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.HashMap;
  20 import java.util.HashSet;
  21 import java.util.LinkedHashSet;
  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.stereotype.Service;
  39 import org.springframework.transaction.annotation.Transactional;
  40
  41 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
  42 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeConfigurator;
  43 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeNotSupportedException;
  44 import eu.etaxonomy.cdm.api.service.DeleteResult.DeleteStatus;
  45 import eu.etaxonomy.cdm.api.service.config.SpecimenDeleteConfigurator;
  46 import eu.etaxonomy.cdm.api.service.dto.DerivateHierarchyDTO;
  47 import eu.etaxonomy.cdm.api.service.dto.DerivateHierarchyDTO.ContigFile;
  48 import eu.etaxonomy.cdm.api.service.dto.DerivateHierarchyDTO.MolecularData;
  49 import eu.etaxonomy.cdm.api.service.exception.ReferencedObjectUndeletableException;
  50 import eu.etaxonomy.cdm.api.service.molecular.ISequenceService;
  51 import eu.etaxonomy.cdm.api.service.pager.Pager;
  52 import eu.etaxonomy.cdm.api.service.pager.impl.DefaultPagerImpl;
  53 import eu.etaxonomy.cdm.api.service.search.ILuceneIndexToolProvider;
  54 import eu.etaxonomy.cdm.api.service.search.ISearchResultBuilder;
  55 import eu.etaxonomy.cdm.api.service.search.LuceneSearch;
  56 import eu.etaxonomy.cdm.api.service.search.LuceneSearch.TopGroupsWithMaxScore;
  57 import eu.etaxonomy.cdm.api.service.search.QueryFactory;
  58 import eu.etaxonomy.cdm.api.service.search.SearchResult;
  59 import eu.etaxonomy.cdm.api.service.search.SearchResultBuilder;
  60 import eu.etaxonomy.cdm.api.service.util.TaxonRelationshipEdge;
  61 import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
  62 import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
  63 import eu.etaxonomy.cdm.model.CdmBaseType;
  64 import eu.etaxonomy.cdm.model.agent.AgentBase;
  65 import eu.etaxonomy.cdm.model.common.CdmBase;
  66 import eu.etaxonomy.cdm.model.common.DefinedTerm;
  67 import eu.etaxonomy.cdm.model.common.DefinedTermBase;
  68 import eu.etaxonomy.cdm.model.common.ICdmBase;
  69 import eu.etaxonomy.cdm.model.common.Language;
  70 import eu.etaxonomy.cdm.model.common.UuidAndTitleCache;
  71 import eu.etaxonomy.cdm.model.description.DescriptionBase;
  72 import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
  73 import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
  74 import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
  75 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  76 import eu.etaxonomy.cdm.model.location.Country;
  77 import eu.etaxonomy.cdm.model.location.NamedArea;
  78 import eu.etaxonomy.cdm.model.media.Media;
  79 import eu.etaxonomy.cdm.model.media.MediaRepresentation;
  80 import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;
  81 import eu.etaxonomy.cdm.model.media.MediaUtils;
  82 import eu.etaxonomy.cdm.model.molecular.DnaSample;
  83 import eu.etaxonomy.cdm.model.molecular.Sequence;
  84 import eu.etaxonomy.cdm.model.molecular.SingleRead;
  85 import eu.etaxonomy.cdm.model.name.NameTypeDesignation;
  86 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
  87 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  88 import eu.etaxonomy.cdm.model.name.TypeDesignationBase;
  89 import eu.etaxonomy.cdm.model.name.TypeDesignationStatusBase;
  90 import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
  91 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  92 import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
  93 import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
  94 import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
  95 import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen;
  96 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  97 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
  98 import eu.etaxonomy.cdm.model.taxon.Taxon;
  99 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
 100 import eu.etaxonomy.cdm.persistence.dao.common.ICdmGenericDao;
 101 import eu.etaxonomy.cdm.persistence.dao.common.IDefinedTermDao;
 102 import eu.etaxonomy.cdm.persistence.dao.initializer.AbstractBeanInitializer;
 103 import eu.etaxonomy.cdm.persistence.dao.occurrence.IOccurrenceDao;
 104 import eu.etaxonomy.cdm.persistence.query.OrderHint;
 105 import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
 106
 107 /**
 108  * @author a.babadshanjan
 109  * @created 01.09.2008
 110  */
 111 @Service
 112 @Transactional(readOnly = true)
 113 public class OccurrenceServiceImpl extends IdentifiableServiceBase<SpecimenOrObservationBase,IOccurrenceDao> implements IOccurrenceService {
 114
 115     static private final Logger logger = Logger.getLogger(OccurrenceServiceImpl.class);
 116
 117     @Autowired
 118     private IDefinedTermDao definedTermDao;
 119
 120     @Autowired
 121     private IDescriptionService descriptionService;
 122
 123     @Autowired
 124     private ITaxonService taxonService;
 125
 126     @Autowired
 127     private ITermService termService;
 128
 129     @Autowired
 130     private INameService nameService;
 131
 132     @Autowired
 133     private ISequenceService sequenceService;
 134
 135     @Autowired
 136     private AbstractBeanInitializer beanInitializer;
 137
 138     @Autowired
 139     private ILuceneIndexToolProvider luceneIndexToolProvider;
 140
 141     @Autowired
 142     private ICdmGenericDao genericDao;
 143
 144
 145     public OccurrenceServiceImpl() {
 146         logger.debug("Load OccurrenceService Bean");
 147     }
 148
 149
 150     /* (non-Javadoc)
 151      * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#updateTitleCache(java.lang.Integer, eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy)
 152      */
 153     @Override
 154     @Transactional(readOnly = false)
 155     public void updateTitleCache(Class<? extends SpecimenOrObservationBase> clazz, Integer stepSize, IIdentifiableEntityCacheStrategy<SpecimenOrObservationBase> cacheStrategy, IProgressMonitor monitor) {
 156         if (clazz == null){
 157             clazz = SpecimenOrObservationBase.class;
 158         }
 159         super.updateTitleCacheImpl(clazz, stepSize, cacheStrategy, monitor);
 160     }
 161
 162
 163     /**
 164      * FIXME Candidate for harmonization
 165      * move to termService
 166      */
 167     @Override
 168     public Country getCountryByIso(String iso639) {
 169         return this.definedTermDao.getCountryByIso(iso639);
