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.ICdmGenericDao;
 100 import eu.etaxonomy.cdm.persistence.dao.common.IDefinedTermDao;
 101 import eu.etaxonomy.cdm.persistence.dao.initializer.AbstractBeanInitializer;
 102 import eu.etaxonomy.cdm.persistence.dao.occurrence.IOccurrenceDao;
 103 import eu.etaxonomy.cdm.persistence.query.OrderHint;
 104 import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
 105
 106 /**
 107  * @author a.babadshanjan
 108  * @created 01.09.2008
 109  */
 110 @Service
 111 @Transactional(readOnly = true)
 112 public class OccurrenceServiceImpl extends IdentifiableServiceBase<SpecimenOrObservationBase,IOccurrenceDao> implements IOccurrenceService {
 113
 114     static private final Logger logger = Logger.getLogger(OccurrenceServiceImpl.class);
 115
 116     @Autowired
 117     private IDefinedTermDao definedTermDao;
 118
 119     @Autowired
 120     private IDescriptionService descriptionService;
 121
 122     @Autowired
 123     private ITaxonService taxonService;
 124
 125     @Autowired
 126     private ITermService termService;
 127
 128     @Autowired
 129     private INameService nameService;
 130
 131     @Autowired
 132     private ISequenceService sequenceService;
 133
 134     @Autowired
 135     private AbstractBeanInitializer beanInitializer;
 136
 137     @Autowired
 138     private ILuceneIndexToolProvider luceneIndexToolProvider;
 139
 140     @Autowired
 141     private ICdmGenericDao genericDao;
 142
 143
 144     public OccurrenceServiceImpl() {
 145         logger.debug("Load OccurrenceService Bean");
 146     }
 147
 148
 149     /* (non-Javadoc)
 150      * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#updateTitleCache(java.lang.Integer, eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy)
 151      */
 152     @Override
 153     @Transactional(readOnly = false)
 154     public void updateTitleCache(Class<? extends SpecimenOrObservationBase> clazz, Integer stepSize, IIdentifiableEntityCacheStrategy<SpecimenOrObservationBase> cacheStrategy, IProgressMonitor monitor) {
 155         if (clazz == null){
 156             clazz = SpecimenOrObservationBase.class;
 157         }
 158         super.updateTitleCacheImpl(clazz, stepSize, cacheStrategy, monitor);
 159     }
 160
 161
 162     /**
 163      * FIXME Candidate for harmonization
 164      * move to termService
 165      */
 166     @Override
 167     public Country getCountryByIso(String iso639) {
 168         return this.definedTermDao.getCountryByIso(iso639);
 169
 170     }
 171
 172     /**
 173      * FIXME Candidate for harmonization
 174      * move to termService
 175      */
 176     @Override
 177     public List<Country> getCountryByName(String name) {
 178         List<? extends DefinedTermBase> terms = this.definedTermDao.findByTitle(Country.class, name, null, null, null, null, null, null) ;
 179         List<Country> countries = new ArrayList<Country>();
 180         for (int i=0;i<terms.size();i++){
 181             countries.add((Country)terms.get(i));
 182         }
 183         return countries;
 184     }
 185
 186     @Override
 187     @Autowired
 188     protected void setDao(IOccurrenceDao dao) {
 189         this.dao = dao;
 190     }
 191
 192     @Override
 193     public Pager<DerivationEvent> getDerivationEvents(SpecimenOrObservationBase occurence, Integer pageSize,Integer pageNumber, List<String> propertyPaths) {
 194         Integer numberOfResults = dao.countDerivationEvents(occurence);
 195
 196         List<DerivationEvent> results = new ArrayList<DerivationEvent>();
 197         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 198             results = dao.getDerivationEvents(occurence, pageSize, pageNumber,propertyPaths);
 199         }
 200
 201         return new DefaultPagerImpl<DerivationEvent>(pageNumber, numberOfResults, pageSize, results);
 202     }
 203
 204     /* (non-Javadoc)
 205      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#countDeterminations(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase, eu.etaxonomy.cdm.model.taxon.TaxonBase)
 206      */
 207     @Override
 208     public int countDeterminations(SpecimenOrObservationBase occurence, TaxonBase taxonbase) {
 209         return dao.countDeterminations(occurence, taxonbase);
 210     }
 211
 212     @Override
 213     public Pager<DeterminationEvent> getDeterminations(SpecimenOrObservationBase occurrence, TaxonBase taxonBase, Integer pageSize,Integer pageNumber, List<String> propertyPaths) {
 214         Integer numberOfResults = dao.countDeterminations(occurrence, taxonBase);
 215
 216         List<DeterminationEvent> results = new ArrayList<DeterminationEvent>();
 217         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 218             results = dao.getDeterminations(occurrence,taxonBase, pageSize, pageNumber, propertyPaths);
 219         }
 220
 221         return new DefaultPagerImpl<DeterminationEvent>(pageNumber, numberOfResults, pageSize, results);
 222     }
 223
 224     @Override
 225     public Pager<Media> getMedia(SpecimenOrObservationBase occurence,Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
 226         Integer numberOfResults = dao.countMedia(occurence);
 227
 228         List<Media> results = new ArrayList<Media>();
 229         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 230             results = dao.getMedia(occurence, pageSize, pageNumber, propertyPaths);
 231         }
 232
 233         return new DefaultPagerImpl<Media>(pageNumber, numberOfResults, pageSize, results);
 234     }
 235
 236     /* (non-Javadoc)
 237      * @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)
 238      */
 239     @Override
 240     public Pager<SpecimenOrObservationBase> list(Class<? extends SpecimenOrObservationBase> type, TaxonBase determinedAs, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 241         Integer numberOfResults = dao.count(type,determinedAs);
 242         List<SpecimenOrObservationBase> results = new ArrayList<SpecimenOrObservationBase>();
 243         pageNumber = pageNumber == null ? 0 : pageNumber;
 244         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 245             Integer start = pageSize == null ? 0 : pageSize * pageNumber;
 246             results = dao.list(type,determinedAs, pageSize, start, orderHints,propertyPaths);
 247         }
 248         return new DefaultPagerImpl<SpecimenOrObservationBase>(pageNumber, numberOfResults, pageSize, results);
 249     }
 250
 251     @Override
 252     public List<UuidAndTitleCache<DerivedUnit>> getDerivedUnitUuidAndTitleCache() {
 253         return dao.getDerivedUnitUuidAndTitleCache();
 254     }
 255
 256     @Override
 257     public List<UuidAndTitleCache<FieldUnit>> getFieldUnitUuidAndTitleCache() {
 258         return dao.getFieldUnitUuidAndTitleCache();
 259     }
 260
 261     /* (non-Javadoc)
