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.List;
  22 import java.util.Map;
  23 import java.util.Map.Entry;
  24 import java.util.Set;
  25 import java.util.UUID;
  26
  27 import org.apache.log4j.Logger;
  28 import org.apache.lucene.index.CorruptIndexException;
  29 import org.apache.lucene.queryParser.ParseException;
  30 import org.apache.lucene.search.BooleanClause.Occur;
  31 import org.apache.lucene.search.BooleanQuery;
  32 import org.apache.lucene.search.SortField;
  33 import org.hibernate.TransientObjectException;
  34 import org.hibernate.search.spatial.impl.Rectangle;
  35 import org.joda.time.Partial;
  36 import org.springframework.beans.factory.annotation.Autowired;
  37 import org.springframework.stereotype.Service;
  38 import org.springframework.transaction.annotation.Transactional;
  39
  40 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
  41 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeConfigurator;
  42 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeNotSupportedException;
  43 import eu.etaxonomy.cdm.api.service.DeleteResult.DeleteStatus;
  44 import eu.etaxonomy.cdm.api.service.config.DeleteConfiguratorBase;
  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.IndividualsAssociation;
  74 import eu.etaxonomy.cdm.model.description.SpecimenDescription;
  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.AmplificationResult;
  83 import eu.etaxonomy.cdm.model.molecular.DnaSample;
  84 import eu.etaxonomy.cdm.model.molecular.Sequence;
  85 import eu.etaxonomy.cdm.model.molecular.SingleRead;
  86 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
  87 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  88 import eu.etaxonomy.cdm.model.name.TypeDesignationStatusBase;
  89 import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
  90 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  91 import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
  92 import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
  93 import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
  94 import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen;
  95 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  96 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
  97 import eu.etaxonomy.cdm.model.taxon.Taxon;
  98 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  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 ISequenceService sequenceService;
 126
 127     @Autowired
 128     private AbstractBeanInitializer beanInitializer;
 129
 130     @Autowired
 131     private ILuceneIndexToolProvider luceneIndexToolProvider;
 132
 133     public OccurrenceServiceImpl() {
 134         logger.debug("Load OccurrenceService Bean");
 135     }
 136
 137
 138     /* (non-Javadoc)
 139      * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#updateTitleCache(java.lang.Integer, eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy)
 140      */
 141     @Override
 142     @Transactional(readOnly = false)
 143     public void updateTitleCache(Class<? extends SpecimenOrObservationBase> clazz, Integer stepSize, IIdentifiableEntityCacheStrategy<SpecimenOrObservationBase> cacheStrategy, IProgressMonitor monitor) {
 144         if (clazz == null){
 145             clazz = SpecimenOrObservationBase.class;
 146         }
 147         super.updateTitleCacheImpl(clazz, stepSize, cacheStrategy, monitor);
 148     }
 149
 150
 151     /**
 152      * FIXME Candidate for harmonization
 153      * move to termService
 154      */
 155     @Override
 156     public Country getCountryByIso(String iso639) {
 157         return this.definedTermDao.getCountryByIso(iso639);
 158
 159     }
 160
 161     /**
 162      * FIXME Candidate for harmonization
 163      * move to termService
 164      */
 165     @Override
 166     public List<Country> getCountryByName(String name) {
 167         List<? extends DefinedTermBase> terms = this.definedTermDao.findByTitle(Country.class, name, null, null, null, null, null, null) ;
 168         List<Country> countries = new ArrayList<Country>();
 169         for (int i=0;i<terms.size();i++){
 170             countries.add((Country)terms.get(i));
 171         }
 172         return countries;
 173     }
 174
 175     @Override
 176     @Autowired
 177     protected void setDao(IOccurrenceDao dao) {
 178         this.dao = dao;
 179     }
 180
 181     @Override
 182     public Pager<DerivationEvent> getDerivationEvents(SpecimenOrObservationBase occurence, Integer pageSize,Integer pageNumber, List<String> propertyPaths) {
 183         Integer numberOfResults = dao.countDerivationEvents(occurence);
 184
 185         List<DerivationEvent> results = new ArrayList<DerivationEvent>();
 186         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 187             results = dao.getDerivationEvents(occurence, pageSize, pageNumber,propertyPaths);
 188         }
 189
 190         return new DefaultPagerImpl<DerivationEvent>(pageNumber, numberOfResults, pageSize, results);
 191     }
 192
 193     /* (non-Javadoc)
 194      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#countDeterminations(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase, eu.etaxonomy.cdm.model.taxon.TaxonBase)
 195      */
 196     @Override
 197     public int countDeterminations(SpecimenOrObservationBase occurence, TaxonBase taxonbase) {
 198         return dao.countDeterminations(occurence, taxonbase);
 199     }
 200
 201     @Override
 202     public Pager<DeterminationEvent> getDeterminations(SpecimenOrObservationBase occurrence, TaxonBase taxonBase, Integer pageSize,Integer pageNumber, List<String> propertyPaths) {
 203         Integer numberOfResults = dao.countDeterminations(occurrence, taxonBase);
 204
 205         List<DeterminationEvent> results = new ArrayList<DeterminationEvent>();
 206         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 207             results = dao.getDeterminations(occurrence,taxonBase, pageSize, pageNumber, propertyPaths);
 208         }
 209
 210         return new DefaultPagerImpl<DeterminationEvent>(pageNumber, numberOfResults, pageSize, results);
 211     }
 212
 213     @Override
 214     public Pager<Media> getMedia(SpecimenOrObservationBase occurence,Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
 215         Integer numberOfResults = dao.countMedia(occurence);
 216
 217         List<Media> results = new ArrayList<Media>();
 218         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 219             results = dao.getMedia(occurence, pageSize, pageNumber, propertyPaths);
 220         }
 221
 222         return new DefaultPagerImpl<Media>(pageNumber, numberOfResults, pageSize, results);
 223     }
 224
 225     /* (non-Javadoc)
 226      * @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)
 227      */
 228     @Override
 229     public Pager<SpecimenOrObservationBase> list(Class<? extends SpecimenOrObservationBase> type, TaxonBase determinedAs, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 230         Integer numberOfResults = dao.count(type,determinedAs);
