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

   1 // $Id$
   2 /**
   3  * Copyright (C) 2007 EDIT
   4  * European Distributed Institute of Taxonomy
   5  * http://www.e-taxonomy.eu
   6  *
   7  * The contents of this file are subject to the Mozilla Public License Version 1.1
   8  * See LICENSE.TXT at the top of this package for the full license terms.
   9  */
  10
  11 package eu.etaxonomy.cdm.api.service;
  12
  13 import java.io.IOException;
  14 import java.net.URI;
  15 import java.net.URISyntaxException;
  16 import java.util.ArrayList;
  17 import java.util.Arrays;
  18 import java.util.Collection;
  19 import java.util.HashMap;
  20 import java.util.HashSet;
  21 import java.util.LinkedHashSet;
  22 import java.util.List;
  23 import java.util.Map;
  24 import java.util.Map.Entry;
  25 import java.util.Set;
  26 import java.util.UUID;
  27
  28 import org.apache.log4j.Logger;
  29 import org.apache.lucene.index.CorruptIndexException;
  30 import org.apache.lucene.queryParser.ParseException;
  31 import org.apache.lucene.search.BooleanClause.Occur;
  32 import org.apache.lucene.search.BooleanQuery;
  33 import org.apache.lucene.search.SortField;
  34 import org.hibernate.TransientObjectException;
  35 import org.hibernate.search.spatial.impl.Rectangle;
  36 import org.joda.time.Partial;
  37 import org.springframework.beans.factory.annotation.Autowired;
  38 import org.springframework.stereotype.Service;
  39 import org.springframework.transaction.annotation.Transactional;
  40
  41 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
  42 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeConfigurator;
  43 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeNotSupportedException;
  44 import eu.etaxonomy.cdm.api.service.dto.DerivateHierarchyDTO;
  45 import eu.etaxonomy.cdm.api.service.molecular.ISequenceService;
  46 import eu.etaxonomy.cdm.api.service.pager.Pager;
  47 import eu.etaxonomy.cdm.api.service.pager.impl.DefaultPagerImpl;
  48 import eu.etaxonomy.cdm.api.service.search.ILuceneIndexToolProvider;
  49 import eu.etaxonomy.cdm.api.service.search.ISearchResultBuilder;
  50 import eu.etaxonomy.cdm.api.service.search.LuceneSearch;
  51 import eu.etaxonomy.cdm.api.service.search.LuceneSearch.TopGroupsWithMaxScore;
  52 import eu.etaxonomy.cdm.api.service.search.QueryFactory;
  53 import eu.etaxonomy.cdm.api.service.search.SearchResult;
  54 import eu.etaxonomy.cdm.api.service.search.SearchResultBuilder;
  55 import eu.etaxonomy.cdm.api.service.util.TaxonRelationshipEdge;
  56 import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
  57 import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
  58 import eu.etaxonomy.cdm.model.CdmBaseType;
  59 import eu.etaxonomy.cdm.model.agent.AgentBase;
  60 import eu.etaxonomy.cdm.model.common.DefinedTerm;
  61 import eu.etaxonomy.cdm.model.common.DefinedTermBase;
  62 import eu.etaxonomy.cdm.model.common.ICdmBase;
  63 import eu.etaxonomy.cdm.model.common.Language;
  64 import eu.etaxonomy.cdm.model.common.UuidAndTitleCache;
  65 import eu.etaxonomy.cdm.model.description.DescriptionBase;
  66 import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
  67 import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
  68 import eu.etaxonomy.cdm.model.location.Country;
  69 import eu.etaxonomy.cdm.model.location.NamedArea;
  70 import eu.etaxonomy.cdm.model.media.Media;
  71 import eu.etaxonomy.cdm.model.media.MediaRepresentation;
  72 import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;
  73 import eu.etaxonomy.cdm.model.molecular.DnaSample;
  74 import eu.etaxonomy.cdm.model.molecular.Sequence;
  75 import eu.etaxonomy.cdm.model.molecular.SingleRead;
  76 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
  77 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  78 import eu.etaxonomy.cdm.model.name.TypeDesignationStatusBase;
  79 import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
  80 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  81 import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
  82 import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
  83 import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
  84 import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen;
  85 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  86 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
  87 import eu.etaxonomy.cdm.model.taxon.Taxon;
  88 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  89 import eu.etaxonomy.cdm.persistence.dao.common.IDefinedTermDao;
  90 import eu.etaxonomy.cdm.persistence.dao.initializer.AbstractBeanInitializer;
  91 import eu.etaxonomy.cdm.persistence.dao.occurrence.IOccurrenceDao;