 262      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getDerivedUnitFacade(eu.etaxonomy.cdm.model.occurrence.DerivedUnit)
 263      */
 264     @Override
 265     public DerivedUnitFacade getDerivedUnitFacade(DerivedUnit derivedUnit, List<String> propertyPaths) throws DerivedUnitFacadeNotSupportedException {
 266         derivedUnit = (DerivedUnit)dao.load(derivedUnit.getUuid(), null);
 267         DerivedUnitFacadeConfigurator config = DerivedUnitFacadeConfigurator.NewInstance();
 268         config.setThrowExceptionForNonSpecimenPreservationMethodRequest(false);
 269         DerivedUnitFacade derivedUnitFacade = DerivedUnitFacade.NewInstance(derivedUnit, config);
 270         beanInitializer.initialize(derivedUnitFacade, propertyPaths);
 271         return derivedUnitFacade;
 272     }
 273
 274     /* (non-Javadoc)
 275      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#listDerivedUnitFacades(eu.etaxonomy.cdm.model.description.DescriptionBase, java.util.List)
 276      */
 277     @Override
 278     public List<DerivedUnitFacade> listDerivedUnitFacades(
 279             DescriptionBase description, List<String> propertyPaths) {
 280
 281         List<DerivedUnitFacade> derivedUnitFacadeList = new ArrayList<DerivedUnitFacade>();
 282         IndividualsAssociation tempIndividualsAssociation;
 283         SpecimenOrObservationBase tempSpecimenOrObservationBase;
 284         List<DescriptionElementBase> elements = descriptionService.listDescriptionElements(description, null, IndividualsAssociation.class, null, 0, Arrays.asList(new String []{"associatedSpecimenOrObservation"}));
 285         for(DescriptionElementBase element : elements){
 286             if(element.isInstanceOf(IndividualsAssociation.class)){
 287                 tempIndividualsAssociation = HibernateProxyHelper.deproxy(element, IndividualsAssociation.class);
 288                 if(tempIndividualsAssociation.getAssociatedSpecimenOrObservation() != null){
 289                     tempSpecimenOrObservationBase = HibernateProxyHelper.deproxy(tempIndividualsAssociation.getAssociatedSpecimenOrObservation(), SpecimenOrObservationBase.class);
 290                     if(tempSpecimenOrObservationBase.isInstanceOf(DerivedUnit.class)){
 291                         try {
 292                             derivedUnitFacadeList.add(DerivedUnitFacade.NewInstance(HibernateProxyHelper.deproxy(tempSpecimenOrObservationBase, DerivedUnit.class)));
 293                         } catch (DerivedUnitFacadeNotSupportedException e) {
 294                             logger.warn(tempIndividualsAssociation.getAssociatedSpecimenOrObservation().getTitleCache() + " : " +e.getMessage());
 295                         }
 296                     }
 297                 }
 298
 299             }
 300         }
 301
 302         beanInitializer.initializeAll(derivedUnitFacadeList, propertyPaths);
 303
 304         return derivedUnitFacadeList;
 305     }
 306
 307
 308     /* (non-Javadoc)
 309      * @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)
 310      */
 311     @Override
 312     public <T extends SpecimenOrObservationBase> List<T> listByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
 313             Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 314
 315         return pageByAssociatedTaxon(type, includeRelationships, associatedTaxon, maxDepth, pageSize, pageNumber, orderHints, propertyPaths).getRecords();
 316     }
 317
 318     /* (non-Javadoc)
 319      * @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)
 320      */
 321     @Override
 322     public Collection<FieldUnit> listFieldUnitsByAssociatedTaxon(Set<TaxonRelationshipEdge> includeRelationships,
 323             Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 324
 325         if(!getSession().contains(associatedTaxon)){
 326             associatedTaxon = (Taxon) taxonService.load(associatedTaxon.getUuid());
 327         }
 328
 329         Set<FieldUnit> fieldUnits = new HashSet<FieldUnit>();
 330
 331         List<SpecimenOrObservationBase> records = pageByAssociatedTaxon(null, includeRelationships, associatedTaxon, maxDepth, pageSize, pageNumber, orderHints, propertyPaths).getRecords();
 332         for(SpecimenOrObservationBase<?> specimen:records){
 333             fieldUnits.addAll(getFieldUnits(specimen.getUuid()));
 334         }
 335         return fieldUnits;
 336     }
 337
 338     @Override
 339     public DerivateHierarchyDTO assembleDerivateHierarchyDTO(FieldUnit fieldUnit, UUID associatedTaxonUuid){
 340
 341         if(!getSession().contains(fieldUnit)){
 342             fieldUnit = (FieldUnit) load(fieldUnit.getUuid());
 343         }
 344         TaxonBase associatedTaxon = taxonService.load(associatedTaxonUuid);
 345
 346         DerivateHierarchyDTO dto = new DerivateHierarchyDTO();
 347         Map<UUID, TypeDesignationStatusBase> typeSpecimenUUIDtoTypeDesignationStatus = new HashMap<UUID, TypeDesignationStatusBase>();
 348
 349         //gather types for this taxon name
 350         TaxonNameBase<?,?> name = associatedTaxon.getName();
 351         Set<?> typeDesignations = name.getSpecimenTypeDesignations();
 352         for (Object object : typeDesignations) {
 353             if(object instanceof CdmBase && ((CdmBase)object).isInstanceOf(SpecimenTypeDesignation.class)){
 354                 SpecimenTypeDesignation specimenTypeDesignation = HibernateProxyHelper.deproxy(object, SpecimenTypeDesignation.class);
 355                 DerivedUnit typeSpecimen = specimenTypeDesignation.getTypeSpecimen();
 356                 final TypeDesignationStatusBase typeStatus = specimenTypeDesignation.getTypeStatus();
 357                 typeSpecimenUUIDtoTypeDesignationStatus.put(typeSpecimen.getUuid(), typeStatus);
 358             }
 359         }
 360
 361         if(fieldUnit.getGatheringEvent()!=null){
 362             GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
 363             //Country
 364             final NamedArea country = gatheringEvent.getCountry();
 365             dto.setCountry(country!=null?country.getDescription():"");
 366             //Collection
 367             final AgentBase collector = gatheringEvent.getCollector();
 368             final String fieldNumber = fieldUnit.getFieldNumber();
 369             dto.setCollection(((collector!=null?collector:"") + " " + (fieldNumber!=null?fieldNumber:"")).trim());
 370             //Date
 371             final Partial gatheringDate = gatheringEvent.getGatheringDate();
 372             dto.setDate(gatheringDate!=null?gatheringDate.toString():"");
 373         }
 374
 375         //Taxon Name
 376         dto.setTaxonName(associatedTaxon.getName().getFullTitleCache());
 377
 378
 379         Collection<DerivedUnit> derivedUnits = new ArrayList<DerivedUnit>();
 380         getDerivedUnitsFor(fieldUnit, derivedUnits);
 381