 170
 171     }
 172
 173     /**
 174      * FIXME Candidate for harmonization
 175      * move to termService
 176      */
 177     @Override
 178     public List<Country> getCountryByName(String name) {
 179         List<? extends DefinedTermBase> terms = this.definedTermDao.findByTitle(Country.class, name, null, null, null, null, null, null) ;
 180         List<Country> countries = new ArrayList<Country>();
 181         for (int i=0;i<terms.size();i++){
 182             countries.add((Country)terms.get(i));
 183         }
 184         return countries;
 185     }
 186
 187     @Override
 188     @Autowired
 189     protected void setDao(IOccurrenceDao dao) {
 190         this.dao = dao;
 191     }
 192
 193     @Override
 194     public Pager<DerivationEvent> getDerivationEvents(SpecimenOrObservationBase occurence, Integer pageSize,Integer pageNumber, List<String> propertyPaths) {
 195         Integer numberOfResults = dao.countDerivationEvents(occurence);
 196
 197         List<DerivationEvent> results = new ArrayList<DerivationEvent>();
 198         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 199             results = dao.getDerivationEvents(occurence, pageSize, pageNumber,propertyPaths);
 200         }
 201
 202         return new DefaultPagerImpl<DerivationEvent>(pageNumber, numberOfResults, pageSize, results);
 203     }
 204
 205     /* (non-Javadoc)
 206      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#countDeterminations(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase, eu.etaxonomy.cdm.model.taxon.TaxonBase)
 207      */
 208     @Override
 209     public int countDeterminations(SpecimenOrObservationBase occurence, TaxonBase taxonbase) {
 210         return dao.countDeterminations(occurence, taxonbase);
 211     }
 212
 213     @Override
 214     public Pager<DeterminationEvent> getDeterminations(SpecimenOrObservationBase occurrence, TaxonBase taxonBase, Integer pageSize,Integer pageNumber, List<String> propertyPaths) {
 215         Integer numberOfResults = dao.countDeterminations(occurrence, taxonBase);
 216
 217         List<DeterminationEvent> results = new ArrayList<DeterminationEvent>();
 218         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 219             results = dao.getDeterminations(occurrence,taxonBase, pageSize, pageNumber, propertyPaths);
 220         }
 221
 222         return new DefaultPagerImpl<DeterminationEvent>(pageNumber, numberOfResults, pageSize, results);
 223     }
 224
 225     @Override
 226     public Pager<Media> getMedia(SpecimenOrObservationBase occurence,Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
 227         Integer numberOfResults = dao.countMedia(occurence);
 228
 229         List<Media> results = new ArrayList<Media>();
 230         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 231             results = dao.getMedia(occurence, pageSize, pageNumber, propertyPaths);
 232         }
 233
 234         return new DefaultPagerImpl<Media>(pageNumber, numberOfResults, pageSize, results);
 235     }
 236
 237     /* (non-Javadoc)
 238      * @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)
 239      */
 240     @Override
 241     public Pager<SpecimenOrObservationBase> list(Class<? extends SpecimenOrObservationBase> type, TaxonBase determinedAs, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 242         Integer numberOfResults = dao.count(type,determinedAs);
 243         List<SpecimenOrObservationBase> results = new ArrayList<SpecimenOrObservationBase>();
 244         pageNumber = pageNumber == null ? 0 : pageNumber;
 245         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 246             Integer start = pageSize == null ? 0 : pageSize * pageNumber;
 247             results = dao.list(type,determinedAs, pageSize, start, orderHints,propertyPaths);
 248         }
 249         return new DefaultPagerImpl<SpecimenOrObservationBase>(pageNumber, numberOfResults, pageSize, results);
 250     }
 251
 252     @Override
 253     public List<UuidAndTitleCache<DerivedUnit>> getDerivedUnitUuidAndTitleCache() {
 254         return dao.getDerivedUnitUuidAndTitleCache();
 255     }
 256
 257     @Override
 258     public List<UuidAndTitleCache<FieldUnit>> getFieldUnitUuidAndTitleCache() {
 259         return dao.getFieldUnitUuidAndTitleCache();
 260     }
 261
 262     /* (non-Javadoc)
 263      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getDerivedUnitFacade(eu.etaxonomy.cdm.model.occurrence.DerivedUnit)
 264      */
 265     @Override
 266     public DerivedUnitFacade getDerivedUnitFacade(DerivedUnit derivedUnit, List<String> propertyPaths) throws DerivedUnitFacadeNotSupportedException {
 267         derivedUnit = (DerivedUnit)dao.load(derivedUnit.getUuid(), null);
 268         DerivedUnitFacadeConfigurator config = DerivedUnitFacadeConfigurator.NewInstance();
 269         config.setThrowExceptionForNonSpecimenPreservationMethodRequest(false);
 270         DerivedUnitFacade derivedUnitFacade = DerivedUnitFacade.NewInstance(derivedUnit, config);
 271         beanInitializer.initialize(derivedUnitFacade, propertyPaths);
 272         return derivedUnitFacade;
 273     }
 274
 275     /* (non-Javadoc)
 276      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#listDerivedUnitFacades(eu.etaxonomy.cdm.model.description.DescriptionBase, java.util.List)
 277      */
 278     @Override
 279     public List<DerivedUnitFacade> listDerivedUnitFacades(
 280             DescriptionBase description, List<String> propertyPaths) {
 281
 282         List<DerivedUnitFacade> derivedUnitFacadeList = new ArrayList<DerivedUnitFacade>();
 283         IndividualsAssociation tempIndividualsAssociation;
 284         SpecimenOrObservationBase tempSpecimenOrObservationBase;
 285         List<DescriptionElementBase> elements = descriptionService.listDescriptionElements(description, null, IndividualsAssociation.class, null, 0, Arrays.asList(new String []{"associatedSpecimenOrObservation"}));
 286         for(DescriptionElementBase element : elements){
 287             if(element instanceof IndividualsAssociation){
 288                 tempIndividualsAssociation = (IndividualsAssociation)element;
 289                 if(tempIndividualsAssociation.getAssociatedSpecimenOrObservation() != null){
 290                     tempSpecimenOrObservationBase = HibernateProxyHelper.deproxy(tempIndividualsAssociation.getAssociatedSpecimenOrObservation(), SpecimenOrObservationBase.class);
