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.FindOccurrencesConfigurator;
  48 import eu.etaxonomy.cdm.api.service.config.IIdentifiableEntityServiceConfigurator;
  49 import eu.etaxonomy.cdm.api.service.config.SpecimenDeleteConfigurator;
  50 import eu.etaxonomy.cdm.api.service.dto.DerivateDTO;
  51 import eu.etaxonomy.cdm.api.service.dto.DerivateDataDTO;
  52 import eu.etaxonomy.cdm.api.service.dto.DerivateDataDTO.ContigFile;
  53 import eu.etaxonomy.cdm.api.service.dto.DerivateDataDTO.MolecularData;
  54 import eu.etaxonomy.cdm.api.service.dto.FieldUnitDTO;
  55 import eu.etaxonomy.cdm.api.service.dto.PreservedSpecimenDTO;
  56 import eu.etaxonomy.cdm.api.service.exception.ReferencedObjectUndeletableException;
  57 import eu.etaxonomy.cdm.api.service.molecular.ISequenceService;
  58 import eu.etaxonomy.cdm.api.service.pager.Pager;
  59 import eu.etaxonomy.cdm.api.service.pager.impl.DefaultPagerImpl;
  60 import eu.etaxonomy.cdm.api.service.search.ILuceneIndexToolProvider;
  61 import eu.etaxonomy.cdm.api.service.search.ISearchResultBuilder;
  62 import eu.etaxonomy.cdm.api.service.search.LuceneSearch;
  63 import eu.etaxonomy.cdm.api.service.search.LuceneSearch.TopGroupsWithMaxScore;
  64 import eu.etaxonomy.cdm.api.service.search.QueryFactory;
  65 import eu.etaxonomy.cdm.api.service.search.SearchResult;
  66 import eu.etaxonomy.cdm.api.service.search.SearchResultBuilder;
  67 import eu.etaxonomy.cdm.api.service.util.TaxonRelationshipEdge;
  68 import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
  69 import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
  70 import eu.etaxonomy.cdm.model.CdmBaseType;
  71 import eu.etaxonomy.cdm.model.agent.AgentBase;
  72 import eu.etaxonomy.cdm.model.common.CdmBase;
  73 import eu.etaxonomy.cdm.model.common.DefinedTerm;
  74 import eu.etaxonomy.cdm.model.common.DefinedTermBase;
  75 import eu.etaxonomy.cdm.model.common.ICdmBase;
  76 import eu.etaxonomy.cdm.model.common.Language;
  77 import eu.etaxonomy.cdm.model.description.CategoricalData;
  78 import eu.etaxonomy.cdm.model.description.DescriptionBase;
  79 import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
  80 import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
  81 import eu.etaxonomy.cdm.model.description.QuantitativeData;
  82 import eu.etaxonomy.cdm.model.description.SpecimenDescription;
  83 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  84 import eu.etaxonomy.cdm.model.location.Country;
  85 import eu.etaxonomy.cdm.model.location.NamedArea;
  86 import eu.etaxonomy.cdm.model.media.Media;
  87 import eu.etaxonomy.cdm.model.media.MediaRepresentation;
  88 import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;
  89 import eu.etaxonomy.cdm.model.media.MediaUtils;
  90 import eu.etaxonomy.cdm.model.molecular.AmplificationResult;
  91 import eu.etaxonomy.cdm.model.molecular.DnaSample;
  92 import eu.etaxonomy.cdm.model.molecular.Sequence;
  93 import eu.etaxonomy.cdm.model.molecular.SingleRead;
  94 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
  95 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  96 import eu.etaxonomy.cdm.model.name.TypeDesignationStatusBase;
  97 import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
  98 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  99 import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
 100 import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
 101 import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
 102 import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen;
 103 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
 104 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
 105 import eu.etaxonomy.cdm.model.taxon.Taxon;
 106 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
 107 import eu.etaxonomy.cdm.persistence.dao.common.IDefinedTermDao;
 108 import eu.etaxonomy.cdm.persistence.dao.initializer.AbstractBeanInitializer;
 109 import eu.etaxonomy.cdm.persistence.dao.occurrence.IOccurrenceDao;
 110 import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
 111 import eu.etaxonomy.cdm.persistence.query.OrderHint;
 112 import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
 113
 114 /**
 115  * @author a.babadshanjan
 116  * @created 01.09.2008
 117  */
 118 @Service
 119 @Transactional(readOnly = true)
 120 public class OccurrenceServiceImpl extends IdentifiableServiceBase<SpecimenOrObservationBase, IOccurrenceDao> implements IOccurrenceService {
 121
 122     static private final Logger logger = Logger.getLogger(OccurrenceServiceImpl.class);
 123
 124     @Autowired
 125     private IDefinedTermDao definedTermDao;
 126
 127     @Autowired
 128     private IDescriptionService descriptionService;
 129
 130     @Autowired
 131     private ITaxonService taxonService;
 132
 133     @Autowired
 134     private ISequenceService sequenceService;
 135
 136     @Autowired
 137     private AbstractBeanInitializer beanInitializer;
 138
 139     @Autowired
 140     private ILuceneIndexToolProvider luceneIndexToolProvider;
 141
 142     private static final String SEPARATOR_STRING = ", ";
 143
 144     public OccurrenceServiceImpl() {
 145         logger.debug("Load OccurrenceService Bean");
 146     }
 147
 148
 149     @Override
 150     @Transactional(readOnly = false)
 151     public void updateTitleCache(Class<? extends SpecimenOrObservationBase> clazz, Integer stepSize, IIdentifiableEntityCacheStrategy<SpecimenOrObservationBase> cacheStrategy, IProgressMonitor monitor) {
 152         if (clazz == null) {
 153             clazz = SpecimenOrObservationBase.class;
 154         }
 155         super.updateTitleCacheImpl(clazz, stepSize, cacheStrategy, monitor);
 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     @Override
 201     public int countDeterminations(SpecimenOrObservationBase occurence, TaxonBase taxonbase) {
 202         return dao.countDeterminations(occurence, taxonbase);
 203     }
 204
 205     @Override
 206     public Pager<DeterminationEvent> getDeterminations(SpecimenOrObservationBase occurrence, TaxonBase taxonBase, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
 207         Integer numberOfResults = dao.countDeterminations(occurrence, taxonBase);
 208
 209         List<DeterminationEvent> results = new ArrayList<DeterminationEvent>();
 210         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 211             results = dao.getDeterminations(occurrence, taxonBase, pageSize, pageNumber, propertyPaths);
 212         }
 213
 214         return new DefaultPagerImpl<DeterminationEvent>(pageNumber, numberOfResults, pageSize, results);
 215     }
 216
 217     @Override
 218     public Pager<Media> getMedia(SpecimenOrObservationBase occurence, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
 219         Integer numberOfResults = dao.countMedia(occurence);
 220
 221         List<Media> results = new ArrayList<Media>();
 222         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 223             results = dao.getMedia(occurence, pageSize, pageNumber, propertyPaths);
 224         }
 225
 226         return new DefaultPagerImpl<Media>(pageNumber, numberOfResults, pageSize, results);
 227     }
 228
 229     @Override
 230     public Pager<SpecimenOrObservationBase> list(Class<? extends SpecimenOrObservationBase> type, TaxonBase determinedAs, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 231         Integer numberOfResults = dao.count(type, determinedAs);
 232         List<SpecimenOrObservationBase> results = new ArrayList<SpecimenOrObservationBase>();
 233         pageNumber = pageNumber == null ? 0 : pageNumber;
 234         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 235             Integer start = pageSize == null ? 0 : pageSize * pageNumber;
 236             results = dao.list(type, determinedAs, pageSize, start, orderHints, propertyPaths);
 237         }
 238         return new DefaultPagerImpl<SpecimenOrObservationBase>(pageNumber, numberOfResults, pageSize, results);
 239     }
 240
 241     @Override
 242     public List<UuidAndTitleCache<DerivedUnit>> getDerivedUnitUuidAndTitleCache() {
 243         return dao.getDerivedUnitUuidAndTitleCache();
 244     }
 245
 246     @Override
 247     public List<UuidAndTitleCache<FieldUnit>> getFieldUnitUuidAndTitleCache() {
 248         return dao.getFieldUnitUuidAndTitleCache();
 249     }
 250
 251     @Override
 252     public DerivedUnitFacade getDerivedUnitFacade(DerivedUnit derivedUnit, List<String> propertyPaths) throws DerivedUnitFacadeNotSupportedException {
 253         derivedUnit = (DerivedUnit) dao.load(derivedUnit.getUuid(), null);