 382         //Herbaria map
 383         Map<eu.etaxonomy.cdm.model.occurrence.Collection, Integer> collectionToCountMap = new HashMap<eu.etaxonomy.cdm.model.occurrence.Collection, Integer>();
 384         //List of accession numbers for citation
 385         List<String> preservedSpecimenAccessionNumbers = new ArrayList<String>();
 386
 387         //iterate over sub derivates
 388         for (DerivedUnit derivedUnit : derivedUnits) {
 389             //current accession number
 390             String currentAccessionNumber = derivedUnit.getAccessionNumber()!=null?derivedUnit.getAccessionNumber():"";
 391             //current herbarium
 392             String currentHerbarium = "";
 393             eu.etaxonomy.cdm.model.occurrence.Collection collection = derivedUnit.getCollection();
 394             if(collection!=null){
 395                 currentHerbarium = collection.getCode()!=null?collection.getCode():"";
 396                 //count herbaria
 397                 Integer count = collectionToCountMap.get(collection);
 398                 if(count==null){
 399                     count = 1;
 400                 }
 401                 else{
 402                     count++;
 403                 }
 404                 collectionToCountMap.put(collection, count);
 405             }
 406             //check if derived unit is a type
 407             if(typeSpecimenUUIDtoTypeDesignationStatus.keySet().contains(derivedUnit.getUuid())){
 408                 dto.setHasType(true);
 409                 TypeDesignationStatusBase typeDesignationStatus = typeSpecimenUUIDtoTypeDesignationStatus.get(derivedUnit.getUuid());
 410                 String typeStatus = typeDesignationStatus.getLabel();
 411                 dto.addTypes(typeStatus, currentAccessionNumber);
 412             }
 413             //assemble molecular data
 414             //pattern: DNAMarker [contig1, primer1_1, primer1_2, ...][contig2, primer2_1, ...]...
 415             if(derivedUnit.isInstanceOf(DnaSample.class)){
 416                 if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.TissueSample){
 417                     //TODO implement TissueSample assembly for web service
 418                 }
 419                 if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.DnaSample){
 420
 421                     DnaSample dna = HibernateProxyHelper.deproxy(derivedUnit, DnaSample.class);
 422                     if(!dna.getSequences().isEmpty()){
 423                         dto.setHasDna(true);
 424                     }
 425                     for(Sequence sequence:dna.getSequences()){
 426                         URI boldUri = null;
 427                         try {
 428                             boldUri = sequence.getBoldUri();
 429                         } catch (URISyntaxException e1) {
 430                             logger.error("Could not create BOLD URI", e1);
 431                         }
 432                         final DefinedTerm dnaMarker = sequence.getDnaMarker();
 433                         MolecularData molecularData = dto.addProviderLink(boldUri!=null?boldUri:null,dnaMarker!=null?dnaMarker.getLabel():"[no marker]");
 434
 435                         //contig file FIXME show primer although contig not present?
 436                         if(sequence.getContigFile()!=null){
 437                             MediaRepresentationPart contigMediaRepresentationPart = MediaUtils.getFirstMediaRepresentationPart(sequence.getContigFile());
 438                             if(contigMediaRepresentationPart!=null){
 439                                 ContigFile contigFile = molecularData.addContigFile(contigMediaRepresentationPart.getUri(), "contig");
 440                                 //primer files
 441                                 if(sequence.getSingleReads()!=null){
 442                                     for (SingleRead singleRead : sequence.getSingleReads()) {
 443                                         MediaRepresentationPart pherogramMediaRepresentationPart = MediaUtils.getFirstMediaRepresentationPart(singleRead.getPherogram());
 444                                         if(pherogramMediaRepresentationPart!=null){
 445                                             contigFile.addPrimerLink(pherogramMediaRepresentationPart.getUri(), "primer");
 446                                         }
 447                                     }
 448                                 }
 449                             }
 450                         }
 451                     }
 452                 }
 453             }
 454             //assemble media data
 455             else if(derivedUnit.isInstanceOf(MediaSpecimen.class)){
 456
 457                 MediaSpecimen media = HibernateProxyHelper.deproxy(derivedUnit, MediaSpecimen.class);
 458                 String mediaUriString = getMediaUriString(media);
 459                 if(media.getKindOfUnit()!=null){
 460                     //specimen scan
 461                     if(media.getKindOfUnit().getUuid().equals(UUID.fromString("acda15be-c0e2-4ea8-8783-b9b0c4ad7f03"))){
 462                         dto.setHasSpecimenScan(true);
 463                             final String imageLinkText = currentHerbarium+" "+currentAccessionNumber;
 464                             dto.addSpecimenScan(mediaUriString==null?"":mediaUriString, !imageLinkText.equals(" ")?imageLinkText:"[no accession]");
 465                     }
 466                     //detail image
 467                     else if(media.getKindOfUnit().getUuid().equals(UUID.fromString("31eb8d02-bf5d-437c-bcc6-87a626445f34"))){
 468                         dto.setHasDetailImage(true);
 469                         String motif = "";
 470                         if(media.getMediaSpecimen()!=null && media.getMediaSpecimen().getTitle()!=null){
 471                             motif = media.getMediaSpecimen().getTitle().getText();
 472                         }
 473                         dto.addDetailImage(mediaUriString==null?"":mediaUriString, motif!=null?motif:"[no motif]");
 474                     }
 475                 }
 476             }
 477             //assemble preserved specimen data
 478             else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.PreservedSpecimen){
 479                 if(!currentAccessionNumber.isEmpty()){
 480                     preservedSpecimenAccessionNumbers.add(currentAccessionNumber);
 481                 }
 482             }
 483         }
 484
 485         final String separator = ", ";
 486         //assemble citation
 487         String citation = "";
 488         citation += !dto.getCountry().isEmpty()?dto.getCountry()+separator:"";
 489         if(fieldUnit.getGatheringEvent()!=null){
 490             if(fieldUnit.getGatheringEvent().getLocality()!=null){
 491                 citation += fieldUnit.getGatheringEvent().getLocality().getText();