 291                     if(tempSpecimenOrObservationBase instanceof DerivedUnit){
 292                         try {
 293                             derivedUnitFacadeList.add(DerivedUnitFacade.NewInstance((DerivedUnit)tempSpecimenOrObservationBase));
 294                         } catch (DerivedUnitFacadeNotSupportedException e) {
 295                             logger.warn(tempIndividualsAssociation.getAssociatedSpecimenOrObservation().getTitleCache() + " : " +e.getMessage());
 296                         }
 297                     }
 298                 }
 299
 300             }
 301         }
 302
 303         beanInitializer.initializeAll(derivedUnitFacadeList, propertyPaths);
 304
 305         return derivedUnitFacadeList;
 306     }
 307
 308
 309     /* (non-Javadoc)
 310      * @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)
 311      */
 312     @Override
 313     public <T extends SpecimenOrObservationBase> List<T> listByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
 314             Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 315
 316         return pageByAssociatedTaxon(type, includeRelationships, associatedTaxon, maxDepth, pageSize, pageNumber, orderHints, propertyPaths).getRecords();
 317     }
 318
 319     /* (non-Javadoc)
 320      * @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)
 321      */
 322     @Override
 323     public Collection<FieldUnit> listFieldUnitsByAssociatedTaxon(Set<TaxonRelationshipEdge> includeRelationships,
 324             Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 325
 326         if(!getSession().contains(associatedTaxon)){
 327             associatedTaxon = (Taxon) taxonService.load(associatedTaxon.getUuid());
 328         }
 329
 330         Set<FieldUnit> fieldUnits = new HashSet<FieldUnit>();
 331
 332         List<SpecimenOrObservationBase> records = pageByAssociatedTaxon(null, includeRelationships, associatedTaxon, maxDepth, pageSize, pageNumber, orderHints, propertyPaths).getRecords();
 333         for(SpecimenOrObservationBase<?> specimen:records){
 334             fieldUnits.addAll(getFieldUnits(specimen.getUuid()));
 335         }
 336         return fieldUnits;
 337     }
 338
 339     @Override
 340     public DerivateHierarchyDTO assembleDerivateHierarchyDTO(FieldUnit fieldUnit, UUID associatedTaxonUuid){
 341
 342         if(!getSession().contains(fieldUnit)){
 343             fieldUnit = (FieldUnit) load(fieldUnit.getUuid());
 344         }
 345         TaxonBase associatedTaxon = taxonService.load(associatedTaxonUuid);
 346
 347         DerivateHierarchyDTO dto = new DerivateHierarchyDTO();
 348         Map<UUID, TypeDesignationStatusBase> typeSpecimenUUIDtoTypeDesignationStatus = new HashMap<UUID, TypeDesignationStatusBase>();
 349
 350         //gather types for this taxon name
 351         TaxonNameBase<?,?> name = associatedTaxon.getName();
 352         Set<?> typeDesignations = name.getSpecimenTypeDesignations();
 353         for (Object object : typeDesignations) {
 354             if(object instanceof SpecimenTypeDesignation){
 355                 SpecimenTypeDesignation specimenTypeDesignation = (SpecimenTypeDesignation)object;
 356                 DerivedUnit typeSpecimen = specimenTypeDesignation.getTypeSpecimen();
 357                 final TypeDesignationStatusBase typeStatus = specimenTypeDesignation.getTypeStatus();
 358                 typeSpecimenUUIDtoTypeDesignationStatus.put(typeSpecimen.getUuid(), typeStatus);
 359             }
 360         }
 361
 362         if(fieldUnit.getGatheringEvent()!=null){
 363             GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
 364             //Country
 365             final NamedArea country = gatheringEvent.getCountry();
 366             dto.setCountry(country!=null?country.getDescription():"");
 367             //Collection
 368             final AgentBase collector = gatheringEvent.getCollector();
 369             final String fieldNumber = fieldUnit.getFieldNumber();
 370             dto.setCollection(((collector!=null?collector:"") + " " + (fieldNumber!=null?fieldNumber:"")).trim());
 371             //Date
 372             final Partial gatheringDate = gatheringEvent.getGatheringDate();
 373             dto.setDate(gatheringDate!=null?gatheringDate.toString():"");
 374         }
 375
 376         //Taxon Name
 377         dto.setTaxonName(associatedTaxon.getName().getFullTitleCache());
 378
 379
 380         Collection<DerivedUnit> derivedUnits = new ArrayList<DerivedUnit>();
 381         getDerivedUnitsFor(fieldUnit, derivedUnits);
 382
 383         //Herbaria map
 384         Map<eu.etaxonomy.cdm.model.occurrence.Collection, Integer> collectionToCountMap = new HashMap<eu.etaxonomy.cdm.model.occurrence.Collection, Integer>();
 385         //List of accession numbers for citation
 386         List<String> preservedSpecimenAccessionNumbers = new ArrayList<String>();
 387
 388         //iterate over sub derivates
 389         for (DerivedUnit derivedUnit : derivedUnits) {
 390             //current accession number
 391             String currentAccessionNumber = derivedUnit.getAccessionNumber()!=null?derivedUnit.getAccessionNumber():"";
 392             //current herbarium
 393             String currentHerbarium = "";
 394             eu.etaxonomy.cdm.model.occurrence.Collection collection = derivedUnit.getCollection();
 395             if(collection!=null){
 396                 currentHerbarium = collection.getCode()!=null?collection.getCode():"";
 397                 //count herbaria
 398                 Integer count = collectionToCountMap.get(collection);
 399                 if(count==null){
 400                     count = 1;
 401                 }
 402                 else{
 403                     count++;
 404                 }
 405                 collectionToCountMap.put(collection, count);
 406             }
 407             //check if derived unit is a type
 408             if(typeSpecimenUUIDtoTypeDesignationStatus.keySet().contains(derivedUnit.getUuid())){
 409                 dto.setHasType(true);
 410                 TypeDesignationStatusBase typeDesignationStatus = typeSpecimenUUIDtoTypeDesignationStatus.get(derivedUnit.getUuid());
 411                 String typeStatus = typeDesignationStatus.getLabel();
 412                 dto.addTypes(typeStatus, currentAccessionNumber);
 413             }
 414             //assemble molecular data
 415             //pattern: DNAMarker [contig1, primer1_1, primer1_2, ...][contig2, primer2_1, ...]...