 254         DerivedUnitFacadeConfigurator config = DerivedUnitFacadeConfigurator.NewInstance();
 255         config.setThrowExceptionForNonSpecimenPreservationMethodRequest(false);
 256         DerivedUnitFacade derivedUnitFacade = DerivedUnitFacade.NewInstance(derivedUnit, config);
 257         beanInitializer.initialize(derivedUnitFacade, propertyPaths);
 258         return derivedUnitFacade;
 259     }
 260
 261     @Override
 262     public List<DerivedUnitFacade> listDerivedUnitFacades(
 263             DescriptionBase description, List<String> propertyPaths) {
 264
 265         List<DerivedUnitFacade> derivedUnitFacadeList = new ArrayList<DerivedUnitFacade>();
 266         IndividualsAssociation tempIndividualsAssociation;
 267         SpecimenOrObservationBase tempSpecimenOrObservationBase;
 268         List<DescriptionElementBase> elements = descriptionService.listDescriptionElements(description, null, IndividualsAssociation.class, null, 0, Arrays.asList(new String []{"associatedSpecimenOrObservation"}));
 269         for (DescriptionElementBase element : elements) {
 270             if (element.isInstanceOf(IndividualsAssociation.class)) {
 271                 tempIndividualsAssociation = HibernateProxyHelper.deproxy(element, IndividualsAssociation.class);
 272                 if (tempIndividualsAssociation.getAssociatedSpecimenOrObservation() != null) {
 273                     tempSpecimenOrObservationBase = HibernateProxyHelper.deproxy(tempIndividualsAssociation.getAssociatedSpecimenOrObservation(), SpecimenOrObservationBase.class);
 274                     if (tempSpecimenOrObservationBase.isInstanceOf(DerivedUnit.class)) {
 275                         try {
 276                             derivedUnitFacadeList.add(DerivedUnitFacade.NewInstance(HibernateProxyHelper.deproxy(tempSpecimenOrObservationBase, DerivedUnit.class)));
 277                         } catch (DerivedUnitFacadeNotSupportedException e) {
 278                             logger.warn(tempIndividualsAssociation.getAssociatedSpecimenOrObservation().getTitleCache() + " : " + e.getMessage());
 279                         }
 280                     }
 281                 }
 282
 283             }
 284         }
 285
 286         beanInitializer.initializeAll(derivedUnitFacadeList, propertyPaths);
 287
 288         return derivedUnitFacadeList;
 289     }
 290
 291
 292     @Override
 293     public <T extends SpecimenOrObservationBase> List<T> listByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
 294             Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 295
 296         return pageByAssociatedTaxon(type, includeRelationships, associatedTaxon, maxDepth, pageSize, pageNumber, orderHints, propertyPaths).getRecords();
 297     }
 298
 299     @Override
 300     public Collection<SpecimenOrObservationBase> listFieldUnitsByAssociatedTaxon(Taxon associatedTaxon, List<OrderHint> orderHints, List<String> propertyPaths) {
 301         return pageFieldUnitsByAssociatedTaxon(null, associatedTaxon, null, null, null, null, propertyPaths).getRecords();
 302     }
 303
 304     @Override
 305     public Pager<SpecimenOrObservationBase> pageFieldUnitsByAssociatedTaxon(Set<TaxonRelationshipEdge> includeRelationships,
 306             Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
 307             List<String> propertyPaths) {
 308
 309         if (!getSession().contains(associatedTaxon)) {
 310             associatedTaxon = (Taxon) taxonService.load(associatedTaxon.getUuid());
 311         }
 312
 313         // gather the IDs of all relevant field units
 314         Set<Integer> fieldUnitIds = new HashSet<Integer>();
 315         List<SpecimenOrObservationBase> records = listByAssociatedTaxon(null, includeRelationships, associatedTaxon, maxDepth, null, null, orderHints, propertyPaths);
 316         for (SpecimenOrObservationBase<?> specimen : records) {
 317             for (FieldUnit fieldUnit : getFieldUnits(specimen.getUuid())) {
 318                 fieldUnitIds.add(fieldUnit.getId());
 319             }
 320         }
 321         //dao.listByIds() does the paging of the field units. Passing the field units directly to the Pager would not work
 322         List<SpecimenOrObservationBase> fieldUnits = dao.listByIds(fieldUnitIds, pageSize, pageNumber, orderHints, propertyPaths);
 323         return new DefaultPagerImpl<SpecimenOrObservationBase>(pageNumber, fieldUnitIds.size(), pageSize, fieldUnits);
 324     }
 325
 326     @Override
 327     public FieldUnitDTO assembleFieldUnitDTO(FieldUnit fieldUnit, UUID associatedTaxonUuid) {
 328
 329         if (!getSession().contains(fieldUnit)) {
 330             fieldUnit = (FieldUnit) load(fieldUnit.getUuid());
 331         }
 332         TaxonBase associatedTaxon = taxonService.load(associatedTaxonUuid);
 333
 334         FieldUnitDTO fieldUnitDTO = new FieldUnitDTO();
 335
 336         if (fieldUnit.getGatheringEvent() != null) {
 337             GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
 338             // Country
 339             NamedArea country = gatheringEvent.getCountry();
 340             fieldUnitDTO.setCountry(country != null ? country.getDescription() : null);
 341             // Collection
 342             AgentBase collector = gatheringEvent.getCollector();
 343             String fieldNumber = fieldUnit.getFieldNumber();
 344             String collectionString = "";
 345             if (collector != null || fieldNumber != null) {
 346                 collectionString += collector != null ? collector : "";
 347                 if (!collectionString.isEmpty()) {
 348                     collectionString += " ";
 349                 }
 350                 collectionString += (fieldNumber != null ? fieldNumber : "");
 351                 collectionString.trim();
 352             }
 353             fieldUnitDTO.setCollection(collectionString);
 354             // Date
 355             Partial gatheringDate = gatheringEvent.getGatheringDate();
 356             String dateString = null;
 357             if (gatheringDate != null) {
 358                 gatheringDate.toString();
 359             }
 360             else if(gatheringEvent.getTimeperiod()!=null && gatheringEvent.getTimeperiod().getFreeText()!=null){
 361                 dateString = gatheringEvent.getTimeperiod().getFreeText();
 362             }
 363             fieldUnitDTO.setDate(dateString);
 364         }
 365
 366         // Taxon Name
 367         fieldUnitDTO.setTaxonName(associatedTaxon.getName().getTitleCache());
 368
 369         // Herbaria map
 370         Map<eu.etaxonomy.cdm.model.occurrence.Collection, Integer> collectionToCountMap = new HashMap<eu.etaxonomy.cdm.model.occurrence.Collection, Integer>();
 371         // List of accession numbers for citation
 372         List<String> preservedSpecimenAccessionNumbers = new ArrayList<String>();
 373
 374         // assemble preserved specimen DTOs
 375         Set<DerivationEvent> derivationEvents = fieldUnit.getDerivationEvents();
 376         for (DerivationEvent derivationEvent : derivationEvents) {
 377             Set<DerivedUnit> derivatives = derivationEvent.getDerivatives();
 378             for (DerivedUnit derivedUnit : derivatives) {
 379                 // collect accession numbers for citation
 380                 String mostSignificantIdentifier = getMostSignificantIdentifier(derivedUnit);
 381                 if (mostSignificantIdentifier != null) {
 382                     preservedSpecimenAccessionNumbers.add(mostSignificantIdentifier);
 383                 }
 384                 // collect collections for herbaria column
 385                 if (derivedUnit.getCollection() != null) {
 386                     Integer herbariumCount = collectionToCountMap.get(derivedUnit.getCollection());
 387                     if (herbariumCount == null) {
 388                         herbariumCount = 0;
 389                     }
 390                     collectionToCountMap.put(derivedUnit.getCollection(), herbariumCount + 1);
 391                 }
 392                 if (derivedUnit.getRecordBasis().equals(SpecimenOrObservationType.PreservedSpecimen)) {
 393                     PreservedSpecimenDTO preservedSpecimenDTO = assemblePreservedSpecimenDTO(derivedUnit, fieldUnitDTO);
 394                     fieldUnitDTO.addPreservedSpecimenDTO(preservedSpecimenDTO);
 395                     fieldUnitDTO.setHasCharacterData(fieldUnitDTO.isHasCharacterData() || preservedSpecimenDTO.isHasCharacterData());
 396                     fieldUnitDTO.setHasDetailImage(fieldUnitDTO.isHasDetailImage() || preservedSpecimenDTO.isHasDetailImage());