 492                 citation += separator;
 493             }
 494             if(fieldUnit.getGatheringEvent().getExactLocation()!=null
 495                     && fieldUnit.getGatheringEvent().getExactLocation().getLatitude()!=null
 496                     && fieldUnit.getGatheringEvent().getExactLocation().getLongitude()!=null){
 497                 citation += fieldUnit.getGatheringEvent().getExactLocation().getLatitude().toString();
 498                 citation += separator;
 499                 citation += fieldUnit.getGatheringEvent().getExactLocation().getLongitude().toString();
 500                 citation += separator;
 501             }
 502         }
 503         citation += !dto.getCollection().isEmpty()?dto.getCollection():"";
 504         if(!preservedSpecimenAccessionNumbers.isEmpty()){
 505             citation += " (";
 506             for(String accessionNumber:preservedSpecimenAccessionNumbers){
 507                 if(!accessionNumber.isEmpty()){
 508                     citation += accessionNumber+separator;
 509                 }
 510             }
 511             citation = removeTail(citation, separator);
 512             citation += ")";
 513         }
 514         citation = removeTail(citation, separator);
 515         dto.setCitation(citation);
 516
 517         //assemble herbaria string
 518         String herbariaString = "";
 519         for(Entry<eu.etaxonomy.cdm.model.occurrence.Collection, Integer> e:collectionToCountMap.entrySet()){
 520             eu.etaxonomy.cdm.model.occurrence.Collection collection = e.getKey();
 521             if(collection.getCode()!=null){
 522                 herbariaString += collection.getCode();
 523             }
 524             if(e.getValue()>1){
 525                 herbariaString += "("+e.getValue()+")";
 526             }
 527             herbariaString += separator;
 528         }
 529         herbariaString = removeTail(herbariaString, separator);
 530         dto.setHerbarium(herbariaString);
 531
 532         return dto;
 533     }
 534
 535
 536     /**
 537      * @param string
 538      * @param tail
 539      * @return
 540      */
 541     private String removeTail(String string, final String tail) {
 542         if(string.endsWith(tail)){
 543             string = string.substring(0, string.length()-tail.length());
 544         }
 545         return string;
 546     }
 547
 548     private String getMediaUriString(MediaSpecimen mediaSpecimen){
 549         String mediaUri = null;
 550         Collection<MediaRepresentation> mediaRepresentations = mediaSpecimen.getMediaSpecimen().getRepresentations();
 551         if(mediaRepresentations!=null && !mediaRepresentations.isEmpty()){
 552             Collection<MediaRepresentationPart> mediaRepresentationParts = mediaRepresentations.iterator().next().getParts();
 553             if(mediaRepresentationParts!=null && !mediaRepresentationParts.isEmpty()){
 554                 MediaRepresentationPart part = mediaRepresentationParts.iterator().next();
 555                 if(part.getUri()!=null){
 556                     mediaUri = part.getUri().toASCIIString();
 557                 }
 558             }
 559         }
 560         return mediaUri;
 561     }
 562
 563     private void getDerivedUnitsFor(SpecimenOrObservationBase<?> specimen, Collection<DerivedUnit> derivedUnits){
 564         for(DerivationEvent derivationEvent:specimen.getDerivationEvents()){
 565             for(DerivedUnit derivative:derivationEvent.getDerivatives()){
 566                 derivedUnits.add(derivative);
 567                 getDerivedUnitsFor(derivative, derivedUnits);
 568             }
 569         }
 570     }
 571
 572
 573     /* (non-Javadoc)
 574      * @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)
 575      */
 576     @SuppressWarnings("unchecked")
 577     @Override
 578     public <T extends SpecimenOrObservationBase> Pager<T> pageByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
 579             Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 580
 581         Set<Taxon> taxa = new HashSet<Taxon>();
 582         Set<Integer> occurrenceIds = new HashSet<Integer>();
 583         List<T> occurrences = new ArrayList<T>();
 584
 585 //        Integer limit = PagerUtils.limitFor(pageSize);
 586 //        Integer start = PagerUtils.startFor(pageSize, pageNumber);
 587
 588         if(!getSession().contains(associatedTaxon)){
 589             associatedTaxon = (Taxon) taxonService.load(associatedTaxon.getUuid());
 590         }
 591
 592         if(includeRelationships != null) {
 593             taxa = taxonService.listRelatedTaxa(associatedTaxon, includeRelationships, maxDepth, null, null, propertyPaths);
 594         }
 595
 596         taxa.add(associatedTaxon);
 597
 598         for (Taxon taxon : taxa) {
 599             List<T> perTaxonOccurrences = dao.listByAssociatedTaxon(type, taxon, null, null, orderHints, propertyPaths);
 600             for (SpecimenOrObservationBase o : perTaxonOccurrences) {
 601                 occurrenceIds.add(o.getId());
 602             }
 603         }
 604         occurrences = (List<T>) dao.listByIds(occurrenceIds, pageSize, pageNumber, orderHints, propertyPaths);
 605
 606         return new DefaultPagerImpl<T>(pageNumber, occurrenceIds.size(), pageSize, occurrences);
 607
 608     }
 609
 610
 611     @Override
 612     public <T extends SpecimenOrObservationBase> Pager<T> pageByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
 613             String taxonUUID, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 614
 615         UUID uuid = UUID.fromString(taxonUUID);
 616         Taxon tax = (Taxon) taxonService.load(uuid);
 617        //TODO REMOVE NULL STATEMENT
 618         type=null;
 619         return pageByAssociatedTaxon( type,includeRelationships,tax, maxDepth, pageSize, pageNumber, orderHints, propertyPaths );
 620
 621     }
 622
 623
 624     @Override
 625     public Pager<SearchResult<SpecimenOrObservationBase>> findByFullText(
 626             Class<? extends SpecimenOrObservationBase> clazz, String queryString, Rectangle boundingBox, List<Language> languages,
 627             boolean highlightFragments, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
 628             List<String> propertyPaths) throws CorruptIndexException, IOException, ParseException {
 629
 630         LuceneSearch luceneSearch = prepareByFullTextSearch(clazz, queryString, boundingBox, languages, highlightFragments);
 631
 632         // --- execute search
 633         TopGroupsWithMaxScore topDocsResultSet = luceneSearch.executeSearch(pageSize, pageNumber);
 634
 635         Map<CdmBaseType, String> idFieldMap = new HashMap<CdmBaseType, String>();
 636         idFieldMap.put(CdmBaseType.SPECIMEN_OR_OBSERVATIONBASE, "id");
 637
 638         // --- initialize taxa, highlight matches ....