  92 import eu.etaxonomy.cdm.persistence.query.OrderHint;
  93 import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
  94
  95 /**
  96  * @author a.babadshanjan
  97  * @created 01.09.2008
  98  */
  99 @Service
 100 @Transactional(readOnly = true)
 101 public class OccurrenceServiceImpl extends IdentifiableServiceBase<SpecimenOrObservationBase,IOccurrenceDao> implements IOccurrenceService {
 102
 103     static private final Logger logger = Logger.getLogger(OccurrenceServiceImpl.class);
 104
 105     @Autowired
 106     private IDefinedTermDao definedTermDao;
 107
 108     @Autowired
 109     private IDescriptionService descriptionService;
 110
 111     @Autowired
 112     private ITaxonService taxonService;
 113
 114     @Autowired
 115     private ITermService termService;
 116
 117     @Autowired
 118     private INameService nameService;
 119
 120     @Autowired
 121     private ISequenceService sequenceService;
 122
 123     @Autowired
 124     private AbstractBeanInitializer beanInitializer;
 125
 126     @Autowired
 127     private ILuceneIndexToolProvider luceneIndexToolProvider;
 128
 129
 130     public OccurrenceServiceImpl() {
 131         logger.debug("Load OccurrenceService Bean");
 132     }
 133
 134
 135     /* (non-Javadoc)
 136      * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#updateTitleCache(java.lang.Integer, eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy)
 137      */
 138     @Override
 139     @Transactional(readOnly = false)
 140     public void updateTitleCache(Class<? extends SpecimenOrObservationBase> clazz, Integer stepSize, IIdentifiableEntityCacheStrategy<SpecimenOrObservationBase> cacheStrategy, IProgressMonitor monitor) {
 141         if (clazz == null){
 142             clazz = SpecimenOrObservationBase.class;
 143         }
 144         super.updateTitleCacheImpl(clazz, stepSize, cacheStrategy, monitor);
 145     }
 146
 147
 148     /**
 149      * FIXME Candidate for harmonization
 150      * move to termService
 151      */
 152     @Override
 153     public Country getCountryByIso(String iso639) {
 154         return this.definedTermDao.getCountryByIso(iso639);
 155
 156     }
 157
 158     /**
 159      * FIXME Candidate for harmonization
 160      * move to termService
 161      */
 162     @Override
 163     public List<Country> getCountryByName(String name) {
 164         List<? extends DefinedTermBase> terms = this.definedTermDao.findByTitle(Country.class, name, null, null, null, null, null, null) ;
 165         List<Country> countries = new ArrayList<Country>();
 166         for (int i=0;i<terms.size();i++){
 167             countries.add((Country)terms.get(i));
 168         }
 169         return countries;
 170     }
 171
 172     @Override
 173     @Autowired
 174     protected void setDao(IOccurrenceDao dao) {
 175         this.dao = dao;
 176     }
 177
 178     @Override
 179     public Pager<DerivationEvent> getDerivationEvents(SpecimenOrObservationBase occurence, Integer pageSize,Integer pageNumber, List<String> propertyPaths) {
 180         Integer numberOfResults = dao.countDerivationEvents(occurence);
 181
 182         List<DerivationEvent> results = new ArrayList<DerivationEvent>();
 183         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 184             results = dao.getDerivationEvents(occurence, pageSize, pageNumber,propertyPaths);
 185         }
 186
 187         return new DefaultPagerImpl<DerivationEvent>(pageNumber, numberOfResults, pageSize, results);
 188     }
 189
 190     /* (non-Javadoc)
 191      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#countDeterminations(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase, eu.etaxonomy.cdm.model.taxon.TaxonBase)
 192      */
 193     @Override
 194     public int countDeterminations(SpecimenOrObservationBase occurence, TaxonBase taxonbase) {
 195         return dao.countDeterminations(occurence, taxonbase);
 196     }
 197
 198     @Override
 199     public Pager<DeterminationEvent> getDeterminations(SpecimenOrObservationBase occurrence, TaxonBase taxonBase, Integer pageSize,Integer pageNumber, List<String> propertyPaths) {
 200         Integer numberOfResults = dao.countDeterminations(occurrence, taxonBase);
 201
 202         List<DeterminationEvent> results = new ArrayList<DeterminationEvent>();
 203         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 204             results = dao.getDeterminations(occurrence,taxonBase, pageSize, pageNumber, propertyPaths);
 205         }
 206
 207         return new DefaultPagerImpl<DeterminationEvent>(pageNumber, numberOfResults, pageSize, results);
 208     }
 209
 210     @Override