 397                     fieldUnitDTO.setHasDna(fieldUnitDTO.isHasDna() || preservedSpecimenDTO.isHasDna());
 398                     fieldUnitDTO.setHasSpecimenScan(fieldUnitDTO.isHasSpecimenScan() || preservedSpecimenDTO.isHasSpecimenScan());
 399                 }
 400             }
 401         }
 402         // assemble derivate data DTO
 403         assembleDerivateDataDTO(fieldUnitDTO, fieldUnit);
 404
 405         // assemble citation
 406         String citation = fieldUnit.getTitleCache();
 407         if (!preservedSpecimenAccessionNumbers.isEmpty()) {
 408             citation += " (";
 409             for (String accessionNumber : preservedSpecimenAccessionNumbers) {
 410                 if (!accessionNumber.isEmpty()) {
 411                     citation += accessionNumber + SEPARATOR_STRING;
 412                 }
 413             }
 414             citation = removeTail(citation, SEPARATOR_STRING);
 415             citation += ")";
 416         }
 417         fieldUnitDTO.setCitation(citation);
 418
 419         // assemble herbaria string
 420         String herbariaString = "";
 421         for (Entry<eu.etaxonomy.cdm.model.occurrence.Collection, Integer> e : collectionToCountMap.entrySet()) {
 422             eu.etaxonomy.cdm.model.occurrence.Collection collection = e.getKey();
 423             if (collection.getCode() != null) {
 424                 herbariaString += collection.getCode();
 425             }
 426             if (e.getValue() > 1) {
 427                 herbariaString += "(" + e.getValue() + ")";
 428             }
 429             herbariaString += SEPARATOR_STRING;
 430         }
 431         herbariaString = removeTail(herbariaString, SEPARATOR_STRING);
 432         fieldUnitDTO.setHerbarium(herbariaString);
 433
 434         return fieldUnitDTO;
 435     }
 436
 437     @Override
 438     public PreservedSpecimenDTO assemblePreservedSpecimenDTO(DerivedUnit derivedUnit) {
 439         return assemblePreservedSpecimenDTO(derivedUnit, null);
 440     }
 441
 442     @Override
 443     public String getMostSignificantIdentifier(DerivedUnit derivedUnit) {
 444         if (derivedUnit.getAccessionNumber() != null && !derivedUnit.getAccessionNumber().isEmpty()) {
 445             return derivedUnit.getAccessionNumber();
 446         }
 447         else if(derivedUnit.getBarcode()!=null && !derivedUnit.getBarcode().isEmpty()){
 448             return derivedUnit.getBarcode();
 449         }
 450         else if(derivedUnit.getCatalogNumber()!=null && !derivedUnit.getCatalogNumber().isEmpty()){
 451             return derivedUnit.getCatalogNumber();
 452         }
 453         return null;
 454     }
 455
 456     public PreservedSpecimenDTO assemblePreservedSpecimenDTO(DerivedUnit derivedUnit, FieldUnitDTO fieldUnitDTO) {
 457         if (!getSession().contains(derivedUnit)) {
 458             derivedUnit = (DerivedUnit) load(derivedUnit.getUuid());
 459         }
 460         PreservedSpecimenDTO preservedSpecimenDTO = new PreservedSpecimenDTO();
 461
 462         // check identifiers in priority order accNo>barCode>catalogNumber
 463         if (derivedUnit.getAccessionNumber() != null && !derivedUnit.getAccessionNumber().isEmpty()) {
 464             preservedSpecimenDTO.setAccessionNumber(derivedUnit.getAccessionNumber());
 465         }
 466         else if(derivedUnit.getBarcode()!=null && !derivedUnit.getBarcode().isEmpty()){
 467             preservedSpecimenDTO.setAccessionNumber(derivedUnit.getBarcode());
 468         }
 469         else if(derivedUnit.getCatalogNumber()!=null && !derivedUnit.getCatalogNumber().isEmpty()){
 470             preservedSpecimenDTO.setAccessionNumber(derivedUnit.getCatalogNumber());
 471         }
 472         preservedSpecimenDTO.setUuid(derivedUnit.getUuid().toString());
 473
 474         // citation
 475         Collection<FieldUnit> fieldUnits = getFieldUnits(derivedUnit);
 476         if (fieldUnits.size() == 1) {
 477             preservedSpecimenDTO.setCitation(fieldUnits.iterator().next().getTitleCache());
 478         }
 479         else{
 480             preservedSpecimenDTO.setCitation("No Citation available. This specimen either has no or multiple field units.");
 481         }
 482
 483         // character state data
 484         Collection<DescriptionElementBase> characterDataForSpecimen = getCharacterDataForSpecimen(derivedUnit);
 485         if (!characterDataForSpecimen.isEmpty()) {
 486             if (fieldUnitDTO != null) {
 487                 fieldUnitDTO.setHasCharacterData(true);
 488             }
 489         }
 490         for (DescriptionElementBase descriptionElementBase : characterDataForSpecimen) {
 491             String character = descriptionElementBase.getFeature().getLabel();
 492             ArrayList<Language> languages = new ArrayList<Language>(Collections.singleton(Language.DEFAULT()));
 493             if (descriptionElementBase instanceof QuantitativeData) {
 494                 QuantitativeData quantitativeData = (QuantitativeData) descriptionElementBase;
 495                 DefaultQuantitativeDescriptionBuilder builder = new DefaultQuantitativeDescriptionBuilder();
 496                 String state = builder.build(quantitativeData, languages).getText(Language.DEFAULT());
 497                 preservedSpecimenDTO.addCharacterData(character, state);
 498             }
 499             else if(descriptionElementBase instanceof CategoricalData){
 500                 CategoricalData categoricalData = (CategoricalData) descriptionElementBase;
 501                 DefaultCategoricalDescriptionBuilder builder = new DefaultCategoricalDescriptionBuilder();
 502                 String state = builder.build(categoricalData, languages).getText(Language.DEFAULT());
 503                 preservedSpecimenDTO.addCharacterData(character, state);
 504             }
 505         }
 506         // check type designations
 507         Collection<SpecimenTypeDesignation> specimenTypeDesignations = listTypeDesignations(derivedUnit, null, null, null, null);
 508         for (SpecimenTypeDesignation specimenTypeDesignation : specimenTypeDesignations) {
 509             if (fieldUnitDTO != null) {
 510                 fieldUnitDTO.setHasType(true);
 511             }
 512             TypeDesignationStatusBase<?> typeStatus = specimenTypeDesignation.getTypeStatus();
 513             if (typeStatus != null) {
 514                 List<String> typedTaxaNames = new ArrayList<String>();
 515                 String label = typeStatus.getLabel();
 516                 Set<TaxonNameBase> typifiedNames = specimenTypeDesignation.getTypifiedNames();
 517                 for (TaxonNameBase taxonNameBase : typifiedNames) {
 518                     typedTaxaNames.add(taxonNameBase.getFullTitleCache());
 519                 }
 520                 preservedSpecimenDTO.addTypes(label, typedTaxaNames);
 521             }
 522         }
 523
 524         // individuals associations
 525         Collection<IndividualsAssociation> individualsAssociations = listIndividualsAssociations(derivedUnit, null, null, null, null);
 526         for (IndividualsAssociation individualsAssociation : individualsAssociations) {
 527             if (individualsAssociation.getInDescription() != null) {
 528                 if (individualsAssociation.getInDescription().isInstanceOf(TaxonDescription.class)) {
 529                     TaxonDescription taxonDescription = HibernateProxyHelper.deproxy(individualsAssociation.getInDescription(), TaxonDescription.class);
 530                     Taxon taxon = taxonDescription.getTaxon();
 531                     if (taxon != null && taxon.getName() != null) {
 532                         preservedSpecimenDTO.addAssociatedTaxon(taxon.getName().getTitleCache());
 533                     }
 534                 }
 535             }
 536         }
 537         // assemble sub derivates
 538         preservedSpecimenDTO.setDerivateDataDTO(assembleDerivateDataDTO(preservedSpecimenDTO, derivedUnit));
 539         return preservedSpecimenDTO;
 540     }
 541
 542     private DerivateDataDTO assembleDerivateDataDTO(DerivateDTO derivateDTO, SpecimenOrObservationBase<?> specimenOrObservation) {
 543         DerivateDataDTO derivateDataDTO = new DerivateDataDTO();
 544         Collection<DerivedUnit> childDerivates = getDerivedUnitsFor(specimenOrObservation);
 545         for (DerivedUnit childDerivate : childDerivates) {
 546             // assemble molecular data
 547             //pattern: DNAMarker [contig1, primer1_1, primer1_2, ...][contig2, primer2_1, ...]...