 639         ISearchResultBuilder searchResultBuilder = new SearchResultBuilder(luceneSearch, luceneSearch.getQuery());
 640         @SuppressWarnings("rawtypes")
 641         List<SearchResult<SpecimenOrObservationBase>> searchResults = searchResultBuilder.createResultSet(
 642                 topDocsResultSet, luceneSearch.getHighlightFields(), dao, idFieldMap, propertyPaths);
 643
 644         int totalHits = topDocsResultSet != null ? topDocsResultSet.topGroups.totalGroupCount : 0;
 645
 646         return new DefaultPagerImpl<SearchResult<SpecimenOrObservationBase>>(pageNumber, totalHits, pageSize,
 647                 searchResults);
 648
 649     }
 650
 651
 652     /**
 653      * @param clazz
 654      * @param queryString
 655      * @param languages
 656      * @param highlightFragments
 657      * @return
 658      */
 659     private LuceneSearch prepareByFullTextSearch(Class<? extends SpecimenOrObservationBase> clazz, String queryString, Rectangle bbox,
 660             List<Language> languages, boolean highlightFragments) {
 661
 662         BooleanQuery finalQuery = new BooleanQuery();
 663         BooleanQuery textQuery = new BooleanQuery();
 664
 665         LuceneSearch luceneSearch = new LuceneSearch(luceneIndexToolProvider, FieldUnit.class);
 666         QueryFactory queryFactory = luceneIndexToolProvider.newQueryFactoryFor(FieldUnit.class);
 667
 668         // --- criteria
 669         luceneSearch.setCdmTypRestriction(clazz);
 670         if(queryString != null){
 671             textQuery.add(queryFactory.newTermQuery("titleCache", queryString), Occur.SHOULD);
 672             finalQuery.add(textQuery, Occur.MUST);
 673         }
 674
 675         // --- spacial query
 676         if(bbox != null){
 677             finalQuery.add(QueryFactory.buildSpatialQueryByRange(bbox, "gatheringEvent.exactLocation.point"), Occur.MUST);
 678         }
 679
 680         luceneSearch.setQuery(finalQuery);
 681
 682         // --- sorting
 683         SortField[] sortFields = new  SortField[]{SortField.FIELD_SCORE, new SortField("titleCache__sort", SortField.STRING, false)};
 684         luceneSearch.setSortFields(sortFields);
 685
 686         if(highlightFragments){
 687             luceneSearch.setHighlightFields(queryFactory.getTextFieldNamesAsArray());
 688         }
 689         return luceneSearch;
 690     }
 691
 692
 693     /* (non-Javadoc)
 694      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getFieldUnits(eu.etaxonomy.cdm.model.occurrence.DerivedUnit)
 695      */
 696     @Override
 697     public Collection<FieldUnit> getFieldUnits(UUID derivedUnitUuid) {
 698         //It will search recursively over all {@link DerivationEvent}s and get the "originals" ({@link SpecimenOrObservationBase})
 699         //from which this DerivedUnit was derived until all FieldUnits are found.
 700
 701         //FIXME: use HQL queries to increase performance
 702         SpecimenOrObservationBase<?> specimen = load(derivedUnitUuid);
 703 //        specimen = HibernateProxyHelper.deproxy(specimen, SpecimenOrObservationBase.class);
 704         Collection<FieldUnit> fieldUnits = new ArrayList<FieldUnit>();
 705
 706         if(specimen.isInstanceOf(FieldUnit.class)){
 707             fieldUnits.add(HibernateProxyHelper.deproxy(specimen, FieldUnit.class));
 708         }
 709         else if(specimen.isInstanceOf(DerivedUnit.class)){
 710             fieldUnits.addAll(getFieldUnits(HibernateProxyHelper.deproxy(specimen, DerivedUnit.class)));
 711         }
 712         return fieldUnits;
 713     }
 714
 715
 716     /**
 717      * @param original
 718      * @param fieldUnits
 719      */
 720     private Collection<FieldUnit> getFieldUnits(DerivedUnit derivedUnit) {
 721         Collection<FieldUnit> fieldUnits = new HashSet<FieldUnit>();
 722         Set<SpecimenOrObservationBase> originals = derivedUnit.getOriginals();
 723         if(originals!=null && !originals.isEmpty()){
 724             for(SpecimenOrObservationBase<?> original:originals){
 725                 if(original.isInstanceOf(FieldUnit.class)){
 726                     fieldUnits.add(HibernateProxyHelper.deproxy(original, FieldUnit.class));
 727                 }
 728                 else if(original.isInstanceOf(DerivedUnit.class)){
 729                     fieldUnits.addAll(getFieldUnits(HibernateProxyHelper.deproxy(original, DerivedUnit.class)));
 730                 }
 731             }
 732         }
 733         return fieldUnits;
 734     }
 735
 736     /* (non-Javadoc)
 737      * @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)
 738      */
 739     @Override
 740     public boolean moveSequence(DnaSample from, DnaSample to, Sequence sequence) {
 741         //reload specimens to avoid session conflicts
 742         from = (DnaSample) load(from.getUuid());
 743         to = (DnaSample) load(to.getUuid());
 744         sequence = sequenceService.load(sequence.getUuid());
 745
 746         if(from==null || to==null || sequence==null){
 747             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" +
 748                     "Operation was move "+sequence+ " from "+from+" to "+to);
 749         }
 750         from.removeSequence(sequence);
 751         saveOrUpdate(from);
 752         to.addSequence(sequence);
 753         saveOrUpdate(to);
 754         return true;
 755     }
 756
 757     /* (non-Javadoc)
 758      * @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)
 759      */
 760     @Override
 761     public boolean moveDerivate(SpecimenOrObservationBase<?> from, SpecimenOrObservationBase<?> to, DerivedUnit derivate) {
 762         //reload specimens to avoid session conflicts
 763         from = load(from.getUuid());
 764         to = load(to.getUuid());
 765         derivate = (DerivedUnit) load(derivate.getUuid());
 766
 767         if(from==null || to==null || derivate==null){
 768             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" +
 769                         "Operation was move "+derivate+ " from "+from+" to "+to);
 770         }
 771
 772         SpecimenOrObservationType derivateType = derivate.getRecordBasis();
 773         SpecimenOrObservationType toType = to.getRecordBasis();
 774         //check if type is a sub derivate type
 775         if(toType==SpecimenOrObservationType.FieldUnit //moving to FieldUnit always works
 776                 || derivateType==SpecimenOrObservationType.Media //moving media always works
 777                 || (derivateType.isKindOf(toType) && toType!=derivateType)){ //moving only to parent derivate type
 778             //remove derivation event from parent specimen of dragged object
 779             DerivationEvent eventToRemove = null;
 780             for(DerivationEvent event:from.getDerivationEvents()){
 781                 if(event.getDerivatives().contains(derivate)){