 416             if(derivedUnit instanceof DnaSample){
 417                 if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.TissueSample){
 418                     //TODO implement TissueSample assembly for web service
 419                 }
 420                 if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.DnaSample){
 421
 422                     DnaSample dna = (DnaSample)derivedUnit;
 423                     if(!dna.getSequences().isEmpty()){
 424                         dto.setHasDna(true);
 425                     }
 426                     for(Sequence sequence:dna.getSequences()){
 427                         URI boldUri = null;
 428                         try {
 429                             boldUri = sequence.getBoldUri();
 430                         } catch (URISyntaxException e1) {
 431                             logger.error("Could not create BOLD URI", e1);
 432                         }
 433                         final DefinedTerm dnaMarker = sequence.getDnaMarker();
 434                         MolecularData molecularData = dto.addProviderLink(boldUri!=null?boldUri:null,dnaMarker!=null?dnaMarker.getLabel():"[no marker]");
 435
 436                         //contig file FIXME show primer although contig not present?
 437                         if(sequence.getContigFile()!=null){
 438                             MediaRepresentationPart contigMediaRepresentationPart = MediaUtils.getFirstMediaRepresentationPart(sequence.getContigFile());
 439                             if(contigMediaRepresentationPart!=null){
 440                                 ContigFile contigFile = molecularData.addContigFile(contigMediaRepresentationPart.getUri(), "contig");
 441                                 //primer files
 442                                 if(sequence.getSingleReads()!=null){
 443                                     for (SingleRead singleRead : sequence.getSingleReads()) {
 444                                         MediaRepresentationPart pherogramMediaRepresentationPart = MediaUtils.getFirstMediaRepresentationPart(singleRead.getPherogram());
 445                                         if(pherogramMediaRepresentationPart!=null){
 446                                             contigFile.addPrimerLink(pherogramMediaRepresentationPart.getUri(), "primer");
 447                                         }
 448                                     }
 449                                 }
 450                             }
 451                         }
 452                     }
 453                 }
 454             }
 455             //assemble media data
 456             else if(derivedUnit instanceof MediaSpecimen){
 457
 458                 MediaSpecimen media = (MediaSpecimen)derivedUnit;
 459                 String mediaUriString = getMediaUriString(media);
 460                 if(media.getKindOfUnit()!=null){
 461                     //specimen scan
 462                     if(media.getKindOfUnit().getUuid().equals(UUID.fromString("acda15be-c0e2-4ea8-8783-b9b0c4ad7f03"))){
 463                         dto.setHasSpecimenScan(true);
 464                             final String imageLinkText = currentHerbarium+" "+currentAccessionNumber;
 465                             dto.addSpecimenScan(mediaUriString==null?"":mediaUriString, !imageLinkText.equals(" ")?imageLinkText:"[no accession]");
 466                     }
 467                     //detail image
 468                     else if(media.getKindOfUnit().getUuid().equals(UUID.fromString("31eb8d02-bf5d-437c-bcc6-87a626445f34"))){
 469                         dto.setHasDetailImage(true);
 470                         String motif = "";
 471                         if(media.getMediaSpecimen()!=null && media.getMediaSpecimen().getTitle()!=null){
 472                             motif = media.getMediaSpecimen().getTitle().getText();
 473                         }
 474                         dto.addDetailImage(mediaUriString==null?"":mediaUriString, motif!=null?motif:"[no motif]");
 475                     }
 476                 }
 477             }
 478             //assemble preserved specimen data
 479             else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.PreservedSpecimen){
 480                 if(!currentAccessionNumber.isEmpty()){
 481                     preservedSpecimenAccessionNumbers.add(currentAccessionNumber);
 482                 }
 483             }
 484         }
 485
 486         final String separator = ", ";
 487         //assemble citation
 488         String citation = "";
 489         citation += !dto.getCountry().isEmpty()?dto.getCountry()+separator:"";
 490         if(fieldUnit.getGatheringEvent()!=null){
 491             if(fieldUnit.getGatheringEvent().getLocality()!=null){
 492                 citation += fieldUnit.getGatheringEvent().getLocality().getText();
 493                 citation += separator;
 494             }
 495             if(fieldUnit.getGatheringEvent().getExactLocation()!=null
 496                     && fieldUnit.getGatheringEvent().getExactLocation().getLatitude()!=null
 497                     && fieldUnit.getGatheringEvent().getExactLocation().getLongitude()!=null){
 498                 citation += fieldUnit.getGatheringEvent().getExactLocation().getLatitude().toString();
 499                 citation += separator;
 500                 citation += fieldUnit.getGatheringEvent().getExactLocation().getLongitude().toString();
 501                 citation += separator;
 502             }
 503         }
 504         citation += !dto.getCollection().isEmpty()?dto.getCollection():"";
 505         if(!preservedSpecimenAccessionNumbers.isEmpty()){
 506             citation += " (";
 507             for(String accessionNumber:preservedSpecimenAccessionNumbers){
 508                 if(!accessionNumber.isEmpty()){
 509                     citation += accessionNumber+separator;
 510                 }
 511             }
 512             citation = removeTail(citation, separator);
 513             citation += ")";
 514         }
 515         citation = removeTail(citation, separator);
 516         dto.setCitation(citation);
 517
 518         //assemble herbaria string
 519         String herbariaString = "";
 520         for(Entry<eu.etaxonomy.cdm.model.occurrence.Collection, Integer> e:collectionToCountMap.entrySet()){
 521             eu.etaxonomy.cdm.model.occurrence.Collection collection = e.getKey();
 522             if(collection.getCode()!=null){
 523                 herbariaString += collection.getCode();
 524             }
 525             if(e.getValue()>1){
 526                 herbariaString += "("+e.getValue()+")";
 527             }
 528             herbariaString += separator;
 529         }
 530         herbariaString = removeTail(herbariaString, separator);
 531         dto.setHerbarium(herbariaString);
 532
 533         return dto;
 534     }
 535
 536
 537     /**
 538      * @param string
 539      * @param tail
 540      * @return
 541      */
 542     private String removeTail(String string, final String tail) {
 543         if(string.endsWith(tail)){
 544             string = string.substring(0, string.length()-tail.length());
 545         }
 546         return string;
 547     }
 548