 231         List<SpecimenOrObservationBase> results = new ArrayList<SpecimenOrObservationBase>();
 232         pageNumber = pageNumber == null ? 0 : pageNumber;
 233         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 234             Integer start = pageSize == null ? 0 : pageSize * pageNumber;
 235             results = dao.list(type,determinedAs, pageSize, start, orderHints,propertyPaths);
 236         }
 237         return new DefaultPagerImpl<SpecimenOrObservationBase>(pageNumber, numberOfResults, pageSize, results);
 238     }
 239
 240     @Override
 241     public List<UuidAndTitleCache<DerivedUnit>> getDerivedUnitUuidAndTitleCache() {
 242         return dao.getDerivedUnitUuidAndTitleCache();
 243     }
 244
 245     @Override
 246     public List<UuidAndTitleCache<FieldUnit>> getFieldUnitUuidAndTitleCache() {
 247         return dao.getFieldUnitUuidAndTitleCache();
 248     }
 249
 250     /* (non-Javadoc)
 251      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getDerivedUnitFacade(eu.etaxonomy.cdm.model.occurrence.DerivedUnit)
 252      */
 253     @Override
 254     public DerivedUnitFacade getDerivedUnitFacade(DerivedUnit derivedUnit, List<String> propertyPaths) throws DerivedUnitFacadeNotSupportedException {
 255         derivedUnit = (DerivedUnit)dao.load(derivedUnit.getUuid(), null);
 256         DerivedUnitFacadeConfigurator config = DerivedUnitFacadeConfigurator.NewInstance();
 257         config.setThrowExceptionForNonSpecimenPreservationMethodRequest(false);
 258         DerivedUnitFacade derivedUnitFacade = DerivedUnitFacade.NewInstance(derivedUnit, config);
 259         beanInitializer.initialize(derivedUnitFacade, propertyPaths);
 260         return derivedUnitFacade;
 261     }
 262
 263     /* (non-Javadoc)
 264      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#listDerivedUnitFacades(eu.etaxonomy.cdm.model.description.DescriptionBase, java.util.List)
 265      */
 266     @Override
 267     public List<DerivedUnitFacade> listDerivedUnitFacades(
 268             DescriptionBase description, List<String> propertyPaths) {
 269
 270         List<DerivedUnitFacade> derivedUnitFacadeList = new ArrayList<DerivedUnitFacade>();
 271         IndividualsAssociation tempIndividualsAssociation;
 272         SpecimenOrObservationBase tempSpecimenOrObservationBase;
 273         List<DescriptionElementBase> elements = descriptionService.listDescriptionElements(description, null, IndividualsAssociation.class, null, 0, Arrays.asList(new String []{"associatedSpecimenOrObservation"}));
 274         for(DescriptionElementBase element : elements){
 275             if(element.isInstanceOf(IndividualsAssociation.class)){
 276                 tempIndividualsAssociation = HibernateProxyHelper.deproxy(element, IndividualsAssociation.class);
 277                 if(tempIndividualsAssociation.getAssociatedSpecimenOrObservation() != null){
 278                     tempSpecimenOrObservationBase = HibernateProxyHelper.deproxy(tempIndividualsAssociation.getAssociatedSpecimenOrObservation(), SpecimenOrObservationBase.class);
 279                     if(tempSpecimenOrObservationBase.isInstanceOf(DerivedUnit.class)){
 280                         try {
 281                             derivedUnitFacadeList.add(DerivedUnitFacade.NewInstance(HibernateProxyHelper.deproxy(tempSpecimenOrObservationBase, DerivedUnit.class)));
 282                         } catch (DerivedUnitFacadeNotSupportedException e) {
 283                             logger.warn(tempIndividualsAssociation.getAssociatedSpecimenOrObservation().getTitleCache() + " : " +e.getMessage());
 284                         }
 285                     }
 286                 }
 287
 288             }
 289         }
 290
 291         beanInitializer.initializeAll(derivedUnitFacadeList, propertyPaths);
 292
 293         return derivedUnitFacadeList;
 294     }
 295
 296
 297     /* (non-Javadoc)
 298      * @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)
 299      */
 300     @Override
 301     public <T extends SpecimenOrObservationBase> List<T> listByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
 302             Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 303
 304         return pageByAssociatedTaxon(type, includeRelationships, associatedTaxon, maxDepth, pageSize, pageNumber, orderHints, propertyPaths).getRecords();
 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 Collection<FieldUnit> listFieldUnitsByAssociatedTaxon(Set<TaxonRelationshipEdge> includeRelationships,
 312             Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 313
 314         if(!getSession().contains(associatedTaxon)){
 315             associatedTaxon = (Taxon) taxonService.load(associatedTaxon.getUuid());
 316         }
 317
 318         Set<FieldUnit> fieldUnits = new HashSet<FieldUnit>();
 319
 320         List<SpecimenOrObservationBase> records = pageByAssociatedTaxon(null, includeRelationships, associatedTaxon, maxDepth, pageSize, pageNumber, orderHints, propertyPaths).getRecords();
 321         for(SpecimenOrObservationBase<?> specimen:records){
 322             fieldUnits.addAll(getFieldUnits(specimen.getUuid()));
 323         }
 324         return fieldUnits;
 325     }
 326
 327     @Override
 328     public DerivateHierarchyDTO assembleDerivateHierarchyDTO(FieldUnit fieldUnit, UUID associatedTaxonUuid){
 329
 330         if(!getSession().contains(fieldUnit)){
 331             fieldUnit = (FieldUnit) load(fieldUnit.getUuid());
 332         }
 333         TaxonBase associatedTaxon = taxonService.load(associatedTaxonUuid);
 334
 335         DerivateHierarchyDTO dto = new DerivateHierarchyDTO();
 336         Map<UUID, TypeDesignationStatusBase> typeSpecimenUUIDtoTypeDesignationStatus = new HashMap<UUID, TypeDesignationStatusBase>();
 337
 338         //gather types for this taxon name
 339         TaxonNameBase<?,?> name = associatedTaxon.getName();
 340         Set<?> typeDesignations = name.getSpecimenTypeDesignations();
 341         for (Object object : typeDesignations) {
 342             if(object instanceof CdmBase && ((CdmBase)object).isInstanceOf(SpecimenTypeDesignation.class)){
 343                 SpecimenTypeDesignation specimenTypeDesignation = HibernateProxyHelper.deproxy(object, SpecimenTypeDesignation.class);
 344                 DerivedUnit typeSpecimen = specimenTypeDesignation.getTypeSpecimen();
 345                 final TypeDesignationStatusBase typeStatus = specimenTypeDesignation.getTypeStatus();
 346                 typeSpecimenUUIDtoTypeDesignationStatus.put(typeSpecimen.getUuid(), typeStatus);
 347             }
 348         }
 349
 350         if(fieldUnit.getGatheringEvent()!=null){
 351             GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
 352             //Country
 353             final NamedArea country = gatheringEvent.getCountry();
 354             dto.setCountry(country!=null?country.getDescription():"");
 355             //Collection
 356             final AgentBase collector = gatheringEvent.getCollector();
 357             final String fieldNumber = fieldUnit.getFieldNumber();
 358             dto.setCollection(((collector!=null?collector:"") + " " + (fieldNumber!=null?fieldNumber:"")).trim());