 548             if (childDerivate.isInstanceOf(DnaSample.class)) {
 549                 if (childDerivate.getRecordBasis() == SpecimenOrObservationType.TissueSample) {
 550                     // TODO implement TissueSample assembly for web service
 551                 }
 552                 if (childDerivate.getRecordBasis() == SpecimenOrObservationType.DnaSample) {
 553
 554                     DnaSample dna = HibernateProxyHelper.deproxy(childDerivate, DnaSample.class);
 555                     if (!dna.getSequences().isEmpty()) {
 556                         derivateDTO.setHasDna(true);
 557                     }
 558                     for (Sequence sequence : dna.getSequences()) {
 559                         URI boldUri = null;
 560                         try {
 561                             boldUri = sequence.getBoldUri();
 562                         } catch (URISyntaxException e1) {
 563                             logger.error("Could not create BOLD URI", e1);
 564                         }
 565                         final DefinedTerm dnaMarker = sequence.getDnaMarker();
 566                         MolecularData molecularData = derivateDataDTO.addProviderLink(boldUri != null ? boldUri : null, dnaMarker != null ? dnaMarker.getLabel() : "[no marker]");
 567
 568                         //contig file
 569                         ContigFile contigFile = null;
 570                         if (sequence.getContigFile() != null) {
 571                             MediaRepresentationPart contigMediaRepresentationPart = MediaUtils.getFirstMediaRepresentationPart(sequence.getContigFile());
 572                             if (contigMediaRepresentationPart != null) {
 573                                 contigFile = molecularData.addContigFile(contigMediaRepresentationPart.getUri(), "contig");
 574                             }
 575                         }
 576                         if(contigFile==null){
 577                             contigFile = molecularData.addContigFile(null, "[no contig]");
 578                         }
 579                         // primer files
 580                         if (sequence.getSingleReads() != null) {
 581                             int readCount = 1;
 582                             for (SingleRead singleRead : sequence.getSingleReads()) {
 583                                 MediaRepresentationPart pherogramMediaRepresentationPart = MediaUtils.getFirstMediaRepresentationPart(singleRead.getPherogram());
 584                                 if (pherogramMediaRepresentationPart != null) {
 585                                     contigFile.addPrimerLink(pherogramMediaRepresentationPart.getUri(), "read"+readCount++);
 586                                 }
 587                             }
 588                         }
 589                     }
 590                 }
 591             }
 592             // assemble media data
 593             else if (childDerivate.isInstanceOf(MediaSpecimen.class)) {
 594                 MediaSpecimen media = HibernateProxyHelper.deproxy(childDerivate, MediaSpecimen.class);
 595
 596                 String mediaUriString = getMediaUriString(media);
 597                 if (media.getKindOfUnit() != null) {
 598                     // specimen scan
 599                     if (media.getKindOfUnit().getUuid().equals(UUID.fromString("acda15be-c0e2-4ea8-8783-b9b0c4ad7f03"))) {
 600                         derivateDataDTO.addSpecimenScanUuid(media.getMediaSpecimen().getUuid());
 601                         derivateDTO.setHasSpecimenScan(true);
 602                         String imageLinkText = "scan";
 603                         if (derivateDTO instanceof PreservedSpecimenDTO && ((PreservedSpecimenDTO) derivateDTO).getAccessionNumber() != null) {
 604                             imageLinkText = ((PreservedSpecimenDTO) derivateDTO).getAccessionNumber();
 605                         }
 606                         derivateDataDTO.addSpecimenScan(mediaUriString == null ? "" : mediaUriString, imageLinkText);
 607                     }
 608                     // detail image
 609                     else if (media.getKindOfUnit().getUuid().equals(UUID.fromString("31eb8d02-bf5d-437c-bcc6-87a626445f34"))) {
 610                         derivateDataDTO.addDetailImageUuid(media.getMediaSpecimen().getUuid());
 611                         derivateDTO.setHasDetailImage(true);
 612                         String motif = "";
 613                         if (media.getMediaSpecimen() != null && media.getMediaSpecimen().getTitle() != null) {
 614                             motif = media.getMediaSpecimen().getTitle().getText();
 615                         }
 616                         derivateDataDTO.addDetailImage(mediaUriString == null ? "" : mediaUriString, motif != null ? motif : "[no motif]");
 617                     }
 618                 }
 619             }
 620         }
 621         return derivateDataDTO;
 622     }
 623
 624     private String removeTail(String string, final String tail) {
 625         if (string.endsWith(tail)) {
 626             string = string.substring(0, string.length() - tail.length());
 627         }
 628         return string;
 629     }
 630
 631     private String getMediaUriString(MediaSpecimen mediaSpecimen) {
 632         String mediaUri = null;
 633         Collection<MediaRepresentation> mediaRepresentations = mediaSpecimen.getMediaSpecimen().getRepresentations();
 634         if (mediaRepresentations != null && !mediaRepresentations.isEmpty()) {
 635             Collection<MediaRepresentationPart> mediaRepresentationParts = mediaRepresentations.iterator().next().getParts();
 636             if (mediaRepresentationParts != null && !mediaRepresentationParts.isEmpty()) {
 637                 MediaRepresentationPart part = mediaRepresentationParts.iterator().next();
 638                 if (part.getUri() != null) {
 639                     mediaUri = part.getUri().toASCIIString();
 640                 }
 641             }
 642         }
 643         return mediaUri;
 644     }
 645
 646     private Collection<DerivedUnit> getDerivedUnitsFor(SpecimenOrObservationBase<?> specimen) {
 647         Collection<DerivedUnit> derivedUnits = new ArrayList<DerivedUnit>();
 648         for (DerivationEvent derivationEvent : specimen.getDerivationEvents()) {
 649             for (DerivedUnit derivative : derivationEvent.getDerivatives()) {
 650                 derivedUnits.add(derivative);
 651                 derivedUnits.addAll(getDerivedUnitsFor(derivative));
 652             }
 653         }
 654         return derivedUnits;
 655     }
 656
 657
 658     @SuppressWarnings("unchecked")
 659     @Override
 660     public <T extends SpecimenOrObservationBase> Pager<T> pageByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
 661             Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 662
 663         Set<Taxon> taxa = new HashSet<Taxon>();
 664         Set<Integer> occurrenceIds = new HashSet<Integer>();
 665         List<T> occurrences = new ArrayList<T>();
 666
 667         // Integer limit = PagerUtils.limitFor(pageSize);
 668         // Integer start = PagerUtils.startFor(pageSize, pageNumber);
 669
 670         if (!getSession().contains(associatedTaxon)) {
 671             associatedTaxon = (Taxon) taxonService.load(associatedTaxon.getUuid());
 672         }
 673
 674         if (includeRelationships != null) {
 675             taxa = taxonService.listRelatedTaxa(associatedTaxon, includeRelationships, maxDepth, null, null, propertyPaths);
 676         }
 677
 678         taxa.add(associatedTaxon);
 679
 680         for (Taxon taxon : taxa) {
 681             List<T> perTaxonOccurrences = dao.listByAssociatedTaxon(type, taxon, null, null, orderHints, propertyPaths);
 682             for (SpecimenOrObservationBase o : perTaxonOccurrences) {
 683                 occurrenceIds.add(o.getId());
 684             }
 685         }
 686         occurrences = (List<T>) dao.listByIds(occurrenceIds, pageSize, pageNumber, orderHints, propertyPaths);
 687
 688         return new DefaultPagerImpl<T>(pageNumber, occurrenceIds.size(), pageSize, occurrences);
 689
 690     }
 691
 692     @Override
 693     public <T extends SpecimenOrObservationBase> Pager<T> pageByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
 694             String taxonUUID, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 695
 696         UUID uuid = UUID.fromString(taxonUUID);
 697         Taxon tax = (Taxon) taxonService.load(uuid);
 698         // TODO REMOVE NULL STATEMENT
 699         type = null;
 700         return pageByAssociatedTaxon(type, includeRelationships, tax, maxDepth, pageSize, pageNumber, orderHints, propertyPaths);
 701
 702     }
 703
 704     @Override
 705     public Pager<SearchResult<SpecimenOrObservationBase>> findByFullText(
 706             Class<? extends SpecimenOrObservationBase> clazz, String queryString, Rectangle boundingBox, List<Language> languages,
 707             boolean highlightFragments, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
 708             List<String> propertyPaths) throws CorruptIndexException, IOException, ParseException {
 709
 710         LuceneSearch luceneSearch = prepareByFullTextSearch(clazz, queryString, boundingBox, languages, highlightFragments);
 711
 712         // --- execute search
 713         TopGroupsWithMaxScore topDocsResultSet = luceneSearch.executeSearch(pageSize, pageNumber);
 714
 715         Map<CdmBaseType, String> idFieldMap = new HashMap<CdmBaseType, String>();
 716         idFieldMap.put(CdmBaseType.SPECIMEN_OR_OBSERVATIONBASE, "id");
 717
 718         // --- initialize taxa, highlight matches ....