 549     private String getMediaUriString(MediaSpecimen mediaSpecimen){
 550         String mediaUri = null;
 551         Collection<MediaRepresentation> mediaRepresentations = mediaSpecimen.getMediaSpecimen().getRepresentations();
 552         if(mediaRepresentations!=null && !mediaRepresentations.isEmpty()){
 553             Collection<MediaRepresentationPart> mediaRepresentationParts = mediaRepresentations.iterator().next().getParts();
 554             if(mediaRepresentationParts!=null && !mediaRepresentationParts.isEmpty()){
 555                 MediaRepresentationPart part = mediaRepresentationParts.iterator().next();
 556                 if(part.getUri()!=null){
 557                     mediaUri = part.getUri().toASCIIString();
 558                 }
 559             }
 560         }
 561         return mediaUri;
 562     }
 563
 564     private void getDerivedUnitsFor(SpecimenOrObservationBase<?> specimen, Collection<DerivedUnit> derivedUnits){
 565         for(DerivationEvent derivationEvent:specimen.getDerivationEvents()){
 566             for(DerivedUnit derivative:derivationEvent.getDerivatives()){
 567                 derivedUnits.add(derivative);
 568                 getDerivedUnitsFor(derivative, derivedUnits);
 569             }
 570         }
 571     }
 572
 573
 574     /* (non-Javadoc)
 575      * @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)
 576      */
 577     @SuppressWarnings("unchecked")
 578     @Override
 579     public <T extends SpecimenOrObservationBase> Pager<T> pageByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
 580             Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 581
 582         Set<Taxon> taxa = new HashSet<Taxon>();
 583         Set<Integer> occurrenceIds = new HashSet<Integer>();
 584         List<T> occurrences = new ArrayList<T>();
 585
 586 //        Integer limit = PagerUtils.limitFor(pageSize);
 587 //        Integer start = PagerUtils.startFor(pageSize, pageNumber);
 588
 589         if(!getSession().contains(associatedTaxon)){
 590             associatedTaxon = (Taxon) taxonService.load(associatedTaxon.getUuid());
 591         }
 592
 593         if(includeRelationships != null) {
 594             taxa = taxonService.listRelatedTaxa(associatedTaxon, includeRelationships, maxDepth, null, null, propertyPaths);
 595         }
 596
 597         taxa.add(associatedTaxon);
 598
 599         for (Taxon taxon : taxa) {
 600             List<T> perTaxonOccurrences = dao.listByAssociatedTaxon(type, taxon, null, null, orderHints, propertyPaths);
 601             for (SpecimenOrObservationBase o : perTaxonOccurrences) {
 602                 occurrenceIds.add(o.getId());
 603             }
 604         }
 605         occurrences = (List<T>) dao.listByIds(occurrenceIds, pageSize, pageNumber, orderHints, propertyPaths);
 606
 607         return new DefaultPagerImpl<T>(pageNumber, occurrenceIds.size(), pageSize, occurrences);
 608
 609     }
 610
 611
 612     @Override
 613     public <T extends SpecimenOrObservationBase> Pager<T> pageByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
 614             String taxonUUID, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 615
 616         UUID uuid = UUID.fromString(taxonUUID);
 617         Taxon tax = (Taxon) taxonService.load(uuid);
 618        //TODO REMOVE NULL STATEMENT
 619         type=null;
 620         return pageByAssociatedTaxon( type,includeRelationships,tax, maxDepth, pageSize, pageNumber, orderHints, propertyPaths );
 621
 622     }
 623
 624
 625     @Override
 626     public Pager<SearchResult<SpecimenOrObservationBase>> findByFullText(
 627             Class<? extends SpecimenOrObservationBase> clazz, String queryString, Rectangle boundingBox, List<Language> languages,
 628             boolean highlightFragments, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
 629             List<String> propertyPaths) throws CorruptIndexException, IOException, ParseException {
 630
 631         LuceneSearch luceneSearch = prepareByFullTextSearch(clazz, queryString, boundingBox, languages, highlightFragments);
 632
 633         // --- execute search
 634         TopGroupsWithMaxScore topDocsResultSet = luceneSearch.executeSearch(pageSize, pageNumber);
 635
 636         Map<CdmBaseType, String> idFieldMap = new HashMap<CdmBaseType, String>();
 637         idFieldMap.put(CdmBaseType.SPECIMEN_OR_OBSERVATIONBASE, "id");
 638
 639         // --- initialize taxa, highlight matches ....
 640         ISearchResultBuilder searchResultBuilder = new SearchResultBuilder(luceneSearch, luceneSearch.getQuery());
 641         @SuppressWarnings("rawtypes")
 642         List<SearchResult<SpecimenOrObservationBase>> searchResults = searchResultBuilder.createResultSet(
 643                 topDocsResultSet, luceneSearch.getHighlightFields(), dao, idFieldMap, propertyPaths);
 644
 645         int totalHits = topDocsResultSet != null ? topDocsResultSet.topGroups.totalGroupCount : 0;
 646
 647         return new DefaultPagerImpl<SearchResult<SpecimenOrObservationBase>>(pageNumber, totalHits, pageSize,
 648                 searchResults);
 649
 650     }
 651
 652
 653     /**
 654      * @param clazz
 655      * @param queryString
 656      * @param languages
 657      * @param highlightFragments
 658      * @return
 659      */
 660     private LuceneSearch prepareByFullTextSearch(Class<? extends SpecimenOrObservationBase> clazz, String queryString, Rectangle bbox,
 661             List<Language> languages, boolean highlightFragments) {
 662
 663         BooleanQuery finalQuery = new BooleanQuery();
 664         BooleanQuery textQuery = new BooleanQuery();
 665
 666         LuceneSearch luceneSearch = new LuceneSearch(luceneIndexToolProvider, FieldUnit.class);
 667         QueryFactory queryFactory = luceneIndexToolProvider.newQueryFactoryFor(FieldUnit.class);
 668
 669         // --- criteria
 670         luceneSearch.setCdmTypRestriction(clazz);
 671         if(queryString != null){
 672             textQuery.add(queryFactory.newTermQuery("titleCache", queryString), Occur.SHOULD);
 673             finalQuery.add(textQuery, Occur.MUST);
 674         }
 675
 676         // --- spacial query
 677         if(bbox != null){
 678             finalQuery.add(QueryFactory.buildSpatialQueryByRange(bbox, "gatheringEvent.exactLocation.point"), Occur.MUST);
 679         }
 680
 681         luceneSearch.setQuery(finalQuery);
 682
 683         // --- sorting
 684         SortField[] sortFields = new  SortField[]{SortField.FIELD_SCORE, new SortField("titleCache__sort", SortField.STRING, false)};
 685         luceneSearch.setSortFields(sortFields);
 686
 687         if(highlightFragments){
 688             luceneSearch.setHighlightFields(queryFactory.getTextFieldNamesAsArray());
 689         }
 690         return luceneSearch;
 691     }
 692
 693
 694     /* (non-Javadoc)
 695      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getFieldUnits(eu.etaxonomy.cdm.model.occurrence.DerivedUnit)
 696      */
 697     @Override
 698     public Collection<FieldUnit> getFieldUnits(UUID derivedUnitUuid) {
 699         //It will search recursively over all {@link DerivationEvent}s and get the "originals" ({@link SpecimenOrObservationBase})
 700         //from which this DerivedUnit was derived until all FieldUnits are found.
