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

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