 719         ISearchResultBuilder searchResultBuilder = new SearchResultBuilder(luceneSearch, luceneSearch.getQuery());
 720         @SuppressWarnings("rawtypes")
 721         List<SearchResult<SpecimenOrObservationBase>> searchResults = searchResultBuilder.createResultSet(
 722                 topDocsResultSet, luceneSearch.getHighlightFields(), dao, idFieldMap, propertyPaths);
 723
 724         int totalHits = topDocsResultSet != null ? topDocsResultSet.topGroups.totalGroupCount : 0;
 725
 726         return new DefaultPagerImpl<SearchResult<SpecimenOrObservationBase>>(pageNumber, totalHits, pageSize,
 727                 searchResults);
 728
 729     }
 730
 731     private LuceneSearch prepareByFullTextSearch(Class<? extends SpecimenOrObservationBase> clazz, String queryString, Rectangle bbox,
 732             List<Language> languages, boolean highlightFragments) {
 733
 734         BooleanQuery finalQuery = new BooleanQuery();
 735         BooleanQuery textQuery = new BooleanQuery();
 736
 737         LuceneSearch luceneSearch = new LuceneSearch(luceneIndexToolProvider, FieldUnit.class);
 738         QueryFactory queryFactory = luceneIndexToolProvider.newQueryFactoryFor(FieldUnit.class);
 739
 740         // --- criteria
 741         luceneSearch.setCdmTypRestriction(clazz);
 742         if (queryString != null) {
 743             textQuery.add(queryFactory.newTermQuery("titleCache", queryString), Occur.SHOULD);
 744             finalQuery.add(textQuery, Occur.MUST);
 745         }
 746
 747         // --- spacial query
 748         if (bbox != null) {
 749             finalQuery.add(QueryFactory.buildSpatialQueryByRange(bbox, "gatheringEvent.exactLocation.point"), Occur.MUST);
 750         }
 751
 752         luceneSearch.setQuery(finalQuery);
 753
 754         // --- sorting
 755         SortField[] sortFields = new SortField[] { SortField.FIELD_SCORE, new SortField("titleCache__sort", SortField.STRING, false) };
 756         luceneSearch.setSortFields(sortFields);
 757
 758         if (highlightFragments) {
 759             luceneSearch.setHighlightFields(queryFactory.getTextFieldNamesAsArray());
 760         }
 761         return luceneSearch;
 762     }
 763
 764
 765     @Override
 766     public Collection<FieldUnit> getFieldUnits(UUID derivedUnitUuid) {
 767         //It will search recursively over all {@link DerivationEvent}s and get the "originals" ({@link SpecimenOrObservationBase})
 768         //from which this DerivedUnit was derived until all FieldUnits are found.
 769
 770         // FIXME: use HQL queries to increase performance
 771         SpecimenOrObservationBase<?> specimen = load(derivedUnitUuid);
 772 //        specimen = HibernateProxyHelper.deproxy(specimen, SpecimenOrObservationBase.class);
 773         Collection<FieldUnit> fieldUnits = new ArrayList<FieldUnit>();
 774
 775         if (specimen.isInstanceOf(FieldUnit.class)) {
 776             fieldUnits.add(HibernateProxyHelper.deproxy(specimen, FieldUnit.class));
 777         }
 778         else if(specimen.isInstanceOf(DerivedUnit.class)){
 779             fieldUnits.addAll(getFieldUnits(HibernateProxyHelper.deproxy(specimen, DerivedUnit.class)));
 780         }
 781         return fieldUnits;
 782     }
 783
 784     private Collection<FieldUnit> getFieldUnits(DerivedUnit derivedUnit) {
 785         Collection<FieldUnit> fieldUnits = new HashSet<FieldUnit>();
 786         Set<SpecimenOrObservationBase> originals = derivedUnit.getOriginals();
 787         if (originals != null && !originals.isEmpty()) {
 788             for (SpecimenOrObservationBase<?> original : originals) {
 789                 if (original.isInstanceOf(FieldUnit.class)) {
 790                     fieldUnits.add(HibernateProxyHelper.deproxy(original, FieldUnit.class));
 791                 }
 792                 else if(original.isInstanceOf(DerivedUnit.class)){
 793                     fieldUnits.addAll(getFieldUnits(HibernateProxyHelper.deproxy(original, DerivedUnit.class)));
 794                 }
 795             }
 796         }
 797         return fieldUnits;
 798     }
 799
 800     @Override
 801     public boolean moveSequence(DnaSample from, DnaSample to, Sequence sequence) {
 802         // reload specimens to avoid session conflicts
 803         from = (DnaSample) load(from.getUuid());
 804         to = (DnaSample) load(to.getUuid());
 805         sequence = sequenceService.load(sequence.getUuid());
 806
 807         if (from == null || to == null || sequence == null) {
 808             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" +
 809                     "Operation was move "+sequence+ " from "+from+" to "+to);
 810         }
 811         from.removeSequence(sequence);
 812         saveOrUpdate(from);
 813         to.addSequence(sequence);
 814         saveOrUpdate(to);
 815         return true;
 816     }
 817
 818     @Override
 819     public boolean moveDerivate(SpecimenOrObservationBase<?> from, SpecimenOrObservationBase<?> to, DerivedUnit derivate) {
 820         // reload specimens to avoid session conflicts
 821         from = load(from.getUuid());
 822         to = load(to.getUuid());
 823         derivate = (DerivedUnit) load(derivate.getUuid());
 824
 825         if (from == null || to == null || derivate == null) {
 826             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" +
 827                         "Operation was move "+derivate+ " from "+from+" to "+to);
 828         }
 829
 830         SpecimenOrObservationType derivateType = derivate.getRecordBasis();
 831         SpecimenOrObservationType toType = to.getRecordBasis();
 832         // check if type is a sub derivate type
 833         if(toType==SpecimenOrObservationType.FieldUnit //moving to FieldUnit always works
 834                 || derivateType==SpecimenOrObservationType.Media //moving media always works
 835                 || (derivateType.isKindOf(toType) && toType!=derivateType)){ //moving only to parent derivate type
 836             // remove derivation event from parent specimen of dragged object
 837             DerivationEvent eventToRemove = null;
 838             for (DerivationEvent event : from.getDerivationEvents()) {
 839                 if (event.getDerivatives().contains(derivate)) {
 840                     eventToRemove = event;
 841                     break;
 842                 }
 843             }
 844             from.removeDerivationEvent(eventToRemove);
 845             if(eventToRemove!=null){
 846                 // add new derivation event to target and copy the event parameters of the old one
 847                 DerivationEvent derivedFromNewOriginalEvent = DerivationEvent.NewSimpleInstance(to, derivate, null);
 848                 derivedFromNewOriginalEvent.setActor(eventToRemove.getActor());
 849                 derivedFromNewOriginalEvent.setDescription(eventToRemove.getDescription());
 850                 derivedFromNewOriginalEvent.setInstitution(eventToRemove.getInstitution());
 851                 derivedFromNewOriginalEvent.setTimeperiod(eventToRemove.getTimeperiod());
 852                 derivedFromNewOriginalEvent.setType(eventToRemove.getType());
 853                 to.addDerivationEvent(derivedFromNewOriginalEvent);
 854                 derivate.setDerivedFrom(derivedFromNewOriginalEvent);
 855             }
 856
 857             saveOrUpdate(from);
 858             saveOrUpdate(to);
 859             return true;
 860         }
 861         return false;
 862     }
 863
 864     @Override
 865     public Collection<ICdmBase> getNonCascadedAssociatedElements(SpecimenOrObservationBase<?> specimen) {
 866         // potential fields that are not persisted cascadingly
 867         /*
 868          * SOOB
 869         -DescriptionBase
 870         -determinations
 871         --modifier TERM
 872         -kindOfUnit TERM
 873         -lifeStage TERM
 874         -sex TERM
 875
 876         FieldUnit
 877         -GatheringEvent
 878         --Country TERM
 879         --CollectingAreas TERM
 880
 881         DerivedUnit
 882         -collection
 883         --institute
 884         ---types TERM
 885         -preservationMethod
 886         --medium TERM
 887         -storedUnder CDM TaxonNameBase
 888          */
 889
 890         Collection<ICdmBase> nonCascadedCdmEntities = new HashSet<ICdmBase>();
 891
 892         //Choose the correct entry point to traverse the graph (FieldUnit or DerivedUnit)
 893
 894         // FieldUnit
 895         if (specimen.isInstanceOf(FieldUnit.class)) {