 701
 702         //FIXME: use HQL queries to increase performance
 703         SpecimenOrObservationBase<?> specimen = load(derivedUnitUuid);
 704 //        specimen = HibernateProxyHelper.deproxy(specimen, SpecimenOrObservationBase.class);
 705         Collection<FieldUnit> fieldUnits = new ArrayList<FieldUnit>();
 706
 707         if(specimen instanceof FieldUnit){
 708             fieldUnits.add((FieldUnit) specimen);
 709         }
 710         else if(specimen instanceof DerivedUnit){
 711             getFieldUnits((DerivedUnit) specimen, fieldUnits);
 712         }
 713         return fieldUnits;
 714     }
 715
 716
 717     /**
 718      * @param original
 719      * @param fieldUnits
 720      */
 721     private void getFieldUnits(DerivedUnit derivedUnit, Collection<FieldUnit> fieldUnits) {
 722         Set<SpecimenOrObservationBase> originals = derivedUnit.getOriginals();
 723         if(originals!=null && !originals.isEmpty()){
 724             for(SpecimenOrObservationBase<?> original:originals){
 725                 if(original instanceof FieldUnit){
 726                     fieldUnits.add((FieldUnit) original);
 727                 }
 728                 else if(original instanceof DerivedUnit){
 729                     getFieldUnits((DerivedUnit) original, fieldUnits);
 730                 }
 731             }
 732         }
 733     }
 734
 735     /* (non-Javadoc)
 736      * @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)
 737      */
 738     @Override
 739     public boolean moveSequence(DnaSample from, DnaSample to, Sequence sequence) {
 740         //reload specimens to avoid session conflicts
 741         from = (DnaSample) load(from.getUuid());
 742         to = (DnaSample) load(to.getUuid());
 743         sequence = sequenceService.load(sequence.getUuid());
 744
 745         if(from==null || to==null || sequence==null){
 746             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" +
 747                     "Operation was move "+sequence+ " from "+from+" to "+to);
 748         }
 749         from.removeSequence(sequence);
 750         saveOrUpdate(from);
 751         to.addSequence(sequence);
 752         saveOrUpdate(to);
 753         return true;
 754     }
 755
 756     /* (non-Javadoc)
 757      * @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)
 758      */
 759     @Override
 760     public boolean moveDerivate(SpecimenOrObservationBase<?> from, SpecimenOrObservationBase<?> to, DerivedUnit derivate) {
 761         //reload specimens to avoid session conflicts
 762         from = load(from.getUuid());
 763         to = load(to.getUuid());
 764         derivate = (DerivedUnit) load(derivate.getUuid());
 765
 766         if(from==null || to==null || derivate==null){
 767             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" +
 768                         "Operation was move "+derivate+ " from "+from+" to "+to);
 769         }
 770
 771         SpecimenOrObservationType derivateType = derivate.getRecordBasis();
 772         SpecimenOrObservationType toType = to.getRecordBasis();
 773         //check if type is a sub derivate type
 774         if(toType==SpecimenOrObservationType.FieldUnit //moving to FieldUnit always works
 775                 || derivateType==SpecimenOrObservationType.Media //moving media always works
 776                 || (derivateType.isKindOf(toType) && toType!=derivateType)){ //moving only to parent derivate type
 777             //remove derivation event from parent specimen of dragged object
 778             DerivationEvent eventToRemove = null;
 779             for(DerivationEvent event:from.getDerivationEvents()){
 780                 if(event.getDerivatives().contains(derivate)){
 781                     eventToRemove = event;
 782                     break;
 783                 }
 784             }
 785             from.removeDerivationEvent(eventToRemove);
 786             saveOrUpdate(from);
 787             //add new derivation event to target
 788             DerivationEvent derivedFromNewOriginalEvent = DerivationEvent.NewSimpleInstance(to, derivate, eventToRemove==null?null:eventToRemove.getType());
 789             to.addDerivationEvent(derivedFromNewOriginalEvent);
 790             derivate.setDerivedFrom(derivedFromNewOriginalEvent);
 791             saveOrUpdate(to);
 792             return true;
 793         }
 794         return false;
 795     }
 796
 797     @Override
 798     public Collection<ICdmBase> getNonCascadedAssociatedElements(SpecimenOrObservationBase<?> specimen){
 799         //potential fields that are not persisted cascadingly
 800         /*
 801          * SOOB
 802         -DescriptionBase
 803         -determinations
 804         --modifier TERM
 805         -kindOfUnit TERM
 806         -lifeStage TERM
 807         -sex TERM
 808
 809         FieldUnit
 810         -GatheringEvent
 811         --Country TERM
 812         --CollectingAreas TERM
 813
 814         DerivedUnit
 815         -collection
 816         --institute
 817         ---types TERM
 818         -preservationMethod
 819         --medium TERM
 820         -storedUnder CDM TaxonNameBase
 821         */
 822
 823         Collection<ICdmBase> nonCascadedCdmEntities = new HashSet<ICdmBase>();
 824
 825         //Choose the correct entry point to traverse the graph (FieldUnit or DerivedUnit)
 826
 827         //FieldUnit
 828         if(specimen instanceof FieldUnit){
 829             nonCascadedCdmEntities.addAll(getFieldUnitNonCascadedAssociatedElements((FieldUnit)specimen));
 830         }
 831         //DerivedUnit
 832         else if(specimen instanceof DerivedUnit){
 833             DerivedUnit derivedUnit = (DerivedUnit)specimen;
 834             if(derivedUnit.getDerivedFrom()!=null){
 835                 Collection<FieldUnit> fieldUnits = new ArrayList<FieldUnit>();
 836                 getFieldUnits(derivedUnit, fieldUnits);
 837                 for(FieldUnit fieldUnit:fieldUnits){
 838                     nonCascadedCdmEntities.addAll(getFieldUnitNonCascadedAssociatedElements(fieldUnit));
 839                 }
 840             }
 841         }
 842         return nonCascadedCdmEntities;
 843     }
 844
 845     private Collection<ICdmBase> getFieldUnitNonCascadedAssociatedElements(FieldUnit fieldUnit){
 846         //get non cascaded element on SpecimenOrObservationBase level