 359             //Date
 360             final Partial gatheringDate = gatheringEvent.getGatheringDate();
 361             dto.setDate(gatheringDate!=null?gatheringDate.toString():"");
 362         }
 363
 364         //Taxon Name
 365         dto.setTaxonName(associatedTaxon.getName().getFullTitleCache());
 366
 367
 368         Collection<DerivedUnit> derivedUnits = new ArrayList<DerivedUnit>();
 369         getDerivedUnitsFor(fieldUnit, derivedUnits);
 370
 371         //Herbaria map
 372         Map<eu.etaxonomy.cdm.model.occurrence.Collection, Integer> collectionToCountMap = new HashMap<eu.etaxonomy.cdm.model.occurrence.Collection, Integer>();
 373         //List of accession numbers for citation
 374         List<String> preservedSpecimenAccessionNumbers = new ArrayList<String>();
 375
 376         //iterate over sub derivates
 377         for (DerivedUnit derivedUnit : derivedUnits) {
 378             //current accession number
 379             String currentAccessionNumber = derivedUnit.getAccessionNumber()!=null?derivedUnit.getAccessionNumber():"";
 380             //current herbarium
 381             String currentHerbarium = "";
 382             eu.etaxonomy.cdm.model.occurrence.Collection collection = derivedUnit.getCollection();
 383             if(collection!=null){
 384                 currentHerbarium = collection.getCode()!=null?collection.getCode():"";
 385                 //count herbaria
 386                 Integer count = collectionToCountMap.get(collection);
 387                 if(count==null){
 388                     count = 1;
 389                 }
 390                 else{
 391                     count++;
 392                 }
 393                 collectionToCountMap.put(collection, count);
 394             }
 395             //check if derived unit is a type
 396             if(typeSpecimenUUIDtoTypeDesignationStatus.keySet().contains(derivedUnit.getUuid())){
 397                 dto.setHasType(true);
 398                 TypeDesignationStatusBase typeDesignationStatus = typeSpecimenUUIDtoTypeDesignationStatus.get(derivedUnit.getUuid());
 399                 String typeStatus = typeDesignationStatus.getLabel();
 400                 dto.addTypes(typeStatus, currentAccessionNumber);
 401             }
 402             //assemble molecular data
 403             //pattern: DNAMarker [contig1, primer1_1, primer1_2, ...][contig2, primer2_1, ...]...
 404             if(derivedUnit.isInstanceOf(DnaSample.class)){
 405                 if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.TissueSample){
 406                     //TODO implement TissueSample assembly for web service
 407                 }
 408                 if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.DnaSample){
 409
 410                     DnaSample dna = HibernateProxyHelper.deproxy(derivedUnit, DnaSample.class);
 411                     if(!dna.getSequences().isEmpty()){
 412                         dto.setHasDna(true);
 413                     }
 414                     for(Sequence sequence:dna.getSequences()){
 415                         URI boldUri = null;
 416                         try {
 417                             boldUri = sequence.getBoldUri();
 418                         } catch (URISyntaxException e1) {
 419                             logger.error("Could not create BOLD URI", e1);
 420                         }
 421                         final DefinedTerm dnaMarker = sequence.getDnaMarker();
 422                         MolecularData molecularData = dto.addProviderLink(boldUri!=null?boldUri:null,dnaMarker!=null?dnaMarker.getLabel():"[no marker]");
 423
 424                         //contig file FIXME show primer although contig not present?
 425                         if(sequence.getContigFile()!=null){
 426                             MediaRepresentationPart contigMediaRepresentationPart = MediaUtils.getFirstMediaRepresentationPart(sequence.getContigFile());
 427                             if(contigMediaRepresentationPart!=null){
 428                                 ContigFile contigFile = molecularData.addContigFile(contigMediaRepresentationPart.getUri(), "contig");
 429                                 //primer files
 430                                 if(sequence.getSingleReads()!=null){
 431                                     for (SingleRead singleRead : sequence.getSingleReads()) {
 432                                         MediaRepresentationPart pherogramMediaRepresentationPart = MediaUtils.getFirstMediaRepresentationPart(singleRead.getPherogram());
 433                                         if(pherogramMediaRepresentationPart!=null){
 434                                             contigFile.addPrimerLink(pherogramMediaRepresentationPart.getUri(), "primer");
 435                                         }
 436                                     }
 437                                 }
 438                             }
 439                         }
 440                     }
 441                 }
 442             }
 443             //assemble media data
 444             else if(derivedUnit.isInstanceOf(MediaSpecimen.class)){
 445
 446                 MediaSpecimen media = HibernateProxyHelper.deproxy(derivedUnit, MediaSpecimen.class);
 447                 String mediaUriString = getMediaUriString(media);
 448                 if(media.getKindOfUnit()!=null){
 449                     //specimen scan
 450                     if(media.getKindOfUnit().getUuid().equals(UUID.fromString("acda15be-c0e2-4ea8-8783-b9b0c4ad7f03"))){
 451                         dto.setHasSpecimenScan(true);
 452                             final String imageLinkText = currentHerbarium+" "+currentAccessionNumber;
 453                             dto.addSpecimenScan(mediaUriString==null?"":mediaUriString, !imageLinkText.equals(" ")?imageLinkText:"[no accession]");
 454                     }
 455                     //detail image
 456                     else if(media.getKindOfUnit().getUuid().equals(UUID.fromString("31eb8d02-bf5d-437c-bcc6-87a626445f34"))){
 457                         dto.setHasDetailImage(true);
 458                         String motif = "";
 459                         if(media.getMediaSpecimen()!=null && media.getMediaSpecimen().getTitle()!=null){
 460                             motif = media.getMediaSpecimen().getTitle().getText();
 461                         }
 462                         dto.addDetailImage(mediaUriString==null?"":mediaUriString, motif!=null?motif:"[no motif]");
 463                     }
 464                 }
 465             }
 466             //assemble preserved specimen data
 467             else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.PreservedSpecimen){
 468                 if(!currentAccessionNumber.isEmpty()){
 469                     preservedSpecimenAccessionNumbers.add(currentAccessionNumber);
 470                 }
 471             }
 472         }
 473
 474         final String separator = ", ";
 475         //assemble citation
 476         String citation = "";