 896             nonCascadedCdmEntities.addAll(getFieldUnitNonCascadedAssociatedElements(HibernateProxyHelper.deproxy(specimen, FieldUnit.class)));
 897         }
 898         // DerivedUnit
 899         else if (specimen.isInstanceOf(DerivedUnit.class)) {
 900             DerivedUnit derivedUnit = HibernateProxyHelper.deproxy(specimen, DerivedUnit.class);
 901             if (derivedUnit.getDerivedFrom() != null) {
 902                 Collection<FieldUnit> fieldUnits = getFieldUnits(derivedUnit);
 903                 for (FieldUnit fieldUnit : fieldUnits) {
 904                     nonCascadedCdmEntities.addAll(getFieldUnitNonCascadedAssociatedElements(fieldUnit));
 905                 }
 906             }
 907         }
 908         return nonCascadedCdmEntities;
 909     }
 910
 911     private Collection<ICdmBase> getFieldUnitNonCascadedAssociatedElements(FieldUnit fieldUnit) {
 912         // get non cascaded element on SpecimenOrObservationBase level
 913         Collection<ICdmBase> nonCascadedCdmEntities = getSpecimenOrObservationNonCascadedAssociatedElements(fieldUnit);
 914
 915         // get FieldUnit specific elements
 916         GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
 917         if (gatheringEvent != null) {
 918             // country
 919             if (gatheringEvent.getCountry() != null) {
 920                 nonCascadedCdmEntities.add(gatheringEvent.getCountry());
 921             }
 922             // collecting areas
 923             for (NamedArea namedArea : gatheringEvent.getCollectingAreas()) {
 924                 nonCascadedCdmEntities.add(namedArea);
 925             }
 926         }
 927         for (DerivationEvent derivationEvent : fieldUnit.getDerivationEvents()) {
 928             for (DerivedUnit derivedUnit : derivationEvent.getDerivatives()) {
 929                 nonCascadedCdmEntities.addAll(getDerivedUnitNonCascadedAssociatedElements(derivedUnit));
 930             }
 931         }
 932         return nonCascadedCdmEntities;
 933     }
 934
 935     private Collection<ICdmBase> getDerivedUnitNonCascadedAssociatedElements(DerivedUnit derivedUnit) {
 936         // get non cascaded element on SpecimenOrObservationBase level
 937         Collection<ICdmBase> nonCascadedCdmEntities = getSpecimenOrObservationNonCascadedAssociatedElements(derivedUnit);
 938
 939         // get DerivedUnit specific elements
 940         if (derivedUnit.getCollection() != null && derivedUnit.getCollection().getInstitute() != null) {
 941             for (DefinedTerm type : derivedUnit.getCollection().getInstitute().getTypes()) {
 942                 nonCascadedCdmEntities.add(type);
 943             }
 944         }
 945         if (derivedUnit.getPreservation() != null && derivedUnit.getPreservation().getMedium() != null) {
 946             nonCascadedCdmEntities.add(derivedUnit.getPreservation().getMedium());
 947         }
 948         if (derivedUnit.getStoredUnder() != null) {
 949             nonCascadedCdmEntities.add(derivedUnit.getStoredUnder());
 950         }
 951         return nonCascadedCdmEntities;
 952     }
 953
 954     private Collection<ICdmBase> getSpecimenOrObservationNonCascadedAssociatedElements(
 955             SpecimenOrObservationBase<?> specimen) {
 956         Collection<ICdmBase> nonCascadedCdmEntities = new HashSet<ICdmBase>();
 957         // scan SpecimenOrObservationBase
 958         for (DeterminationEvent determinationEvent : specimen.getDeterminations()) {
 959             // modifier
 960             if (determinationEvent.getModifier() != null) {
 961                 nonCascadedCdmEntities.add(determinationEvent.getModifier());
 962             }
 963         }
 964         // kindOfUnit
 965         if (specimen.getKindOfUnit() != null) {
 966             nonCascadedCdmEntities.add(specimen.getKindOfUnit());
 967         }
 968         // lifeStage
 969         if (specimen.getLifeStage() != null) {
 970             nonCascadedCdmEntities.add(specimen.getLifeStage());
 971         }
 972         // sex
 973         if (specimen.getSex() != null) {
 974             nonCascadedCdmEntities.add(specimen.getSex());
 975         }
 976         return nonCascadedCdmEntities;
 977     }
 978
 979     @Override
 980     public DeleteResult isDeletable(SpecimenOrObservationBase specimen, DeleteConfiguratorBase config) {
 981         DeleteResult deleteResult = new DeleteResult();
 982         SpecimenDeleteConfigurator specimenDeleteConfigurator = (SpecimenDeleteConfigurator) config;
 983
 984         // check elements found by super method
 985         Set<CdmBase> relatedObjects = super.isDeletable(specimen, config).getRelatedObjects();
 986         for (CdmBase cdmBase : relatedObjects) {
 987             // check for type designation
 988             if (cdmBase.isInstanceOf(SpecimenTypeDesignation.class) && !specimenDeleteConfigurator.isDeleteFromTypeDesignation()) {
 989                 deleteResult.setAbort();
 990                 deleteResult.addException(new ReferencedObjectUndeletableException("Specimen is a type specimen."));
 991                 deleteResult.addRelatedObject(cdmBase);
 992                 break;
 993             }
 994             // check for IndividualsAssociations
 995             else if (cdmBase.isInstanceOf(IndividualsAssociation.class) && !specimenDeleteConfigurator.isDeleteFromIndividualsAssociation()) {
 996                 deleteResult.setAbort();
 997                 deleteResult.addException(new ReferencedObjectUndeletableException("Specimen is still associated via IndividualsAssociations"));
 998                 deleteResult.addRelatedObject(cdmBase);
 999                 break;
1000             }
1001             // check for specimen/taxon description
1002             else if((cdmBase.isInstanceOf(SpecimenDescription.class) || cdmBase.isInstanceOf(TaxonDescription.class))
1003                     && !specimenDeleteConfigurator.isDeleteFromDescription()){
1004                 deleteResult.setAbort();
1005                 deleteResult.addException(new ReferencedObjectUndeletableException("Specimen is still used in a Description."));
1006                 deleteResult.addRelatedObject(cdmBase);
1007                 break;
1008             }
1009             // check for children and parents (derivation events)
1010             else if (cdmBase.isInstanceOf(DerivationEvent.class)) {
1011                 DerivationEvent derivationEvent = HibernateProxyHelper.deproxy(cdmBase, DerivationEvent.class);
1012                 // check if derivation event is empty
1013                 if (!derivationEvent.getDerivatives().isEmpty()) {
1014                     if (derivationEvent.getDerivatives().size() == 1 && derivationEvent.getDerivatives().contains(specimen)) {
1015                         //if it is the parent event with only one derivate then the specimen is still deletable
1016                         continue;
1017                     }
1018                     else if(!specimenDeleteConfigurator.isDeleteChildren()){
1019                         //if not and children should not be deleted then it is undeletable
1020                         deleteResult.setAbort();
1021                         deleteResult.addException(new ReferencedObjectUndeletableException("Derivative still has child derivatives."));
1022                         deleteResult.addRelatedObject(cdmBase);
1023                         break;
1024                     }
1025                     else{
1026                         // check all children if they can be deleted
1027                         Set<DerivedUnit> derivatives = derivationEvent.getDerivatives();
1028                         DeleteResult childResult = new DeleteResult();
1029                         for (DerivedUnit derivedUnit : derivatives) {
1030                             childResult.includeResult(isDeletable(derivedUnit, specimenDeleteConfigurator));
1031                         }
1032                         if (!childResult.isOk()) {
1033                             deleteResult.setAbort();
1034                             deleteResult.includeResult(childResult);
1035                             deleteResult.addRelatedObject(cdmBase);
1036                             break;
1037                         }
1038                     }
1039                 }
1040             }
1041             // check for amplification
1042             else if (cdmBase.isInstanceOf(AmplificationResult.class) && !specimenDeleteConfigurator.isDeleteMolecularData()) {
1043                 deleteResult.setAbort();
1044                 deleteResult.addException(new ReferencedObjectUndeletableException("DnaSample is used in amplification results."));