 847         Collection<ICdmBase> nonCascadedCdmEntities = getSpecimenOrObservationNonCascadedAssociatedElements(fieldUnit);
 848
 849         //get FieldUnit specific elements
 850         GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
 851         if(gatheringEvent!=null){
 852             //country
 853             if(gatheringEvent.getCountry()!=null){
 854                 nonCascadedCdmEntities.add(gatheringEvent.getCountry());
 855             }
 856             //collecting areas
 857             for (NamedArea namedArea : gatheringEvent.getCollectingAreas()) {
 858                 nonCascadedCdmEntities.add(namedArea);
 859             }
 860         }
 861         for (DerivationEvent derivationEvent : fieldUnit.getDerivationEvents()) {
 862             for (DerivedUnit derivedUnit : derivationEvent.getDerivatives()) {
 863                 nonCascadedCdmEntities.addAll(getDerivedUnitNonCascadedAssociatedElements(derivedUnit));
 864             }
 865         }
 866         return nonCascadedCdmEntities;
 867     }
 868
 869     private Collection<ICdmBase> getDerivedUnitNonCascadedAssociatedElements(DerivedUnit derivedUnit){
 870         //get non cascaded element on SpecimenOrObservationBase level
 871         Collection<ICdmBase> nonCascadedCdmEntities = getSpecimenOrObservationNonCascadedAssociatedElements(derivedUnit);
 872
 873         //get DerivedUnit specific elements
 874         if(derivedUnit.getCollection()!=null && derivedUnit.getCollection().getInstitute()!=null){
 875             for (DefinedTerm type : derivedUnit.getCollection().getInstitute().getTypes()) {
 876                 nonCascadedCdmEntities.add(type);
 877             }
 878         }
 879         if(derivedUnit.getPreservation()!=null && derivedUnit.getPreservation().getMedium()!=null){
 880             nonCascadedCdmEntities.add(derivedUnit.getPreservation().getMedium());
 881         }
 882         if(derivedUnit.getStoredUnder()!=null){
 883             nonCascadedCdmEntities.add(derivedUnit.getStoredUnder());
 884         }
 885         return nonCascadedCdmEntities;
 886     }
 887
 888     /**
 889      * @param specimen
 890      * @return
 891      */
 892     private Collection<ICdmBase> getSpecimenOrObservationNonCascadedAssociatedElements(
 893             SpecimenOrObservationBase<?> specimen) {
 894         Collection<ICdmBase> nonCascadedCdmEntities = new HashSet<ICdmBase>();
 895         //scan SpecimenOrObservationBase
 896         for(DeterminationEvent determinationEvent:specimen.getDeterminations()){
 897             //modifier
 898             if(determinationEvent.getModifier()!=null){
 899                 nonCascadedCdmEntities.add(determinationEvent.getModifier());
 900             }
 901         }
 902         //kindOfUnit
 903         if(specimen.getKindOfUnit()!=null){
 904             nonCascadedCdmEntities.add(specimen.getKindOfUnit());
 905         }
 906         //lifeStage
 907         if(specimen.getLifeStage()!=null){
 908             nonCascadedCdmEntities.add(specimen.getLifeStage());
 909         }
 910         //sex
 911         if(specimen.getSex()!=null){
 912             nonCascadedCdmEntities.add(specimen.getSex());
 913         }
 914         return nonCascadedCdmEntities;
 915     }
 916
 917
 918     /* (non-Javadoc)
 919      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#delete(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase, eu.etaxonomy.cdm.api.service.config.SpecimenDeleteConfigurator)
 920      */
 921     @Override
 922     public DeleteResult delete(SpecimenOrObservationBase<?> specimen, SpecimenDeleteConfigurator config) {
 923         DeleteResult deleteResult = new DeleteResult();
 924         //check for derivation events
 925         Set<DerivationEvent> derivationEvents = specimen.getDerivationEvents();
 926         for (DerivationEvent derivationEvent : derivationEvents) {
 927             if(!derivationEvent.getDerivatives().isEmpty()){
 928                 deleteResult.setAbort();
 929                 deleteResult.addException(new ReferencedObjectUndeletableException("Derivate with children cannot be deleted."));
 930                 return deleteResult;
 931             }
 932         }
 933         //check for original (parent derivate)
 934         if(specimen instanceof DerivedUnit){
 935             DerivationEvent derivedFromEvent = ((DerivedUnit) specimen).getDerivedFrom();
 936             if(derivedFromEvent!=null){
 937                 derivedFromEvent.removeDerivative((DerivedUnit) specimen);
 938             }
 939         }
 940         //check for IndividualsAssociation (e.g. in TaxonDescriptions)
 941         Collection<TaxonBase<?>> associatedTaxa = listAssociatedTaxa(specimen, null, null, null, null);
 942         if(!associatedTaxa.isEmpty()){
 943             if(config.isDeleteFromIndividualsAssociation()){
 944                 for (TaxonBase<?> taxonBase : associatedTaxa) {
 945                     if(taxonBase instanceof Taxon){
 946                         Set<TaxonDescription> descriptions = ((Taxon) taxonBase).getDescriptions();
 947                         for (TaxonDescription taxonDescription : descriptions) {
 948                             Set<DescriptionElementBase> elements = taxonDescription.getElements();
 949                             for (DescriptionElementBase descriptionElementBase : elements) {
 950                                 if(descriptionElementBase instanceof IndividualsAssociation){
 951                                     IndividualsAssociation individualsAssociation = (IndividualsAssociation) descriptionElementBase;
 952                                     if(individualsAssociation.getAssociatedSpecimenOrObservation().equals(specimen)){
 953                                         individualsAssociation.setAssociatedSpecimenOrObservation(null);
 954                                     }
 955                                 }
 956                             }
 957                         }
 958                     }
 959                 }
 960             }
 961             else{
 962                 deleteResult.addRelatedObjects(new HashSet<CdmBase>(associatedTaxa));
 963                 deleteResult.setAbort();
 964                 deleteResult.addException(new ReferencedObjectUndeletableException("Specimen is still associated with taxa."));
 965                 return deleteResult;
 966             }
 967         }