 477         citation += !dto.getCountry().isEmpty()?dto.getCountry()+separator:"";
 478         if(fieldUnit.getGatheringEvent()!=null){
 479             if(fieldUnit.getGatheringEvent().getLocality()!=null){
 480                 citation += fieldUnit.getGatheringEvent().getLocality().getText();
 481                 citation += separator;
 482             }
 483             if(fieldUnit.getGatheringEvent().getExactLocation()!=null
 484                     && fieldUnit.getGatheringEvent().getExactLocation().getLatitude()!=null
 485                     && fieldUnit.getGatheringEvent().getExactLocation().getLongitude()!=null){
 486                 citation += fieldUnit.getGatheringEvent().getExactLocation().getLatitude().toString();
 487                 citation += separator;
 488                 citation += fieldUnit.getGatheringEvent().getExactLocation().getLongitude().toString();
 489                 citation += separator;
 490             }
 491         }
 492         citation += !dto.getCollection().isEmpty()?dto.getCollection():"";
 493         if(!preservedSpecimenAccessionNumbers.isEmpty()){
 494             citation += " (";
 495             for(String accessionNumber:preservedSpecimenAccessionNumbers){
 496                 if(!accessionNumber.isEmpty()){
 497                     citation += accessionNumber+separator;
 498                 }
 499             }
 500             citation = removeTail(citation, separator);
 501             citation += ")";
 502         }
 503         citation = removeTail(citation, separator);
 504         dto.setCitation(citation);
 505
 506         //assemble herbaria string
 507         String herbariaString = "";
 508         for(Entry<eu.etaxonomy.cdm.model.occurrence.Collection, Integer> e:collectionToCountMap.entrySet()){
 509             eu.etaxonomy.cdm.model.occurrence.Collection collection = e.getKey();
 510             if(collection.getCode()!=null){
 511                 herbariaString += collection.getCode();
 512             }
 513             if(e.getValue()>1){
 514                 herbariaString += "("+e.getValue()+")";
 515             }
 516             herbariaString += separator;
 517         }
 518         herbariaString = removeTail(herbariaString, separator);
 519         dto.setHerbarium(herbariaString);
 520
 521         return dto;
 522     }
 523
 524
 525     /**
 526      * @param string
 527      * @param tail
 528      * @return
 529      */
 530     private String removeTail(String string, final String tail) {
 531         if(string.endsWith(tail)){
 532             string = string.substring(0, string.length()-tail.length());
 533         }
 534         return string;
 535     }
 536
 537     private String getMediaUriString(MediaSpecimen mediaSpecimen){
 538         String mediaUri = null;
 539         Collection<MediaRepresentation> mediaRepresentations = mediaSpecimen.getMediaSpecimen().getRepresentations();
 540         if(mediaRepresentations!=null && !mediaRepresentations.isEmpty()){
 541             Collection<MediaRepresentationPart> mediaRepresentationParts = mediaRepresentations.iterator().next().getParts();
 542             if(mediaRepresentationParts!=null && !mediaRepresentationParts.isEmpty()){
 543                 MediaRepresentationPart part = mediaRepresentationParts.iterator().next();
 544                 if(part.getUri()!=null){
 545                     mediaUri = part.getUri().toASCIIString();
 546                 }
 547             }
 548         }
 549         return mediaUri;
 550     }
 551
 552     private void getDerivedUnitsFor(SpecimenOrObservationBase<?> specimen, Collection<DerivedUnit> derivedUnits){
 553         for(DerivationEvent derivationEvent:specimen.getDerivationEvents()){
 554             for(DerivedUnit derivative:derivationEvent.getDerivatives()){
 555                 derivedUnits.add(derivative);
 556                 getDerivedUnitsFor(derivative, derivedUnits);
 557             }
 558         }
 559     }
 560
 561
 562     /* (non-Javadoc)
 563      * @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)
 564      */
 565     @SuppressWarnings("unchecked")
 566     @Override
 567     public <T extends SpecimenOrObservationBase> Pager<T> pageByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
 568             Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 569
 570         Set<Taxon> taxa = new HashSet<Taxon>();
 571         Set<Integer> occurrenceIds = new HashSet<Integer>();
 572         List<T> occurrences = new ArrayList<T>();
 573
 574 //        Integer limit = PagerUtils.limitFor(pageSize);
 575 //        Integer start = PagerUtils.startFor(pageSize, pageNumber);
 576
 577         if(!getSession().contains(associatedTaxon)){
 578             associatedTaxon = (Taxon) taxonService.load(associatedTaxon.getUuid());
 579         }
 580
 581         if(includeRelationships != null) {
 582             taxa = taxonService.listRelatedTaxa(associatedTaxon, includeRelationships, maxDepth, null, null, propertyPaths);
 583         }
 584
 585         taxa.add(associatedTaxon);
 586
 587         for (Taxon taxon : taxa) {
 588             List<T> perTaxonOccurrences = dao.listByAssociatedTaxon(type, taxon, null, null, orderHints, propertyPaths);
 589             for (SpecimenOrObservationBase o : perTaxonOccurrences) {
 590                 occurrenceIds.add(o.getId());
 591             }
 592         }
 593         occurrences = (List<T>) dao.listByIds(occurrenceIds, pageSize, pageNumber, orderHints, propertyPaths);
 594
 595         return new DefaultPagerImpl<T>(pageNumber, occurrenceIds.size(), pageSize, occurrences);
 596
 597     }
 598
 599
 600     @Override
 601     public <T extends SpecimenOrObservationBase> Pager<T> pageByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
 602             String taxonUUID, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 603
 604         UUID uuid = UUID.fromString(taxonUUID);
 605         Taxon tax = (Taxon) taxonService.load(uuid);
 606        //TODO REMOVE NULL STATEMENT
 607         type=null;
 608         return pageByAssociatedTaxon( type,includeRelationships,tax, maxDepth, pageSize, pageNumber, orderHints, propertyPaths );
 609
 610     }
 611
 612
 613     @Override
 614     public Pager<SearchResult<SpecimenOrObservationBase>> findByFullText(
 615             Class<? extends SpecimenOrObservationBase> clazz, String queryString, Rectangle boundingBox, List<Language> languages,
 616             boolean highlightFragments, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
 617             List<String> propertyPaths) throws CorruptIndexException, IOException, ParseException {
 618
 619         LuceneSearch luceneSearch = prepareByFullTextSearch(clazz, queryString, boundingBox, languages, highlightFragments);
 620
 621         // --- execute search
 622         TopGroupsWithMaxScore topDocsResultSet = luceneSearch.executeSearch(pageSize, pageNumber);
 623
 624         Map<CdmBaseType, String> idFieldMap = new HashMap<CdmBaseType, String>();
 625         idFieldMap.put(CdmBaseType.SPECIMEN_OR_OBSERVATIONBASE, "id");
 626
 627         // --- initialize taxa, highlight matches ....