1045                 deleteResult.addRelatedObject(cdmBase);
1046                 break;
1047             }
1048             // check for sequence
1049             else if (cdmBase.isInstanceOf(Sequence.class) && !specimenDeleteConfigurator.isDeleteMolecularData()) {
1050                 deleteResult.setAbort();
1051                 deleteResult.addException(new ReferencedObjectUndeletableException("DnaSample is used in sequences."));
1052                 deleteResult.addRelatedObject(cdmBase);
1053                 break;
1054             }
1055         }
1056         if (deleteResult.isOk()) {
1057             //add all related object if deletion is OK so they can be handled by the delete() method
1058             deleteResult.addRelatedObjects(relatedObjects);
1059         }
1060         return deleteResult;
1061     }
1062
1063     @Override
1064     public DeleteResult delete(SpecimenOrObservationBase<?> specimen, SpecimenDeleteConfigurator config) {
1065         specimen = HibernateProxyHelper.deproxy(specimen, SpecimenOrObservationBase.class);
1066
1067         if (config.isDeleteChildren()) {
1068             Set<DerivationEvent> derivationEvents = specimen.getDerivationEvents();
1069             for (DerivationEvent derivationEvent : derivationEvents) {
1070                 Set<DerivedUnit> derivatives = derivationEvent.getDerivatives();
1071                 for (DerivedUnit derivedUnit : derivatives) {
1072                     delete(derivedUnit, config);
1073                 }
1074             }
1075         }
1076
1077         DeleteResult deleteResult = isDeletable(specimen, config);
1078         if (!deleteResult.isOk()) {
1079             return deleteResult;
1080         }
1081
1082         // check related objects
1083         Set<CdmBase> relatedObjects = deleteResult.getRelatedObjects();
1084
1085         for (CdmBase relatedObject : relatedObjects) {
1086             // check for TypeDesignations
1087             if (relatedObject.isInstanceOf(SpecimenTypeDesignation.class)) {
1088                 SpecimenTypeDesignation designation = HibernateProxyHelper.deproxy(relatedObject, SpecimenTypeDesignation.class);
1089                 designation.setTypeSpecimen(null);
1090                 Set<TaxonNameBase> typifiedNames = designation.getTypifiedNames();
1091                 for (TaxonNameBase taxonNameBase : typifiedNames) {
1092                     taxonNameBase.removeTypeDesignation(designation);
1093                 }
1094             }
1095             // delete IndividualsAssociation
1096             if (relatedObject.isInstanceOf(IndividualsAssociation.class)) {
1097                 IndividualsAssociation assciation = HibernateProxyHelper.deproxy(relatedObject, IndividualsAssociation.class);
1098                 assciation.setAssociatedSpecimenOrObservation(null);
1099                 assciation.getInDescription().removeElement(assciation);
1100             }
1101             // check for taxon description
1102             if (relatedObject.isInstanceOf(TaxonDescription.class)) {
1103                 TaxonDescription taxonDescription = HibernateProxyHelper.deproxy(relatedObject, TaxonDescription.class);
1104                 taxonDescription.setDescribedSpecimenOrObservation(null);
1105             }
1106             // check for specimen description
1107             if (relatedObject.isInstanceOf(SpecimenDescription.class)) {
1108                 SpecimenDescription specimenDescription = HibernateProxyHelper.deproxy(relatedObject, SpecimenDescription.class);
1109                 // check if specimen is "described" specimen
1110                 if (specimenDescription.getDescribedSpecimenOrObservation().equals(specimen)) {
1111                     specimenDescription.setDescribedSpecimenOrObservation(null);
1112                 }
1113                 // check if description is a description of the given specimen
1114                 if (specimen.getDescriptions().contains(specimenDescription)) {
1115                     specimen.removeDescription(specimenDescription);
1116                 }
1117             }
1118             // check for amplification
1119             if (relatedObject.isInstanceOf(AmplificationResult.class)) {
1120                 AmplificationResult amplificationResult = HibernateProxyHelper.deproxy(relatedObject, AmplificationResult.class);
1121                 amplificationResult.getDnaSample().removeAmplificationResult(amplificationResult);
1122             }
1123             // check for sequence
1124             if (relatedObject.isInstanceOf(Sequence.class)) {
1125                 Sequence sequence = HibernateProxyHelper.deproxy(relatedObject, Sequence.class);
1126                 sequence.getDnaSample().removeSequence(sequence);
1127             }
1128             // check for children and parents (derivation events)
1129             if (relatedObject.isInstanceOf(DerivationEvent.class)) {
1130                 DerivationEvent derivationEvent = HibernateProxyHelper.deproxy(relatedObject, DerivationEvent.class);
1131                 // parent derivation event (derivedFrom)
1132                 if (derivationEvent.getDerivatives().contains(specimen) && specimen.isInstanceOf(DerivedUnit.class)) {
1133                     derivationEvent.removeDerivative(HibernateProxyHelper.deproxy(specimen, DerivedUnit.class));
1134                     if (derivationEvent.getDerivatives().isEmpty()) {
1135                         Set<SpecimenOrObservationBase> originals = derivationEvent.getOriginals();
1136                         for (SpecimenOrObservationBase specimenOrObservationBase : originals) {
1137                             specimenOrObservationBase.removeDerivationEvent(derivationEvent);
1138                         }
1139                     }
1140                 }
1141                 else{
1142                     //child derivation events should not occur since we delete the hierarchy from bottom to top
1143                 }
1144             }
1145         }
1146
1147         deleteResult.includeResult(delete(specimen));
1148         return deleteResult;
1149     }
1150
1151     @Override
1152     public DeleteResult deleteSingleRead(SingleRead singleRead, Sequence sequence){
1153         DeleteResult deleteResult = new DeleteResult();
1154         singleRead = HibernateProxyHelper.deproxy(singleRead, SingleRead.class);
1155         //delete from amplification result
1156         if(singleRead.getAmplificationResult()!=null){
1157             singleRead.getAmplificationResult().removeSingleRead(singleRead);
1158         }
1159         //delete from sequence
1160         sequence.removeSingleRead(singleRead);
1161         deleteResult.setStatus(Status.OK);
1162         return deleteResult;
1163     }
1164
1165     @Override
1166     public DeleteResult deleteDerivateHierarchy(CdmBase from, SpecimenDeleteConfigurator config) {
1167         DeleteResult deleteResult = new DeleteResult();
1168         String deleteMolecularNotAllowed = "Deleting molecular data is not allowed in config";
1169         if (from.isInstanceOf(Sequence.class)) {
1170             if (!config.isDeleteMolecularData()) {
1171                 deleteResult.setAbort();
1172                 deleteResult.addException(new ReferencedObjectUndeletableException(deleteMolecularNotAllowed));
1173                 return deleteResult;
1174             }
1175             Sequence sequence = HibernateProxyHelper.deproxy(from, Sequence.class);
1176             sequence.getDnaSample().removeSequence(sequence);
1177             deleteResult = sequenceService.delete(sequence);
1178         }
1179         else if(from instanceof SingleRead){
1180             SingleRead singleRead = (SingleRead)from;
1181             //delete from amplification result
1182             if(singleRead.getAmplificationResult()!=null){
1183                 singleRead.getAmplificationResult().removeSingleRead(singleRead);
1184             }
1185             deleteResult.setAbort();
1186             deleteResult.addException(new ReferencedObjectUndeletableException("Deleted ONLY from amplification. "
1187                     + "Single read may still be attached to a consensus sequence."));
1188         }
1189         else if(from.isInstanceOf(SpecimenOrObservationBase.class))  {
1190             deleteResult = delete(HibernateProxyHelper.deproxy(from, SpecimenOrObservationBase.class), config);
1191         }
1192         return deleteResult;
1193     }
1194
1195 //    private DeleteResult deepDelete(SpecimenOrObservationBase<?> entity, SpecimenDeleteConfigurator config){
