // check for taxon description
1161             if (relatedObject.isInstanceOf(TaxonDescription.class)) {
1162                 TaxonDescription taxonDescription = HibernateProxyHelper.deproxy(relatedObject, TaxonDescription.class);
1163                 taxonDescription.setDescribedSpecimenOrObservation(null);
1164             }
1165             // check for specimen description
1166             if (relatedObject.isInstanceOf(SpecimenDescription.class)) {
1167                 SpecimenDescription specimenDescription = HibernateProxyHelper.deproxy(relatedObject, SpecimenDescription.class);
1168                 // check if specimen is "described" specimen
1169                 if (specimenDescription.getDescribedSpecimenOrObservation().equals(specimen)) {
1170                     specimenDescription.setDescribedSpecimenOrObservation(null);
1171                 }
1172                 // check if description is a description of the given specimen
1173                 if (specimen.getDescriptions().contains(specimenDescription)) {
1174                     specimen.removeDescription(specimenDescription);
1175                 }
1176             }
1177             // check for amplification
1178             if (relatedObject.isInstanceOf(AmplificationResult.class)) {
1179                 AmplificationResult amplificationResult = HibernateProxyHelper.deproxy(relatedObject, AmplificationResult.class);
1180                 amplificationResult.getDnaSample().removeAmplificationResult(amplificationResult);
1181             }
1182             // check for sequence
1183             if (relatedObject.isInstanceOf(Sequence.class)) {
1184                 Sequence sequence = HibernateProxyHelper.deproxy(relatedObject, Sequence.class);
1185                 sequence.getDnaSample().removeSequence(sequence);
1186             }
1187             // check for children and parents (derivation events)
1188             if (relatedObject.isInstanceOf(DerivationEvent.class)) {
1189                 DerivationEvent derivationEvent = HibernateProxyHelper.deproxy(relatedObject, DerivationEvent.class);
1190                 // parent derivation event (derivedFrom)
1191                 if (derivationEvent.getDerivatives().contains(specimen) && specimen.isInstanceOf(DerivedUnit.class)) {
1192                     derivationEvent.removeDerivative(HibernateProxyHelper.deproxy(specimen, DerivedUnit.class));
1193                     if (derivationEvent.getDerivatives().isEmpty()) {
1194                         Set<SpecimenOrObservationBase> originals = derivationEvent.getOriginals();
1195                         for (SpecimenOrObservationBase specimenOrObservationBase : originals) {
1196                             specimenOrObservationBase.removeDerivationEvent(derivationEvent);
1197                         }
1198                     }
1199                 }
1200                 else{
1201                     //child derivation events should not occur since we delete the hierarchy from bottom to top
1202                 }
1203             }
1204         }
1205
1206         deleteResult.includeResult(delete(specimen));
1207         return deleteResult;
1208     }
1209
1210     /* (non-Javadoc)
1211      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#deleteDerivateHierarchy(eu.etaxonomy.cdm.model.common.ICdmBase)
1212      */
1213     @Override
1214     public DeleteResult deleteDerivateHierarchy(CdmBase from, SpecimenDeleteConfigurator config) {
1215         DeleteResult deleteResult = new DeleteResult();
1216         if (from.isInstanceOf(Sequence.class)) {
1217             if (!config.isDeleteMolecularData()) {
1218                 deleteResult.setAbort();
1219                 deleteResult.addException(new ReferencedObjectUndeletableException("deleting molecur data is not allowed in config"));
1220                 return deleteResult;
1221             }
1222             Sequence sequence = HibernateProxyHelper.deproxy(from, Sequence.class);
1223             sequence.getDnaSample().removeSequence(sequence);
1224             deleteResult = sequenceService.delete(sequence);
1225         }
1226         else if(from.isInstanceOf(SingleRead.class))  {
1227             if (!config.isDeleteMolecularData()) {
1228                 deleteResult.setAbort();
1229                 deleteResult.addException(new ReferencedObjectUndeletableException("deleting molecur data is not allowed in config"));
1230                 return deleteResult;
1231             }
1232             SingleRead singleRead = HibernateProxyHelper.deproxy(from, SingleRead.class);
1233             singleRead.getAmplificationResult().removeSingleRead(singleRead);
1234             deleteResult.setStatus(Status.OK);
1235         }
1236         else if(from.isInstanceOf(SpecimenOrObservationBase.class))  {
1237             deleteResult = delete(HibernateProxyHelper.deproxy(from, SpecimenOrObservationBase.class), config);
1238         }
1239         return deleteResult;
1240     }
1241
1242 //    private DeleteResult deepDelete(SpecimenOrObservationBase<?> entity, SpecimenDeleteConfigurator config){
1243     // Set<DerivationEvent> derivationEvents = entity.getDerivationEvents();
1244     // for (DerivationEvent derivationEvent : derivationEvents) {
1245     // Set<DerivedUnit> derivatives = derivationEvent.getDerivatives();
1246     // for (DerivedUnit derivedUnit : derivatives) {
1247     // DeleteResult deleteResult = deepDelete(derivedUnit, config);
1248     // if(!deleteResult.isOk()){
1249     // return deleteResult;
1250     // }
1251     // }
1252     // }
1253     // return delete(entity, config);
1254     // }
1255
1256     /* (non-Javadoc)
1257      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#listAssociatedTaxa(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase)
1258      */
1259     @Override
1260     public Collection<IndividualsAssociation> listIndividualsAssociations(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