 968         //check for TypeDesignations
 969         Collection<TaxonBase<?>> typedTaxa = listTypedTaxa(specimen, null, null, null, null);
 970         if(!typedTaxa.isEmpty()){
 971             if(config.isdeleteFromTypeDesignation()){
 972                 for (TaxonBase<?> taxonBase : typedTaxa) {
 973                     if(taxonBase.getName()!=null){
 974                         Set<TypeDesignationBase> typeDesignations = taxonBase.getName().getTypeDesignations();
 975                         for (TypeDesignationBase typeDesignationBase : typeDesignations) {
 976                             if(typeDesignationBase instanceof SpecimenTypeDesignation){
 977                                 ((SpecimenTypeDesignation) typeDesignationBase).setTypeSpecimen(null);
 978                             }
 979                         }
 980                     }
 981                 }
 982             }
 983             else{
 984                 deleteResult.addRelatedObjects(new HashSet<CdmBase>(typedTaxa));
 985                 deleteResult.setAbort();
 986                 deleteResult.addException(new ReferencedObjectUndeletableException("Specimen is a type specimen."));
 987                 return deleteResult;
 988             }
 989         }
 990         if(!config.isDeleteChildren()){
 991             Set<CdmBase> referencingObjects = genericDao.getReferencingObjects(specimen);
 992             for (CdmBase referencingObject : referencingObjects){
 993                 //DerivedUnit?.storedUnder
 994                 if (referencingObject.isInstanceOf(DerivedUnit.class)){
 995                     String message = "Name can't be deleted as it is used as derivedUnit#storedUnder by %s. Remove 'stored under' prior to deleting this name";
 996                     message = String.format(message, CdmBase.deproxy(referencingObject, DerivedUnit.class).getTitleCache());
 997                 }
 998                 //DescriptionElementSource#nameUsedInSource
 999                 if (referencingObject.isInstanceOf(DescriptionElementSource.class)){
1000                     String message = "Name can't be deleted as it is used as descriptionElementSource#nameUsedInSource";
1001                 }
1002                 //NameTypeDesignation#typeName
1003                 if (referencingObject.isInstanceOf(NameTypeDesignation.class)){
1004                     String message = "Name can't be deleted as it is used as a name type in a NameTypeDesignation";
1005                 }
1006             }
1007             deleteResult = delete(specimen);
1008         }
1009         else{
1010             //TODO implement deep delete
1011         }
1012         return deleteResult;
1013     }
1014
1015     /* (non-Javadoc)
1016      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#deleteDerivateHierarchy(eu.etaxonomy.cdm.model.common.ICdmBase)
1017      */
1018     @Override
1019     public DeleteResult deleteDerivateHierarchy(ICdmBase from, SpecimenDeleteConfigurator config) {
1020         DeleteResult deleteResult = new DeleteResult();
1021         if(from instanceof Sequence){
1022             Sequence sequence = (Sequence)from;
1023             sequence.getDnaSample().removeSequence(sequence);
1024             deleteResult.setStatus(DeleteStatus.OK);
1025         }
1026         else if(from instanceof SpecimenOrObservationBase<?>)  {
1027             deleteResult = delete((SpecimenOrObservationBase<?>) from, config);
1028         }
1029         return deleteResult;
1030     }
1031
1032     private Set<ICdmBase> collectEntitiesToDelete(ICdmBase entity){
1033         Set<ICdmBase> entitiesToDelete = new LinkedHashSet<ICdmBase>();
1034
1035         if(entity instanceof SpecimenOrObservationBase<?>){
1036             SpecimenOrObservationBase<?> specimen = (SpecimenOrObservationBase<?>) entity;
1037             if(entity instanceof DerivedUnit){
1038                 DerivedUnit derivedUnit = (DerivedUnit)entity;
1039                 DerivationEvent derivedFrom = derivedUnit.getDerivedFrom();
1040                 Set<SpecimenOrObservationBase> originals = derivedFrom.getOriginals();
1041                 for (SpecimenOrObservationBase<?> original: originals) {
1042                         original.removeDerivationEvent(derivedFrom);
1043 //                        saveOrUpdate(original);
1044                 }
1045             }
1046             if(entity instanceof DnaSample && ((DnaSample) entity).getRecordBasis()==SpecimenOrObservationType.DnaSample){
1047                 DnaSample dnaSample = (DnaSample)entity;
1048                 for (Sequence sequence : dnaSample.getSequences()) {
1049                     entitiesToDelete.addAll(collectEntitiesToDelete(sequence));
1050                     dnaSample.removeSequence(sequence);
1051 //                    saveOrUpdate(dnaSample);
1052                 }
1053             }
1054             Set<DerivationEvent> derivationEvents = specimen.getDerivationEvents();
1055             for (DerivationEvent derivationEvent : derivationEvents) {
1056                 for (DerivedUnit derivedUnit : derivationEvent.getDerivatives()) {
1057                     entitiesToDelete.addAll(collectEntitiesToDelete(derivedUnit));
1058                 }
1059             }
1060         }
1061         else if(entity instanceof Sequence){
1062             Sequence sequence = (Sequence)entity;
1063             for (SingleRead singleRead : sequence.getSingleReads()) {
1064                 entitiesToDelete.addAll(collectEntitiesToDelete(singleRead));
1065                 sequence.removeSingleRead(singleRead);
1066             }
1067 //            sequenceService.saveOrUpdate(sequence);
1068         }
1069         entitiesToDelete.add(entity);
1070         return entitiesToDelete;
1071     }
1072
1073     /* (non-Javadoc)
1074      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#listAssociatedTaxa(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase)
1075      */
1076     @Override
1077     public Collection<TaxonBase<?>> listAssociatedTaxa(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
1078         return dao.listAssociatedTaxa(specimen, null, null, null, null);
1079     }
1080
1081     @Override
1082     public Collection<TaxonBase<?>> listTypedTaxa(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
1083         return dao.listTypedTaxa(specimen, limit, start, orderHints, propertyPaths);
1084     }
1085
1086 }