1196     // Set<DerivationEvent> derivationEvents = entity.getDerivationEvents();
1197     // for (DerivationEvent derivationEvent : derivationEvents) {
1198     // Set<DerivedUnit> derivatives = derivationEvent.getDerivatives();
1199     // for (DerivedUnit derivedUnit : derivatives) {
1200     // DeleteResult deleteResult = deepDelete(derivedUnit, config);
1201     // if(!deleteResult.isOk()){
1202     // return deleteResult;
1203     // }
1204     // }
1205     // }
1206     // return delete(entity, config);
1207     // }
1208
1209     @Override
1210     public Collection<IndividualsAssociation> listIndividualsAssociations(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
1211         return dao.listIndividualsAssociations(specimen, null, null, null, null);
1212     }
1213
1214     @Override
1215     public Collection<SpecimenTypeDesignation> listTypeDesignations(SpecimenOrObservationBase<?> specimen,
1216             Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
1217         return dao.listTypeDesignations(specimen, limit, start, orderHints, propertyPaths);
1218     }
1219
1220     @Override
1221     public Collection<DescriptionBase<?>> listDescriptionsWithDescriptionSpecimen(
1222             SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints,
1223             List<String> propertyPaths) {
1224         return dao.listDescriptionsWithDescriptionSpecimen(specimen, limit, start, orderHints, propertyPaths);
1225     }
1226
1227     @Override
1228     public Collection<DescriptionElementBase> getCharacterDataForSpecimen(SpecimenOrObservationBase<?> specimen) {
1229         Collection<DescriptionElementBase> states = new ArrayList<DescriptionElementBase>();
1230         if (specimen != null) {
1231             Set<DescriptionBase> descriptions = specimen.getDescriptions();
1232             for (DescriptionBase<?> descriptionBase : descriptions) {
1233                 if (descriptionBase.isInstanceOf(SpecimenDescription.class)) {
1234                     SpecimenDescription specimenDescription = HibernateProxyHelper.deproxy(descriptionBase, SpecimenDescription.class);
1235                     Set<DescriptionElementBase> elements = specimenDescription.getElements();
1236                     for (DescriptionElementBase descriptionElementBase : elements) {
1237                         if(descriptionElementBase.getFeature().isSupportsCategoricalData()
1238                                 ||descriptionElementBase.getFeature().isSupportsQuantitativeData()){
1239                             states.add(descriptionElementBase);
1240                         }
1241                     }
1242                 }
1243             }
1244         }
1245         return states;
1246     }
1247
1248     @Override
1249     public Collection<DescriptionElementBase> getCharacterDataForSpecimen(UUID specimenUuid) {
1250         SpecimenOrObservationBase<?> specimen = load(specimenUuid);
1251         if (specimen != null) {
1252             return getCharacterDataForSpecimen(specimen);
1253         }
1254         else{
1255             throw new DataRetrievalFailureException("Specimen with the given uuid not found in the data base");
1256         }
1257     }
1258
1259
1260     @Override
1261     public Pager<SpecimenOrObservationBase> findByTitle(
1262             IIdentifiableEntityServiceConfigurator<SpecimenOrObservationBase> config) {
1263         if (config instanceof FindOccurrencesConfigurator) {
1264             FindOccurrencesConfigurator occurrenceConfig = (FindOccurrencesConfigurator) config;
1265             List<SpecimenOrObservationBase> occurrences = new ArrayList<SpecimenOrObservationBase>();
1266             Taxon taxon = null;
1267             if(occurrenceConfig.getAssociatedTaxonUuid()!=null){
1268                 TaxonBase taxonBase = taxonService.load(occurrenceConfig.getAssociatedTaxonUuid());
1269                 if(taxonBase.isInstanceOf(Taxon.class)){
1270                     taxon = HibernateProxyHelper.deproxy(taxonBase, Taxon.class);
1271                 }
1272             }
1273             occurrences.addAll(dao.findOccurrences(occurrenceConfig.getClazz(),
1274                     occurrenceConfig.getTitleSearchString(), occurrenceConfig.getSignificantIdentifier(),
1275                     occurrenceConfig.getSpecimenType(), taxon, occurrenceConfig.getMatchMode(), null, null,
1276                     occurrenceConfig.getOrderHints(), occurrenceConfig.getPropertyPaths()));
1277             // indirectly associated specimens
1278             List<SpecimenOrObservationBase> indirectlyAssociatedOccurrences = new ArrayList<SpecimenOrObservationBase>(occurrences);
1279             if(occurrenceConfig.isRetrieveIndirectlyAssociatedSpecimens()){
1280                 for (SpecimenOrObservationBase specimen : occurrences) {
1281                     List<SpecimenOrObservationBase<?>> allHierarchyDerivates = getAllHierarchyDerivatives(specimen);
1282                     for (SpecimenOrObservationBase<?> specimenOrObservationBase : allHierarchyDerivates) {
1283                         if(!occurrences.contains(specimenOrObservationBase)){
1284                             indirectlyAssociatedOccurrences.add(specimenOrObservationBase);
1285                         }
1286                     }
1287                 }
1288                 occurrences = indirectlyAssociatedOccurrences;
1289             }
1290
1291             return new DefaultPagerImpl<SpecimenOrObservationBase>(config.getPageNumber(), occurrences.size(), config.getPageSize(), occurrences);
1292         }
1293         return super.findByTitle(config);
1294     }
1295
1296     @Override
1297     public List<SpecimenOrObservationBase<?>> getAllHierarchyDerivatives(SpecimenOrObservationBase<?> specimen){
1298         List<SpecimenOrObservationBase<?>> allHierarchyDerivatives = new ArrayList<SpecimenOrObservationBase<?>>();
1299         Collection<FieldUnit> fieldUnits = getFieldUnits(specimen.getUuid());
1300         if(fieldUnits.isEmpty()){
1301             allHierarchyDerivatives.add(specimen);
1302             allHierarchyDerivatives.addAll(getAllChildDerivatives(specimen));
1303         }
1304         else{
1305             for (FieldUnit fieldUnit : fieldUnits) {
1306                 allHierarchyDerivatives.add(fieldUnit);
1307                 allHierarchyDerivatives.addAll(getAllChildDerivatives(fieldUnit));
1308             }
1309         }
1310         return allHierarchyDerivatives;
1311     }
1312
1313     @Override
1314     public List<DerivedUnit> getAllChildDerivatives(SpecimenOrObservationBase<?> specimen){
1315         List<DerivedUnit> childDerivate = new ArrayList<DerivedUnit>();
1316         Set<DerivationEvent> derivationEvents = specimen.getDerivationEvents();
1317         for (DerivationEvent derivationEvent : derivationEvents) {
1318             Set<DerivedUnit> derivatives = derivationEvent.getDerivatives();
1319             for (DerivedUnit derivedUnit : derivatives) {
1320                 childDerivate.add(derivedUnit);
1321                 childDerivate.addAll(getAllChildDerivatives(derivedUnit));
1322             }
1323         }
1324         return childDerivate;
1325     }
1326
1327     @Override
1328     public int countOccurrences(IIdentifiableEntityServiceConfigurator<SpecimenOrObservationBase> config){
1329         if (config instanceof FindOccurrencesConfigurator) {
1330             FindOccurrencesConfigurator occurrenceConfig = (FindOccurrencesConfigurator) config;
1331             Taxon taxon = null;
1332             if(occurrenceConfig.getAssociatedTaxonUuid()!=null){
1333                 TaxonBase taxonBase = taxonService.load(occurrenceConfig.getAssociatedTaxonUuid());
1334                 if(taxonBase.isInstanceOf(Taxon.class)){
1335                     taxon = HibernateProxyHelper.deproxy(taxonBase, Taxon.class);
1336                 }
1337             }
1338             // indirectly associated specimens
1339             if(occurrenceConfig.isRetrieveIndirectlyAssociatedSpecimens()){
1340                 return findByTitle(config).getRecords().size();
1341             }
1342             return dao.countOccurrences(occurrenceConfig.getClazz(), occurrenceConfig.getTitleSearchString(),
1343                     occurrenceConfig.getSignificantIdentifier(), occurrenceConfig.getSpecimenType(), taxon,
1344                     occurrenceConfig.getMatchMode(), null, null, occurrenceConfig.getOrderHints(),
1345                     occurrenceConfig.getPropertyPaths());
1346         }
1347         return super.countByTitle(config);
1348     }
1349
1350 }