 628         ISearchResultBuilder searchResultBuilder = new SearchResultBuilder(luceneSearch, luceneSearch.getQuery());
 629         @SuppressWarnings("rawtypes")
 630         List<SearchResult<SpecimenOrObservationBase>> searchResults = searchResultBuilder.createResultSet(
 631                 topDocsResultSet, luceneSearch.getHighlightFields(), dao, idFieldMap, propertyPaths);
 632
 633         int totalHits = topDocsResultSet != null ? topDocsResultSet.topGroups.totalGroupCount : 0;
 634
 635         return new DefaultPagerImpl<SearchResult<SpecimenOrObservationBase>>(pageNumber, totalHits, pageSize,
 636                 searchResults);
 637
 638     }
 639
 640
 641     /**
 642      * @param clazz
 643      * @param queryString
 644      * @param languages
 645      * @param highlightFragments
 646      * @return
 647      */
 648     private LuceneSearch prepareByFullTextSearch(Class<? extends SpecimenOrObservationBase> clazz, String queryString, Rectangle bbox,
 649             List<Language> languages, boolean highlightFragments) {
 650
 651         BooleanQuery finalQuery = new BooleanQuery();
 652         BooleanQuery textQuery = new BooleanQuery();
 653
 654         LuceneSearch luceneSearch = new LuceneSearch(luceneIndexToolProvider, FieldUnit.class);
 655         QueryFactory queryFactory = luceneIndexToolProvider.newQueryFactoryFor(FieldUnit.class);
 656
 657         // --- criteria
 658         luceneSearch.setCdmTypRestriction(clazz);
 659         if(queryString != null){
 660             textQuery.add(queryFactory.newTermQuery("titleCache", queryString), Occur.SHOULD);
 661             finalQuery.add(textQuery, Occur.MUST);
 662         }
 663
 664         // --- spacial query
 665         if(bbox != null){
 666             finalQuery.add(QueryFactory.buildSpatialQueryByRange(bbox, "gatheringEvent.exactLocation.point"), Occur.MUST);
 667         }
 668
 669         luceneSearch.setQuery(finalQuery);
 670
 671         // --- sorting
 672         SortField[] sortFields = new  SortField[]{SortField.FIELD_SCORE, new SortField("titleCache__sort", SortField.STRING, false)};
 673         luceneSearch.setSortFields(sortFields);
 674
 675         if(highlightFragments){
 676             luceneSearch.setHighlightFields(queryFactory.getTextFieldNamesAsArray());
 677         }
 678         return luceneSearch;
 679     }
 680
 681
 682     /* (non-Javadoc)
 683      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getFieldUnits(eu.etaxonomy.cdm.model.occurrence.DerivedUnit)
 684      */
 685     @Override
 686     public Collection<FieldUnit> getFieldUnits(UUID derivedUnitUuid) {
 687         //It will search recursively over all {@link DerivationEvent}s and get the "originals" ({@link SpecimenOrObservationBase})
 688         //from which this DerivedUnit was derived until all FieldUnits are found.
 689
 690         //FIXME: use HQL queries to increase performance
 691         SpecimenOrObservationBase<?> specimen = load(derivedUnitUuid);
 692 //        specimen = HibernateProxyHelper.deproxy(specimen, SpecimenOrObservationBase.class);
 693         Collection<FieldUnit> fieldUnits = new ArrayList<FieldUnit>();
 694
 695         if(specimen.isInstanceOf(FieldUnit.class)){
 696             fieldUnits.add(HibernateProxyHelper.deproxy(specimen, FieldUnit.class));
 697         }
 698         else if(specimen.isInstanceOf(DerivedUnit.class)){
 699             fieldUnits.addAll(getFieldUnits(HibernateProxyHelper.deproxy(specimen, DerivedUnit.class)));
 700         }
 701         return fieldUnits;
 702     }
 703
 704
 705     /**
 706      * @param original
 707      * @param fieldUnits
 708      */
 709     private Collection<FieldUnit> getFieldUnits(DerivedUnit derivedUnit) {
 710         Collection<FieldUnit> fieldUnits = new HashSet<FieldUnit>();
 711         Set<SpecimenOrObservationBase> originals = derivedUnit.getOriginals();
 712         if(originals!=null && !originals.isEmpty()){
 713             for(SpecimenOrObservationBase<?> original:originals){
 714                 if(original.isInstanceOf(FieldUnit.class)){
 715                     fieldUnits.add(HibernateProxyHelper.deproxy(original, FieldUnit.class));
 716                 }
 717                 else if(original.isInstanceOf(DerivedUnit.class)){
 718                     fieldUnits.addAll(getFieldUnits(HibernateProxyHelper.deproxy(original, DerivedUnit.class)));
 719                 }
 720             }
 721         }
 722         return fieldUnits;
 723     }
 724
 725     /* (non-Javadoc)
 726      * @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)
 727      */
 728     @Override
 729     public boolean moveSequence(DnaSample from, DnaSample to, Sequence sequence) {
 730         //reload specimens to avoid session conflicts
 731         from = (DnaSample) load(from.getUuid());
 732         to = (DnaSample) load(to.getUuid());
 733         sequence = sequenceService.load(sequence.getUuid());
 734
 735         if(from==null || to==null || sequence==null){
 736             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" +
 737                     "Operation was move "+sequence+ " from "+from+" to "+to);
 738         }
 739         from.removeSequence(sequence);
 740         saveOrUpdate(from);
 741         to.addSequence(sequence);
 742         saveOrUpdate(to);
 743         return true;
 744     }
 745
 746     /* (non-Javadoc)
 747      * @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)
 748      */
 749     @Override
 750     public boolean moveDerivate(SpecimenOrObservationBase<?> from, SpecimenOrObservationBase<?> to, DerivedUnit derivate) {
 751         //reload specimens to avoid session conflicts
 752         from = load(from.getUuid());
 753         to = load(to.getUuid());
 754         derivate = (DerivedUnit) load(derivate.getUuid());
 755
 756         if(from==null || to==null || derivate==null){
 757             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" +
 758                         "Operation was move "+derivate+ " from "+from+" to "+to);
 759         }
 760
 761         SpecimenOrObservationType derivateType = derivate.getRecordBasis();
 762         SpecimenOrObservationType toType = to.getRecordBasis();
 763         //check if type is a sub derivate type
 764         if(toType==SpecimenOrObservationType.FieldUnit //moving to FieldUnit always works
 765                 || derivateType==SpecimenOrObservationType.Media //moving media always works
 766                 || (derivateType.isKindOf(toType) && toType!=derivateType)){ //moving only to parent derivate type
 767             //remove derivation event from parent specimen of dragged object
 768             DerivationEvent eventToRemove = null;
 769             for(DerivationEvent event:from.getDerivationEvents()){
 770                 if(event.getDerivatives().contains(derivate)){
 771                     eventToRemove = event;
 772                     break;
 773                 }