 782                     eventToRemove = event;
 783                     break;
 784                 }
 785             }
 786             from.removeDerivationEvent(eventToRemove);
 787             saveOrUpdate(from);
 788             //add new derivation event to target
 789             DerivationEvent derivedFromNewOriginalEvent = DerivationEvent.NewSimpleInstance(to, derivate, eventToRemove==null?null:eventToRemove.getType());
 790             to.addDerivationEvent(derivedFromNewOriginalEvent);
 791             derivate.setDerivedFrom(derivedFromNewOriginalEvent);
 792             saveOrUpdate(to);
 793             return true;
 794         }
 795         return false;
 796     }
 797
 798     @Override
 799     public Collection<ICdmBase> getNonCascadedAssociatedElements(SpecimenOrObservationBase<?> specimen){
 800         //potential fields that are not persisted cascadingly
 801         /*
 802          * SOOB
 803         -DescriptionBase
 804         -determinations
 805         --modifier TERM
 806         -kindOfUnit TERM
 807         -lifeStage TERM
 808         -sex TERM
 809
 810         FieldUnit
 811         -GatheringEvent
 812         --Country TERM
 813         --CollectingAreas TERM
 814
 815         DerivedUnit
 816         -collection
 817         --institute
 818         ---types TERM
 819         -preservationMethod
 820         --medium TERM
 821         -storedUnder CDM TaxonNameBase
 822         */
 823
 824         Collection<ICdmBase> nonCascadedCdmEntities = new HashSet<ICdmBase>();
 825
 826         //Choose the correct entry point to traverse the graph (FieldUnit or DerivedUnit)
 827
 828         //FieldUnit
 829         if(specimen.isInstanceOf(FieldUnit.class)){
 830             nonCascadedCdmEntities.addAll(getFieldUnitNonCascadedAssociatedElements(HibernateProxyHelper.deproxy(specimen, FieldUnit.class)));
 831         }
 832         //DerivedUnit
 833         else if(specimen.isInstanceOf(DerivedUnit.class)){
 834             DerivedUnit derivedUnit = HibernateProxyHelper.deproxy(specimen, DerivedUnit.class);
 835             if(derivedUnit.getDerivedFrom()!=null){
 836                 Collection<FieldUnit> fieldUnits = getFieldUnits(derivedUnit);
 837                 for(FieldUnit fieldUnit:fieldUnits){
 838                     nonCascadedCdmEntities.addAll(getFieldUnitNonCascadedAssociatedElements(fieldUnit));
 839                 }
 840             }
 841         }
 842         return nonCascadedCdmEntities;
 843     }
 844
 845     private Collection<ICdmBase> getFieldUnitNonCascadedAssociatedElements(FieldUnit fieldUnit){
 846         //get non cascaded element on SpecimenOrObservationBase level
 847         Collection<ICdmBase> nonCascadedCdmEntities = getSpecimenOrObservationNonCascadedAssociatedElements(fieldUnit);
 848
 849         //get FieldUnit specific elements
 850         GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
 851         if(gatheringEvent!=null){
 852             //country
 853             if(gatheringEvent.getCountry()!=null){
 854                 nonCascadedCdmEntities.add(gatheringEvent.getCountry());
 855             }
 856             //collecting areas
 857             for (NamedArea namedArea : gatheringEvent.getCollectingAreas()) {
 858                 nonCascadedCdmEntities.add(namedArea);
 859             }
 860         }
 861         for (DerivationEvent derivationEvent : fieldUnit.getDerivationEvents()) {
 862             for (DerivedUnit derivedUnit : derivationEvent.getDerivatives()) {
 863                 nonCascadedCdmEntities.addAll(getDerivedUnitNonCascadedAssociatedElements(derivedUnit));
 864             }
 865         }
 866         return nonCascadedCdmEntities;
 867     }
 868
 869     private Collection<ICdmBase> getDerivedUnitNonCascadedAssociatedElements(DerivedUnit derivedUnit){
 870         //get non cascaded element on SpecimenOrObservationBase level
 871         Collection<ICdmBase> nonCascadedCdmEntities = getSpecimenOrObservationNonCascadedAssociatedElements(derivedUnit);
 872
 873         //get DerivedUnit specific elements
 874         if(derivedUnit.getCollection()!=null && derivedUnit.getCollection().getInstitute()!=null){
 875             for (DefinedTerm type : derivedUnit.getCollection().getInstitute().getTypes()) {
 876                 nonCascadedCdmEntities.add(type);
 877             }
 878         }
 879         if(derivedUnit.getPreservation()!=null && derivedUnit.getPreservation().getMedium()!=null){
 880             nonCascadedCdmEntities.add(derivedUnit.getPreservation().getMedium());
 881         }
 882         if(derivedUnit.getStoredUnder()!=null){
 883             nonCascadedCdmEntities.add(derivedUnit.getStoredUnder());
 884         }
 885         return nonCascadedCdmEntities;
 886     }
 887
 888     /**
 889      * @param specimen
 890      * @return
 891      */
 892     private Collection<ICdmBase> getSpecimenOrObservationNonCascadedAssociatedElements(
 893             SpecimenOrObservationBase<?> specimen) {
 894         Collection<ICdmBase> nonCascadedCdmEntities = new HashSet<ICdmBase>();
 895         //scan SpecimenOrObservationBase
 896         for(DeterminationEvent determinationEvent:specimen.getDeterminations()){
 897             //modifier
 898             if(determinationEvent.getModifier()!=null){
 899                 nonCascadedCdmEntities.add(determinationEvent.getModifier());
 900             }
 901         }
 902         //kindOfUnit
 903         if(specimen.getKindOfUnit()!=null){
 904             nonCascadedCdmEntities.add(specimen.getKindOfUnit());
 905         }
 906         //lifeStage
 907         if(specimen.getLifeStage()!=null){
 908             nonCascadedCdmEntities.add(specimen.getLifeStage());
 909         }
 910         //sex
 911         if(specimen.getSex()!=null){
 912             nonCascadedCdmEntities.add(specimen.getSex());
 913         }
 914         return nonCascadedCdmEntities;
 915     }
 916
 917     /* (non-Javadoc)
 918      * @see eu.etaxonomy.cdm.api.service.VersionableServiceBase#isDeletable(eu.etaxonomy.cdm.model.common.VersionableEntity, eu.etaxonomy.cdm.api.service.config.DeleteConfiguratorBase)
 919      */
 920     @Override
 921     public DeleteResult isDeletable(SpecimenOrObservationBase specimen, DeleteConfiguratorBase config) {
 922         DeleteResult deleteResult = new DeleteResult();
 923         SpecimenDeleteConfigurator specimenDeleteConfigurator = (SpecimenDeleteConfigurator)config;
 924
 925         //check elements found by super method
 926         Set<CdmBase> relatedObjects = super.isDeletable(specimen, config).getRelatedObjects();
 927         for (CdmBase cdmBase : relatedObjects) {
 928             //check for type designation
 929             if(cdmBase.isInstanceOf(SpecimenTypeDesignation.class) && !specimenDeleteConfigurator.isDeleteFromTypeDesignation()){