 211     public Pager<Media> getMedia(SpecimenOrObservationBase occurence,Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
 212         Integer numberOfResults = dao.countMedia(occurence);
 213
 214         List<Media> results = new ArrayList<Media>();
 215         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 216             results = dao.getMedia(occurence, pageSize, pageNumber, propertyPaths);
 217         }
 218
 219         return new DefaultPagerImpl<Media>(pageNumber, numberOfResults, pageSize, results);
 220     }
 221
 222     /* (non-Javadoc)
 223      * @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)
 224      */
 225     @Override
 226     public Pager<SpecimenOrObservationBase> list(Class<? extends SpecimenOrObservationBase> type, TaxonBase determinedAs, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 227         Integer numberOfResults = dao.count(type,determinedAs);
 228         List<SpecimenOrObservationBase> results = new ArrayList<SpecimenOrObservationBase>();
 229         pageNumber = pageNumber == null ? 0 : pageNumber;
 230         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 231             Integer start = pageSize == null ? 0 : pageSize * pageNumber;
 232             results = dao.list(type,determinedAs, pageSize, start, orderHints,propertyPaths);
 233         }
 234         return new DefaultPagerImpl<SpecimenOrObservationBase>(pageNumber, numberOfResults, pageSize, results);
 235     }
 236
 237     @Override
 238     public List<UuidAndTitleCache<DerivedUnit>> getDerivedUnitUuidAndTitleCache() {
 239         return dao.getDerivedUnitUuidAndTitleCache();
 240     }
 241
 242     @Override
 243     public List<UuidAndTitleCache<FieldUnit>> getFieldUnitUuidAndTitleCache() {
 244         return dao.getFieldUnitUuidAndTitleCache();
 245     }
 246
 247     /* (non-Javadoc)
 248      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getDerivedUnitFacade(eu.etaxonomy.cdm.model.occurrence.DerivedUnit)
 249      */
 250     @Override
 251     public DerivedUnitFacade getDerivedUnitFacade(DerivedUnit derivedUnit, List<String> propertyPaths) throws DerivedUnitFacadeNotSupportedException {
 252         derivedUnit = (DerivedUnit)dao.load(derivedUnit.getUuid(), null);
 253         DerivedUnitFacadeConfigurator config = DerivedUnitFacadeConfigurator.NewInstance();
 254         config.setThrowExceptionForNonSpecimenPreservationMethodRequest(false);
 255         DerivedUnitFacade derivedUnitFacade = DerivedUnitFacade.NewInstance(derivedUnit, config);
 256         beanInitializer.initialize(derivedUnitFacade, propertyPaths);
 257         return derivedUnitFacade;
 258     }
 259
 260     /* (non-Javadoc)
 261      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#listDerivedUnitFacades(eu.etaxonomy.cdm.model.description.DescriptionBase, java.util.List)
 262      */
 263     @Override
 264     public List<DerivedUnitFacade> listDerivedUnitFacades(
 265             DescriptionBase description, List<String> propertyPaths) {
 266
 267         List<DerivedUnitFacade> derivedUnitFacadeList = new ArrayList<DerivedUnitFacade>();
 268         IndividualsAssociation tempIndividualsAssociation;
 269         SpecimenOrObservationBase tempSpecimenOrObservationBase;
 270         List<DescriptionElementBase> elements = descriptionService.listDescriptionElements(description, null, IndividualsAssociation.class, null, 0, Arrays.asList(new String []{"associatedSpecimenOrObservation"}));
 271         for(DescriptionElementBase element : elements){
 272             if(element instanceof IndividualsAssociation){
 273                 tempIndividualsAssociation = (IndividualsAssociation)element;
 274                 if(tempIndividualsAssociation.getAssociatedSpecimenOrObservation() != null){
 275                     tempSpecimenOrObservationBase = HibernateProxyHelper.deproxy(tempIndividualsAssociation.getAssociatedSpecimenOrObservation(), SpecimenOrObservationBase.class);
 276                     if(tempSpecimenOrObservationBase instanceof DerivedUnit){
 277                         try {
 278                             derivedUnitFacadeList.add(DerivedUnitFacade.NewInstance((DerivedUnit)tempSpecimenOrObservationBase));
 279                         } catch (DerivedUnitFacadeNotSupportedException e) {
 280                             logger.warn(tempIndividualsAssociation.getAssociatedSpecimenOrObservation().getTitleCache() + " : " +e.getMessage());
 281                         }
 282                     }
 283                 }
 284
 285             }
 286         }
 287
 288         beanInitializer.initializeAll(derivedUnitFacadeList, propertyPaths);
 289