 774             }
 775             from.removeDerivationEvent(eventToRemove);
 776             saveOrUpdate(from);
 777             //add new derivation event to target
 778             DerivationEvent derivedFromNewOriginalEvent = DerivationEvent.NewSimpleInstance(to, derivate, eventToRemove==null?null:eventToRemove.getType());
 779             to.addDerivationEvent(derivedFromNewOriginalEvent);
 780             derivate.setDerivedFrom(derivedFromNewOriginalEvent);
 781             saveOrUpdate(to);
 782             return true;
 783         }
 784         return false;
 785     }
 786
 787     @Override
 788     public Collection<ICdmBase> getNonCascadedAssociatedElements(SpecimenOrObservationBase<?> specimen){
 789         //potential fields that are not persisted cascadingly
 790         /*
 791          * SOOB
 792         -DescriptionBase
 793         -determinations
 794         --modifier TERM
 795         -kindOfUnit TERM
 796         -lifeStage TERM
 797         -sex TERM
 798
 799         FieldUnit
 800         -GatheringEvent
 801         --Country TERM
 802         --CollectingAreas TERM
 803
 804         DerivedUnit
 805         -collection
 806         --institute
 807         ---types TERM
 808         -preservationMethod
 809         --medium TERM
 810         -storedUnder CDM TaxonNameBase
 811         */
 812
 813         Collection<ICdmBase> nonCascadedCdmEntities = new HashSet<ICdmBase>();
 814
 815         //Choose the correct entry point to traverse the graph (FieldUnit or DerivedUnit)
 816
 817         //FieldUnit
 818         if(specimen.isInstanceOf(FieldUnit.class)){
 819             nonCascadedCdmEntities.addAll(getFieldUnitNonCascadedAssociatedElements(HibernateProxyHelper.deproxy(specimen, FieldUnit.class)));
 820         }
 821         //DerivedUnit
 822         else if(specimen.isInstanceOf(DerivedUnit.class)){
 823             DerivedUnit derivedUnit = HibernateProxyHelper.deproxy(specimen, DerivedUnit.class);
 824             if(derivedUnit.getDerivedFrom()!=null){
 825                 Collection<FieldUnit> fieldUnits = getFieldUnits(derivedUnit);
 826                 for(FieldUnit fieldUnit:fieldUnits){
 827                     nonCascadedCdmEntities.addAll(getFieldUnitNonCascadedAssociatedElements(fieldUnit));
 828                 }
 829             }
 830         }
 831         return nonCascadedCdmEntities;
 832     }
 833
 834     private Collection<ICdmBase> getFieldUnitNonCascadedAssociatedElements(FieldUnit fieldUnit){
 835         //get non cascaded element on SpecimenOrObservationBase level
 836         Collection<ICdmBase> nonCascadedCdmEntities = getSpecimenOrObservationNonCascadedAssociatedElements(fieldUnit);
 837
 838         //get FieldUnit specific elements
 839         GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
 840         if(gatheringEvent!=null){
 841             //country
 842             if(gatheringEvent.getCountry()!=null){
 843                 nonCascadedCdmEntities.add(gatheringEvent.getCountry());
 844             }
 845             //collecting areas
 846             for (NamedArea namedArea : gatheringEvent.getCollectingAreas()) {
 847                 nonCascadedCdmEntities.add(namedArea);
 848             }
 849         }
 850         for (DerivationEvent derivationEvent : fieldUnit.getDerivationEvents()) {
 851             for (DerivedUnit derivedUnit : derivationEvent.getDerivatives()) {
 852                 nonCascadedCdmEntities.addAll(getDerivedUnitNonCascadedAssociatedElements(derivedUnit));
 853             }
 854         }
 855         return nonCascadedCdmEntities;
 856     }
 857
 858     private Collection<ICdmBase> getDerivedUnitNonCascadedAssociatedElements(DerivedUnit derivedUnit){
 859         //get non cascaded element on SpecimenOrObservationBase level
 860         Collection<ICdmBase> nonCascadedCdmEntities = getSpecimenOrObservationNonCascadedAssociatedElements(derivedUnit);
 861
 862         //get DerivedUnit specific elements
 863         if(derivedUnit.getCollection()!=null && derivedUnit.getCollection().getInstitute()!=null){
 864             for (DefinedTerm type : derivedUnit.getCollection().getInstitute().getTypes()) {
 865                 nonCascadedCdmEntities.add(type);
 866             }
 867         }
 868         if(derivedUnit.getPreservation()!=null && derivedUnit.getPreservation().getMedium()!=null){
 869             nonCascadedCdmEntities.add(derivedUnit.getPreservation().getMedium());
 870         }
 871         if(derivedUnit.getStoredUnder()!=null){
 872             nonCascadedCdmEntities.add(derivedUnit.getStoredUnder());
 873         }
 874         return nonCascadedCdmEntities;
 875     }
 876
 877     /**
 878      * @param specimen
 879      * @return
 880      */
 881     private Collection<ICdmBase> getSpecimenOrObservationNonCascadedAssociatedElements(
 882             SpecimenOrObservationBase<?> specimen) {
 883         Collection<ICdmBase> nonCascadedCdmEntities = new HashSet<ICdmBase>();
 884         //scan SpecimenOrObservationBase
 885         for(DeterminationEvent determinationEvent:specimen.getDeterminations()){
 886             //modifier
 887             if(determinationEvent.getModifier()!=null){
 888                 nonCascadedCdmEntities.add(determinationEvent.getModifier());
 889             }
 890         }
 891         //kindOfUnit
 892         if(specimen.getKindOfUnit()!=null){
 893             nonCascadedCdmEntities.add(specimen.getKindOfUnit());
 894         }
 895         //lifeStage
 896         if(specimen.getLifeStage()!=null){
 897             nonCascadedCdmEntities.add(specimen.getLifeStage());
 898         }
 899         //sex
 900         if(specimen.getSex()!=null){
 901             nonCascadedCdmEntities.add(specimen.getSex());
 902         }
 903         return nonCascadedCdmEntities;
 904     }
 905
 906     /* (non-Javadoc)
 907      * @see eu.etaxonomy.cdm.api.service.VersionableServiceBase#isDeletable(eu.etaxonomy.cdm.model.common.VersionableEntity, eu.etaxonomy.cdm.api.service.config.DeleteConfiguratorBase)
 908      */
 909     @Override
 910     public DeleteResult isDeletable(SpecimenOrObservationBase specimen, DeleteConfiguratorBase config) {
 911         DeleteResult deleteResult = new DeleteResult();
 912         SpecimenDeleteConfigurator specimenDeleteConfigurator = (SpecimenDeleteConfigurator)config;
 913
 914         //check elements found by super method
 915         Set<CdmBase> relatedObjects = super.isDeletable(specimen, config).getRelatedObjects();
 916         for (CdmBase cdmBase : relatedObjects) {
 917             //check for type designation
 918             if(cdmBase.isInstanceOf(SpecimenTypeDesignation.class) && !specimenDeleteConfigurator.isDeleteFromTypeDesignation()){
 919                 deleteResult.setAbort();
 920                 deleteResult.addException(new ReferencedObjectUndeletableException("Specimen is a type specimen."));