 930                 deleteResult.setAbort();
 931                 deleteResult.addException(new ReferencedObjectUndeletableException("Specimen is a type specimen."));
 932                 deleteResult.addRelatedObject(cdmBase);
 933                 break;
 934             }
 935             //check for IndividualsAssociations
 936             else if(cdmBase.isInstanceOf(IndividualsAssociation.class) && !specimenDeleteConfigurator.isDeleteFromIndividualsAssociation()){
 937                 deleteResult.setAbort();
 938                 deleteResult.addException(new ReferencedObjectUndeletableException("Specimen is still associated via IndividualsAssociations"));
 939                 deleteResult.addRelatedObject(cdmBase);
 940                 break;
 941             }
 942             //check for specimen/taxon description
 943             else if((cdmBase.isInstanceOf(SpecimenDescription.class) || cdmBase.isInstanceOf(TaxonDescription.class))
 944                     && !specimenDeleteConfigurator.isDeleteFromDescription()){
 945                 deleteResult.setAbort();
 946                 deleteResult.addException(new ReferencedObjectUndeletableException("Specimen is still used in a Description."));
 947                 deleteResult.addRelatedObject(cdmBase);
 948                 break;
 949             }
 950             //check for children and parents (derivation events)
 951             else if(cdmBase.isInstanceOf(DerivationEvent.class)){
 952                 DerivationEvent derivationEvent = HibernateProxyHelper.deproxy(cdmBase, DerivationEvent.class);
 953                 //check if derivation event is empty
 954                 if(!derivationEvent.getDerivatives().isEmpty()){
 955                     if(derivationEvent.getDerivatives().size()==1 && derivationEvent.getDerivatives().contains(specimen)){
 956                         //if it is the parent event with only one derivate then the specimen is still deletable
 957                         continue;
 958                     }
 959                     else if(!specimenDeleteConfigurator.isDeleteChildren()){
 960                         //if not and children should not be deleted then it is undeletable
 961                         deleteResult.setAbort();
 962                         deleteResult.addException(new ReferencedObjectUndeletableException("Derivate still has child derivates."));
 963                         deleteResult.addRelatedObject(cdmBase);
 964                         break;
 965                     }
 966                     else{
 967                         //check all children if they can be deleted
 968                         Set<DerivedUnit> derivatives = derivationEvent.getDerivatives();
 969                         DeleteResult childResult = new DeleteResult();
 970                         for (DerivedUnit derivedUnit : derivatives) {
 971                             childResult.includeResult(isDeletable(derivedUnit, specimenDeleteConfigurator));
 972                         }
 973                         if(!childResult.isOk()){
 974                             deleteResult.setAbort();
 975                             deleteResult.includeResult(childResult);
 976                             break;
 977                         }
 978                     }
 979                 }
 980             }
 981             //check for amplification
 982             else if(cdmBase.isInstanceOf(AmplificationResult.class) && !specimenDeleteConfigurator.isDeleteMolecularData()){
 983                 deleteResult.setAbort();
 984                 deleteResult.addException(new ReferencedObjectUndeletableException("DnaSample is used in amplification results."));
 985                 deleteResult.addRelatedObject(cdmBase);
 986                 break;
 987             }
 988             //check for sequence
 989             else if(cdmBase.isInstanceOf(Sequence.class) && !specimenDeleteConfigurator.isDeleteMolecularData()){
 990                 deleteResult.setAbort();
 991                 deleteResult.addException(new ReferencedObjectUndeletableException("DnaSample is used in sequences."));
 992                 deleteResult.addRelatedObject(cdmBase);
 993                 break;
 994             }
 995         }
 996         return deleteResult;
 997     }
 998
 999     /* (non-Javadoc)
1000      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#delete(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase, eu.etaxonomy.cdm.api.service.config.SpecimenDeleteConfigurator)
1001      */
1002     @Override
1003     public DeleteResult delete(SpecimenOrObservationBase<?> specimen, SpecimenDeleteConfigurator config) {
1004         specimen = HibernateProxyHelper.deproxy(specimen, SpecimenOrObservationBase.class);
1005
1006         if(config.isDeleteChildren()){
1007             Set<DerivationEvent> derivationEvents = specimen.getDerivationEvents();
1008             for (DerivationEvent derivationEvent : derivationEvents) {
1009                 Set<DerivedUnit> derivatives = derivationEvent.getDerivatives();
1010                 for (DerivedUnit derivedUnit : derivatives) {
1011                     delete(derivedUnit, config);
1012                 }
1013             }
1014         }
1015
1016         DeleteResult deleteResult = isDeletable(specimen, config);
1017         if(!deleteResult.isOk()){
1018             return deleteResult;
1019         }
1020
1021         //check related objects
1022         Set<CdmBase> relatedObjects = deleteResult.getRelatedObjects();
1023
1024         for (CdmBase relatedObject : relatedObjects) {
1025             //check for TypeDesignations
1026             if(relatedObject.isInstanceOf(SpecimenTypeDesignation.class)){
1027                 SpecimenTypeDesignation designation = HibernateProxyHelper.deproxy(relatedObject, SpecimenTypeDesignation.class);
1028                 designation.setTypeSpecimen(null);
1029                 Set<TaxonNameBase> typifiedNames = designation.getTypifiedNames();
1030                 for (TaxonNameBase taxonNameBase : typifiedNames) {
1031                     taxonNameBase.removeTypeDesignation(designation);
1032                 }
1033             }
1034             //delete IndividualsAssociation
1035             if(relatedObject.isInstanceOf(IndividualsAssociation.class)){
1036                 IndividualsAssociation assciation = HibernateProxyHelper.deproxy(relatedObject, IndividualsAssociation.class);
1037                 assciation.setAssociatedSpecimenOrObservation(null);
1038                 assciation.getInDescription().removeElement(assciation);
1039             }
1040             //check for taxon description
1041             if(relatedObject.isInstanceOf(TaxonDescription.class)){
1042                 TaxonDescription taxonDescription = HibernateProxyHelper.deproxy(relatedObject, TaxonDescription.class);