 290         return derivedUnitFacadeList;
 291     }
 292
 293
 294     /* (non-Javadoc)
 295      * @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)
 296      */
 297     @Override
 298     public <T extends SpecimenOrObservationBase> List<T> listByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
 299             Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 300
 301         return pageByAssociatedTaxon(type, includeRelationships, associatedTaxon, maxDepth, pageSize, pageNumber, orderHints, propertyPaths).getRecords();
 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 Collection<FieldUnit> listFieldUnitsByAssociatedTaxon(Set<TaxonRelationshipEdge> includeRelationships,
 309             Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 310
 311         if(!getSession().contains(associatedTaxon)){
 312             associatedTaxon = (Taxon) taxonService.load(associatedTaxon.getUuid());
 313         }
 314
 315         Set<FieldUnit> fieldUnits = new HashSet<FieldUnit>();
 316
 317         List<SpecimenOrObservationBase> records = pageByAssociatedTaxon(null, includeRelationships, associatedTaxon, maxDepth, pageSize, pageNumber, orderHints, propertyPaths).getRecords();
 318         for(SpecimenOrObservationBase<?> specimen:records){
 319             fieldUnits.addAll(getFieldUnits(specimen.getUuid()));
 320         }
 321         return fieldUnits;
 322     }
 323
 324     @Override
 325     public DerivateHierarchyDTO assembleDerivateHierarchyDTO(FieldUnit fieldUnit, UUID associatedTaxonUuid){
 326
 327         if(!getSession().contains(fieldUnit)){
 328             fieldUnit = (FieldUnit) load(fieldUnit.getUuid());
 329         }
 330         TaxonBase associatedTaxon = taxonService.load(associatedTaxonUuid);
 331
 332         DerivateHierarchyDTO dto = new DerivateHierarchyDTO();
 333         Map<UUID, TypeDesignationStatusBase> typeSpecimenUUIDtoTypeDesignationStatus = new HashMap<UUID, TypeDesignationStatusBase>();
 334
 335         //gather types for this taxon name
 336         TaxonNameBase<?,?> name = associatedTaxon.getName();
 337         Set<?> typeDesignations = name.getSpecimenTypeDesignations();
 338         for (Object object : typeDesignations) {
 339             if(object instanceof SpecimenTypeDesignation){
 340                 SpecimenTypeDesignation specimenTypeDesignation = (SpecimenTypeDesignation)object;
 341                 DerivedUnit typeSpecimen = specimenTypeDesignation.getTypeSpecimen();
 342                 final TypeDesignationStatusBase typeStatus = specimenTypeDesignation.getTypeStatus();
 343                 typeSpecimenUUIDtoTypeDesignationStatus.put(typeSpecimen.getUuid(), typeStatus);
 344             }
 345         }
 346
 347         if(fieldUnit.getGatheringEvent()!=null){
 348             GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
 349             //Country
 350             final NamedArea country = gatheringEvent.getCountry();
 351             dto.setCountry(country!=null?country.getDescription():"");
 352             //Collection
 353             final AgentBase collector = gatheringEvent.getCollector();
 354             final String fieldNumber = fieldUnit.getFieldNumber();
 355             dto.setCollection(((collector!=null?collector:"") + " " + (fieldNumber!=null?fieldNumber:"")).trim());
 356             //Date
 357             final Partial gatheringDate = gatheringEvent.getGatheringDate();
 358             dto.setDate(gatheringDate!=null?gatheringDate.toString():"");
 359         }
 360
 361         //Taxon Name
 362         dto.setTaxonName(associatedTaxon.getName().getFullTitleCache());
 363
 364
 365         Collection<DerivedUnit> derivedUnits = new ArrayList<DerivedUnit>();
 366         getDerivedUnitsFor(fieldUnit, derivedUnits);
 367
 368         //Herbaria map
 369         Map<eu.etaxonomy.cdm.model.occurrence.Collection, Integer> collectionToCountMap = new HashMap<eu.etaxonomy.cdm.model.occurrence.Collection, Integer>();
 370         //List of accession numbers for citation
 371         List<String> preservedSpecimenAccessionNumbers = new ArrayList<String>();
 372
 373         //iterate over sub derivates
 374         for (DerivedUnit derivedUnit : derivedUnits) {
 375             //current accession number
 376             String currentAccessionNumber = derivedUnit.getAccessionNumber()!=null?derivedUnit.getAccessionNumber():"";
 377             //current herbarium
 378             String currentHerbarium = "";
 379             eu.etaxonomy.cdm.model.occurrence.Collection collection = derivedUnit.getCollection();
 380             if(collection!=null){
 381                 currentHerbarium = collection.getCode()!=null?collection.getCode():"";