 921                 deleteResult.addRelatedObject(cdmBase);
 922                 break;
 923             }
 924             //check for IndividualsAssociations
 925             else if(cdmBase.isInstanceOf(IndividualsAssociation.class) && !specimenDeleteConfigurator.isDeleteFromIndividualsAssociation()){
 926                 deleteResult.setAbort();
 927                 deleteResult.addException(new ReferencedObjectUndeletableException("Specimen is still associated via IndividualsAssociations"));
 928                 deleteResult.addRelatedObject(cdmBase);
 929                 break;
 930             }
 931             //check for specimen/taxon description
 932             else if((cdmBase.isInstanceOf(SpecimenDescription.class) || cdmBase.isInstanceOf(TaxonDescription.class))
 933                     && !specimenDeleteConfigurator.isDeleteFromDescription()){
 934                 deleteResult.setAbort();
 935                 deleteResult.addException(new ReferencedObjectUndeletableException("Specimen is still used in a Description."));
 936                 deleteResult.addRelatedObject(cdmBase);
 937                 break;
 938             }
 939             //check for children and parents (derivation events)
 940             else if(cdmBase.isInstanceOf(DerivationEvent.class)){
 941                 DerivationEvent derivationEvent = HibernateProxyHelper.deproxy(cdmBase, DerivationEvent.class);
 942                 //check if derivation event is empty
 943                 if(!derivationEvent.getDerivatives().isEmpty()){
 944                     if(derivationEvent.getDerivatives().size()==1 && derivationEvent.getDerivatives().contains(specimen)){
 945                         //if it is the parent event with only one derivate then the specimen is still deletable
 946                         continue;
 947                     }
 948                     else if(!specimenDeleteConfigurator.isDeleteChildren()){
 949                         //if not and children should not be deleted then it is undeletable
 950                         deleteResult.setAbort();
 951                         deleteResult.addException(new ReferencedObjectUndeletableException("Derivate still has child derivates."));
 952                         deleteResult.addRelatedObject(cdmBase);
 953                         break;
 954                     }
 955                     else{
 956                         //check all children if they can be deleted
 957                         Set<DerivedUnit> derivatives = derivationEvent.getDerivatives();
 958                         DeleteResult childResult = new DeleteResult();
 959                         for (DerivedUnit derivedUnit : derivatives) {
 960                             childResult.includeResult(isDeletable(derivedUnit, specimenDeleteConfigurator));
 961                         }
 962                         if(!childResult.isOk()){
 963                             deleteResult.setAbort();
 964                             deleteResult.includeResult(childResult);
 965                             deleteResult.addRelatedObject(cdmBase);
 966                             break;
 967                         }
 968                     }
 969                 }
 970             }
 971             //check for amplification
 972             else if(cdmBase.isInstanceOf(AmplificationResult.class) && !specimenDeleteConfigurator.isDeleteMolecularData()){
 973                 deleteResult.setAbort();
 974                 deleteResult.addException(new ReferencedObjectUndeletableException("DnaSample is used in amplification results."));
 975                 deleteResult.addRelatedObject(cdmBase);
 976                 break;
 977             }
 978             //check for sequence
 979             else if(cdmBase.isInstanceOf(Sequence.class) && !specimenDeleteConfigurator.isDeleteMolecularData()){
 980                 deleteResult.setAbort();
 981                 deleteResult.addException(new ReferencedObjectUndeletableException("DnaSample is used in sequences."));
 982                 deleteResult.addRelatedObject(cdmBase);
 983                 break;
 984             }
 985         }
 986         if(deleteResult.isOk()){
 987             //add all related object if deletion is OK so they can be handled by the delete() method
 988             deleteResult.addRelatedObjects(relatedObjects);
 989         }
 990         return deleteResult;
 991     }
 992
 993     /* (non-Javadoc)
 994      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#delete(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase, eu.etaxonomy.cdm.api.service.config.SpecimenDeleteConfigurator)
 995      */
 996     @Override
 997     public DeleteResult delete(SpecimenOrObservationBase<?> specimen, SpecimenDeleteConfigurator config) {
 998         specimen = HibernateProxyHelper.deproxy(specimen, SpecimenOrObservationBase.class);
 999
1000         if(config.isDeleteChildren()){
1001             Set<DerivationEvent> derivationEvents = specimen.getDerivationEvents();
1002             for (DerivationEvent derivationEvent : derivationEvents) {
1003                 Set<DerivedUnit> derivatives = derivationEvent.getDerivatives();
1004                 for (DerivedUnit derivedUnit : derivatives) {
1005                     delete(derivedUnit, config);
1006                 }
1007             }
1008         }
1009
1010         DeleteResult deleteResult = isDeletable(specimen, config);
1011         if(!deleteResult.isOk()){
1012             return deleteResult;
1013         }
1014
1015         //check related objects
1016         Set<CdmBase> relatedObjects = deleteResult.getRelatedObjects();
1017
1018         for (CdmBase relatedObject : relatedObjects) {
1019             //check for TypeDesignations
1020             if(relatedObject.isInstanceOf(SpecimenTypeDesignation.class)){
1021                 SpecimenTypeDesignation designation = HibernateProxyHelper.deproxy(relatedObject, SpecimenTypeDesignation.class);
1022                 designation.setTypeSpecimen(null);
1023                 Set<TaxonNameBase> typifiedNames = designation.getTypifiedNames();
1024                 for (TaxonNameBase taxonNameBase : typifiedNames) {
1025                     taxonNameBase.removeTypeDesignation(designation);
1026                 }
1027             }
1028             //delete IndividualsAssociation
1029             if(relatedObject.isInstanceOf(IndividualsAssociation.class)){
1030                 IndividualsAssociation assciation = HibernateProxyHelper.deproxy(relatedObject, IndividualsAssociation.class);
1031                 assciation.setAssociatedSpecimenOrObservation(null);
1032                 assciation.getInDescription().removeElement(assciation);
1033             }
1034             //check for taxon description
1035             if(relatedObject.isInstanceOf(TaxonDescription.class)){
1036                 TaxonDescription taxonDescription = HibernateProxyHelper.deproxy(relatedObject, TaxonDescription.class);