1043                 taxonDescription.setDescribedSpecimenOrObservation(null);
1044             }
1045             //check for specimen description
1046             if(relatedObject.isInstanceOf(SpecimenDescription.class)){
1047                 SpecimenDescription specimenDescription = HibernateProxyHelper.deproxy(relatedObject, SpecimenDescription.class);
1048                 //check if specimen is "described" specimen
1049                 if(specimenDescription.getDescribedSpecimenOrObservation().equals(specimen)){
1050                     specimenDescription.setDescribedSpecimenOrObservation(null);
1051                 }
1052                 //check if description is a description of the given specimen
1053                 if(specimen.getDescriptions().contains(specimenDescription)){
1054                     specimen.removeDescription(specimenDescription);
1055                 }
1056             }
1057             //check for amplification
1058             if(relatedObject.isInstanceOf(AmplificationResult.class)){
1059                 AmplificationResult amplificationResult = HibernateProxyHelper.deproxy(relatedObject, AmplificationResult.class);
1060                 amplificationResult.getDnaSample().removeAmplificationResult(amplificationResult);
1061             }
1062             //check for sequence
1063             if(relatedObject.isInstanceOf(Sequence.class)){
1064                 Sequence sequence = HibernateProxyHelper.deproxy(relatedObject, Sequence.class);
1065                 sequence.getDnaSample().removeSequence(sequence);
1066             }
1067             //check for children and parents (derivation events)
1068             if(relatedObject.isInstanceOf(DerivationEvent.class)){
1069                 DerivationEvent derivationEvent = HibernateProxyHelper.deproxy(relatedObject, DerivationEvent.class);
1070                 //parent derivation event (derivedFrom)
1071                 if(derivationEvent.getDerivatives().contains(specimen) && specimen.isInstanceOf(DerivedUnit.class)){
1072                     derivationEvent.removeDerivative(HibernateProxyHelper.deproxy(specimen, DerivedUnit.class));
1073                     if(derivationEvent.getDerivatives().isEmpty()){
1074                         Set<SpecimenOrObservationBase> originals = derivationEvent.getOriginals();
1075                         for (SpecimenOrObservationBase specimenOrObservationBase : originals) {
1076                             specimenOrObservationBase.removeDerivationEvent(derivationEvent);
1077                         }
1078                     }
1079                 }
1080                 else{
1081                     //child derivation events should not occur since we delete the hierarchy from bottom to top
1082                 }
1083             }
1084         }
1085
1086         deleteResult.includeResult(delete(specimen));
1087         return deleteResult;
1088     }
1089
1090     /* (non-Javadoc)
1091      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#deleteDerivateHierarchy(eu.etaxonomy.cdm.model.common.ICdmBase)
1092      */
1093     @Override
1094     public DeleteResult deleteDerivateHierarchy(CdmBase from, SpecimenDeleteConfigurator config) {
1095         DeleteResult deleteResult = new DeleteResult();
1096         if(from.isInstanceOf(Sequence.class)){
1097             if(!config.isDeleteMolecularData()){
1098                 deleteResult.setAbort();
1099                 deleteResult.addException(new ReferencedObjectUndeletableException("deleting molecur data is not allowed in config"));
1100                 return deleteResult;
1101             }
1102             Sequence sequence = HibernateProxyHelper.deproxy(from, Sequence.class);
1103             sequence.getDnaSample().removeSequence(sequence);
1104             deleteResult = sequenceService.delete(sequence);
1105         }
1106         else if(from.isInstanceOf(SingleRead.class))  {
1107             if(!config.isDeleteMolecularData()){
1108                 deleteResult.setAbort();
1109                 deleteResult.addException(new ReferencedObjectUndeletableException("deleting molecur data is not allowed in config"));
1110                 return deleteResult;
1111             }
1112             SingleRead singleRead = HibernateProxyHelper.deproxy(from, SingleRead.class);
1113             singleRead.getAmplificationResult().removeSingleRead(singleRead);
1114             deleteResult.setStatus(DeleteStatus.OK);
1115         }
1116         else if(from.isInstanceOf(SpecimenOrObservationBase.class))  {
1117             deleteResult = delete(HibernateProxyHelper.deproxy(from, SpecimenOrObservationBase.class), config);
1118         }
1119         return deleteResult;
1120     }
1121
1122 //    private DeleteResult deepDelete(SpecimenOrObservationBase<?> entity, SpecimenDeleteConfigurator config){
1123 //        Set<DerivationEvent> derivationEvents = entity.getDerivationEvents();
1124 //        for (DerivationEvent derivationEvent : derivationEvents) {
1125 //            Set<DerivedUnit> derivatives = derivationEvent.getDerivatives();
1126 //            for (DerivedUnit derivedUnit : derivatives) {
1127 //                DeleteResult deleteResult = deepDelete(derivedUnit, config);
1128 //                if(!deleteResult.isOk()){
1129 //                    return deleteResult;
1130 //                }
1131 //            }
1132 //        }
1133 //        return delete(entity, config);
1134 //    }
1135
1136     /* (non-Javadoc)
1137      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#listAssociatedTaxa(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase)
1138      */
1139     @Override
1140     public Collection<IndividualsAssociation> listIndividualsAssociations(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
1141         return dao.listIndividualsAssociations(specimen, null, null, null, null);
1142     }
1143
1144     /* (non-Javadoc)
1145      * @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)
1146      */
1147     @Override
1148     public Collection<SpecimenTypeDesignation> listTypeDesignations(SpecimenOrObservationBase<?> specimen,
1149             Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
1150         return dao.listTypeDesignations(specimen, limit, start, orderHints, propertyPaths);
1151     }
1152
1153     /* (non-Javadoc)
1154      * @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)
1155      */
1156     @Override
1157     public Collection<DescriptionBase<?>> listDescriptionsWithDescriptionSpecimen(
1158             SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints,
1159             List<String> propertyPaths) {
1160         return dao.listDescriptionsWithDescriptionSpecimen(specimen, limit, start, orderHints, propertyPaths);
1161     }
1162
1163 }