 382                 //count herbaria
 383                 Integer count = collectionToCountMap.get(collection);
 384                 if(count==null){
 385                     count = 1;
 386                 }
 387                 else{
 388                     count++;
 389                 }
 390                 collectionToCountMap.put(collection, count);
 391             }
 392             //check if derived unit is a type
 393             if(typeSpecimenUUIDtoTypeDesignationStatus.keySet().contains(derivedUnit.getUuid())){
 394                 dto.setHasType(true);
 395                 TypeDesignationStatusBase typeDesignationStatus = typeSpecimenUUIDtoTypeDesignationStatus.get(derivedUnit.getUuid());
 396                 String typeStatus = typeDesignationStatus.getLabel();
 397                 dto.addTypes(typeStatus, currentAccessionNumber);
 398             }
 399             //assemble molecular data
 400             if(derivedUnit instanceof DnaSample){
 401                 if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.TissueSample){
 402                     //TODO implement TissueSample assembly for web service
 403                 }
 404                 if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.DnaSample){
 405
 406                     DnaSample dna = (DnaSample)derivedUnit;
 407                     if(!dna.getSequences().isEmpty()){
 408                         dto.setHasDna(true);
 409                     }
 410                     for(Sequence sequence:dna.getSequences()){
 411                         URI boldUri = null;
 412                         try {
 413                             boldUri = sequence.getBoldUri();
 414                         } catch (URISyntaxException e1) {
 415                             logger.error("Could not create BOLD URI", e1);
 416                         }
 417                         final DefinedTerm dnaMarker = sequence.getDnaMarker();
 418                         dto.addProviderLink(boldUri!=null?boldUri:null,dnaMarker!=null?dnaMarker.getLabel():"[no marker]");
 419                     }
 420                 }
 421             }
 422             //assemble media data
 423             else if(derivedUnit instanceof MediaSpecimen){
 424
 425                 MediaSpecimen media = (MediaSpecimen)derivedUnit;
 426                 String mediaUriString = getMediaUriString(media);
 427                 if(media.getKindOfUnit()!=null){
 428                     //specimen scan
 429                     if(media.getKindOfUnit().getUuid().equals(UUID.fromString("acda15be-c0e2-4ea8-8783-b9b0c4ad7f03"))){
 430                         dto.setHasSpecimenScan(true);
 431                             final String imageLinkText = currentHerbarium+" "+currentAccessionNumber;
 432                             dto.addSpecimenScan(mediaUriString==null?"":mediaUriString, !imageLinkText.equals(" ")?imageLinkText:"[no accession]");
 433                     }
 434                     //detail image
 435                     else if(media.getKindOfUnit().getUuid().equals(UUID.fromString("31eb8d02-bf5d-437c-bcc6-87a626445f34"))){
 436                         dto.setHasDetailImage(true);
 437                         String motif = "";
 438                         if(media.getMediaSpecimen()!=null && media.getMediaSpecimen().getTitle()!=null){
 439                             motif = media.getMediaSpecimen().getTitle().getText();
 440                         }
 441                         dto.addDetailImage(mediaUriString==null?"":mediaUriString, motif!=null?motif:"[no motif]");
 442                     }
 443                 }
 444             }
 445             //assemble preserved specimen data
 446             else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.PreservedSpecimen){
 447                 if(!currentAccessionNumber.isEmpty()){
 448                     preservedSpecimenAccessionNumbers.add(currentAccessionNumber);
 449                 }
 450             }
 451         }
 452
 453         final String separator = ", ";
 454         //assemble citation
 455         String citation = "";
 456         citation += !dto.getCountry().isEmpty()?dto.getCountry()+separator:"";
 457         if(fieldUnit.getGatheringEvent()!=null){
 458             if(fieldUnit.getGatheringEvent().getLocality()!=null){
 459                 citation += fieldUnit.getGatheringEvent().getLocality().getText();
 460                 citation += separator;
 461             }
 462             if(fieldUnit.getGatheringEvent().getExactLocation()!=null
 463                     && fieldUnit.getGatheringEvent().getExactLocation().getLatitude()!=null