1037                 taxonDescription.setDescribedSpecimenOrObservation(null);
1038             }
1039             //check for specimen description
1040             if(relatedObject.isInstanceOf(SpecimenDescription.class)){
1041                 SpecimenDescription specimenDescription = HibernateProxyHelper.deproxy(relatedObject, SpecimenDescription.class);
1042                 //check if specimen is "described" specimen
1043                 if(specimenDescription.getDescribedSpecimenOrObservation().equals(specimen)){
1044                     specimenDescription.setDescribedSpecimenOrObservation(null);
1045                 }
1046                 //check if description is a description of the given specimen
1047                 if(specimen.getDescriptions().contains(specimenDescription)){
1048                     specimen.removeDescription(specimenDescription);
1049                 }
1050             }
1051             //check for amplification
1052             if(relatedObject.isInstanceOf(AmplificationResult.class)){
1053                 AmplificationResult amplificationResult = HibernateProxyHelper.deproxy(relatedObject, AmplificationResult.class);
1054                 amplificationResult.getDnaSample().removeAmplificationResult(amplificationResult);
1055             }
1056             //check for sequence
1057             if(relatedObject.isInstanceOf(Sequence.class)){
1058                 Sequence sequence = HibernateProxyHelper.deproxy(relatedObject, Sequence.class);
1059                 sequence.getDnaSample().removeSequence(sequence);
1060             }
1061             //check for children and parents (derivation events)
1062             if(relatedObject.isInstanceOf(DerivationEvent.class)){
1063                 DerivationEvent derivationEvent = HibernateProxyHelper.deproxy(relatedObject, DerivationEvent.class);
1064                 //parent derivation event (derivedFrom)
1065                 if(derivationEvent.getDerivatives().contains(specimen) && specimen.isInstanceOf(DerivedUnit.class)){
1066                     derivationEvent.removeDerivative(HibernateProxyHelper.deproxy(specimen, DerivedUnit.class));
1067                     if(derivationEvent.getDerivatives().isEmpty()){
1068                         Set<SpecimenOrObservationBase> originals = derivationEvent.getOriginals();
1069                         for (SpecimenOrObservationBase specimenOrObservationBase : originals) {
1070                             specimenOrObservationBase.removeDerivationEvent(derivationEvent);
1071                         }
1072                     }
1073                 }
1074                 else{
1075                     //child derivation events should not occur since we delete the hierarchy from bottom to top
1076                 }
1077             }
1078         }
1079
1080         deleteResult.includeResult(delete(specimen));
1081         return deleteResult;
1082     }
1083
1084     /* (non-Javadoc)
1085      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#deleteDerivateHierarchy(eu.etaxonomy.cdm.model.common.ICdmBase)
1086      */
1087     @Override
1088     public DeleteResult deleteDerivateHierarchy(CdmBase from, SpecimenDeleteConfigurator config) {
1089         DeleteResult deleteResult = new DeleteResult();
1090         if(from.isInstanceOf(Sequence.class)){
1091             if(!config.isDeleteMolecularData()){
1092                 deleteResult.setAbort();
1093                 deleteResult.addException(new ReferencedObjectUndeletableException("deleting molecur data is not allowed in config"));
1094                 return deleteResult;
1095             }
1096             Sequence sequence = HibernateProxyHelper.deproxy(from, Sequence.class);
1097             sequence.getDnaSample().removeSequence(sequence);
1098             deleteResult = sequenceService.delete(sequence);
1099         }
1100         else if(from.isInstanceOf(SingleRead.class))  {
1101             if(!config.isDeleteMolecularData()){
1102                 deleteResult.setAbort();
1103                 deleteResult.addException(new ReferencedObjectUndeletableException("deleting molecur data is not allowed in config"));
1104                 return deleteResult;
1105             }
1106             SingleRead singleRead = HibernateProxyHelper.deproxy(from, SingleRead.class);
1107             singleRead.getAmplificationResult().removeSingleRead(singleRead);
1108             deleteResult.setStatus(DeleteStatus.OK);
1109         }
1110         else if(from.isInstanceOf(SpecimenOrObservationBase.class))  {
1111             deleteResult = delete(HibernateProxyHelper.deproxy(from, SpecimenOrObservationBase.class), config);
1112         }
1113         return deleteResult;
1114     }
1115
1116 //    private DeleteResult deepDelete(SpecimenOrObservationBase<?> entity, SpecimenDeleteConfigurator config){
1117 //        Set<DerivationEvent> derivationEvents = entity.getDerivationEvents();
1118 //        for (DerivationEvent derivationEvent : derivationEvents) {
1119 //            Set<DerivedUnit> derivatives = derivationEvent.getDerivatives();
1120 //            for (DerivedUnit derivedUnit : derivatives) {
1121 //                DeleteResult deleteResult = deepDelete(derivedUnit, config);
1122 //                if(!deleteResult.isOk()){
1123 //                    return deleteResult;
1124 //                }
1125 //            }
1126 //        }
1127 //        return delete(entity, config);
1128 //    }
1129
1130     /* (non-Javadoc)
1131      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#listAssociatedTaxa(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase)
1132      */
1133     @Override
1134     public Collection<IndividualsAssociation> listIndividualsAssociations(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
1135         return dao.listIndividualsAssociations(specimen, null, null, null, null);
1136     }
1137
1138     /* (non-Javadoc)
1139      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#listTypeDesignations(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
1140      */
1141     @Override
1142     public Collection<SpecimenTypeDesignation> listTypeDesignations(SpecimenOrObservationBase<?> specimen,
1143             Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
1144         return dao.listTypeDesignations(specimen, limit, start, orderHints, propertyPaths);
1145     }
1146
1147     /* (non-Javadoc)
1148      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#listDescriptionsWithDescriptionSpecimen(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
1149      */
1150     @Override
1151     public Collection<DescriptionBase<?>> listDescriptionsWithDescriptionSpecimen(
1152             SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints,
1153             List<String> propertyPaths) {
1154         return dao.listDescriptionsWithDescriptionSpecimen(specimen, limit, start, orderHints, propertyPaths);
1155     }
1156
1157 }