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