1261         return dao.listIndividualsAssociations(specimen, null, null, null, null);
1262     }
1263
1264     /* (non-Javadoc)
1265      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#listTypeDesignations(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
1266      */
1267     @Override
1268     public Collection<SpecimenTypeDesignation> listTypeDesignations(SpecimenOrObservationBase<?> specimen,
1269             Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
1270         return dao.listTypeDesignations(specimen, limit, start, orderHints, propertyPaths);
1271     }
1272
1273     /* (non-Javadoc)
1274      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#listDescriptionsWithDescriptionSpecimen(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
1275      */
1276     @Override
1277     public Collection<DescriptionBase<?>> listDescriptionsWithDescriptionSpecimen(
1278             SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints,
1279             List<String> propertyPaths) {
1280         return dao.listDescriptionsWithDescriptionSpecimen(specimen, limit, start, orderHints, propertyPaths);
1281     }
1282
1283     /* (non-Javadoc)
1284      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getStatesForSpecimen(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase)
1285      */
1286     @Override
1287     public Collection<DescriptionElementBase> getCharacterDataForSpecimen(SpecimenOrObservationBase<?> specimen) {
1288         Collection<DescriptionElementBase> states = new ArrayList<DescriptionElementBase>();
1289         if (specimen != null) {
1290             Set<DescriptionBase> descriptions = specimen.getDescriptions();
1291             for (DescriptionBase<?> descriptionBase : descriptions) {
1292                 if (descriptionBase.isInstanceOf(SpecimenDescription.class)) {
1293                     SpecimenDescription specimenDescription = HibernateProxyHelper.deproxy(descriptionBase, SpecimenDescription.class);
1294                     Set<DescriptionElementBase> elements = specimenDescription.getElements();
1295                     for (DescriptionElementBase descriptionElementBase : elements) {
1296                         if(descriptionElementBase.getFeature().isSupportsCategoricalData()
1297                                 ||descriptionElementBase.getFeature().isSupportsQuantitativeData()){
1298                             states.add(descriptionElementBase);
1299                         }
1300                     }
1301                 }
1302             }
1303         }
1304         return states;
1305     }
1306
1307     /* (non-Javadoc)
1308      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getStatesForSpecimen(java.util.UUID)
1309      */
1310     @Override
1311     public Collection<DescriptionElementBase> getCharacterDataForSpecimen(UUID specimenUuid) {
1312         SpecimenOrObservationBase<?> specimen = load(specimenUuid);
1313         if (specimen != null) {
1314             return getCharacterDataForSpecimen(specimen);
1315         }
1316         else{
1317             throw new DataRetrievalFailureException("Specimen with the given uuid not found in the data base");
1318         }
1319     }
1320
1321
1322     /* (non-Javadoc)
1323      * @see eu.etaxonomy.cdm.api.service.IdentifiableServiceBase#findByTitle(eu.etaxonomy.cdm.api.service.config.IIdentifiableEntityServiceConfigurator)
1324      */
1325     @Override
1326     public Pager<SpecimenOrObservationBase> findByTitle(
1327             IIdentifiableEntityServiceConfigurator<SpecimenOrObservationBase> config) {
1328         if (config instanceof FindOccurrencesConfigurator) {
1329             FindOccurrencesConfigurator occurrenceConfig = (FindOccurrencesConfigurator) config;
1330             List<SpecimenOrObservationBase> occurrences = new ArrayList<SpecimenOrObservationBase>();
1331             Taxon taxon = null;
1332             if(occurrenceConfig.getAssociatedTaxonUuid()!=null){
1333                 TaxonBase taxonBase = taxonService.load(occurrenceConfig.getAssociatedTaxonUuid());
1334                 if(taxonBase.isInstanceOf(Taxon.class)){
1335                     taxon = HibernateProxyHelper.deproxy(taxonBase, Taxon.class);
1336                 }
1337             }
1338             occurrences.addAll(dao.findOccurrences(occurrenceConfig.getClazz(), occurrenceConfig.getTitleSearchString(), occurrenceConfig.getSpecimenType(),
1339                     taxon, occurrenceConfig.getMatchMode(), null, null, occurrenceConfig.getOrderHints(), occurrenceConfig.getPropertyPaths()));
1340             return new DefaultPagerImpl<SpecimenOrObservationBase>(config.getPageNumber(), occurrences.size(), config.getPageSize(), occurrences);
1341         }
1342         return super.findByTitle(config);
1343     }
1344
1345     @Override
1346     public int countOccurrences(IIdentifiableEntityServiceConfigurator<SpecimenOrObservationBase> config){
1347         if (config instanceof FindOccurrencesConfigurator) {
1348             FindOccurrencesConfigurator occurrenceConfig = (FindOccurrencesConfigurator) config;
1349             Taxon taxon = null;
1350             if(occurrenceConfig.getAssociatedTaxonUuid()!=null){
1351                 TaxonBase taxonBase = taxonService.load(occurrenceConfig.getAssociatedTaxonUuid());
1352                 if(taxonBase.isInstanceOf(Taxon.class)){
1353                     taxon = HibernateProxyHelper.deproxy(taxonBase, Taxon.class);
1354                 }
1355             }
1356             return dao.countOccurrences(occurrenceConfig.getClazz(), occurrenceConfig.getTitleSearchString(), occurrenceConfig.getSpecimenType(),
1357                     taxon, occurrenceConfig.getMatchMode(), null, null, occurrenceConfig.getOrderHints(), occurrenceConfig.getPropertyPaths());
1358         }
1359         return super.countByTitle(config);
1360     }
1361
1362 }