 464                     && fieldUnit.getGatheringEvent().getExactLocation().getLongitude()!=null){
 465                 citation += fieldUnit.getGatheringEvent().getExactLocation().getLatitude().toString();
 466                 citation += separator;
 467                 citation += fieldUnit.getGatheringEvent().getExactLocation().getLongitude().toString();
 468                 citation += separator;
 469             }
 470         }
 471         citation += !dto.getCollection().isEmpty()?dto.getCollection():"";
 472         if(!preservedSpecimenAccessionNumbers.isEmpty()){
 473             citation += " (";
 474             for(String accessionNumber:preservedSpecimenAccessionNumbers){
 475                 if(!accessionNumber.isEmpty()){
 476                     citation += accessionNumber+separator;
 477                 }
 478             }
 479             citation = removeTail(citation, separator);
 480             citation += ")";
 481         }
 482         citation = removeTail(citation, separator);
 483         dto.setCitation(citation);
 484
 485         //assemble herbaria string
 486         String herbariaString = "";
 487         for(Entry<eu.etaxonomy.cdm.model.occurrence.Collection, Integer> e:collectionToCountMap.entrySet()){
 488             eu.etaxonomy.cdm.model.occurrence.Collection collection = e.getKey();
 489             if(collection.getCode()!=null){
 490                 herbariaString += collection.getCode();
 491             }
 492             if(e.getValue()>1){
 493                 herbariaString += "("+e.getValue()+")";
 494             }
 495             herbariaString += separator;
 496         }
 497         herbariaString = removeTail(herbariaString, separator);
 498         dto.setHerbarium(herbariaString);
 499
 500         return dto;
 501     }
 502
 503
 504     /**
 505      * @param string
 506      * @param tail
 507      * @return
 508      */
 509     private String removeTail(String string, final String tail) {
 510         if(string.endsWith(tail)){
 511             string = string.substring(0, string.length()-tail.length());
 512         }
 513         return string;
 514     }
 515
 516     private String getMediaUriString(MediaSpecimen mediaSpecimen){
 517         String mediaUri = null;
 518         Collection<MediaRepresentation> mediaRepresentations = mediaSpecimen.getMediaSpecimen().getRepresentations();
 519         if(mediaRepresentations!=null && !mediaRepresentations.isEmpty()){
 520             Collection<MediaRepresentationPart> mediaRepresentationParts = mediaRepresentations.iterator().next().getParts();
 521             if(mediaRepresentationParts!=null && !mediaRepresentationParts.isEmpty()){
 522                 MediaRepresentationPart part = mediaRepresentationParts.iterator().next();
 523                 if(part.getUri()!=null){
 524                     mediaUri = part.getUri().toASCIIString();
 525                 }
 526             }
 527         }
 528         return mediaUri;
 529     }
 530
 531     private void getDerivedUnitsFor(SpecimenOrObservationBase<?> specimen, Collection<DerivedUnit> derivedUnits){
 532         for(DerivationEvent derivationEvent:specimen.getDerivationEvents()){
 533             for(DerivedUnit derivative:derivationEvent.getDerivatives()){
 534                 derivedUnits.add(derivative);
 535                 getDerivedUnitsFor(derivative, derivedUnits);
 536             }
 537         }
 538     }
 539
 540
 541     /* (non-Javadoc)
 542      * @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)
 543      */
 544     @SuppressWarnings("unchecked")
 545     @Override
 546     public <T extends SpecimenOrObservationBase> Pager<T> pageByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
 547             Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 548
 549         Set<Taxon> taxa = new HashSet<Taxon>();
 550         Set<Integer> occurrenceIds = new HashSet<Integer>();
 551         List<T> occurrences = new ArrayList<T>();
 552
 553 //        Integer limit = PagerUtils.limitFor(pageSize);
 554 //        Integer start = PagerUtils.startFor(pageSize, pageNumber);
 555
 556         if(!getSession().contains(associatedTaxon)){
 557             associatedTaxon = (Taxon) taxonService.load(associatedTaxon.getUuid());
 558         }
 559
 560         if(includeRelationships != null) {
 561             taxa = taxonService.listRelatedTaxa(associatedTaxon, includeRelationships, maxDepth, null, null, propertyPaths);
 562         }
 563
 564         taxa.add(associatedTaxon);
 565
 566         for (Taxon taxon : taxa) {
 567             List<T> perTaxonOccurrences = dao.listByAssociatedTaxon(type, taxon, null, null, orderHints, propertyPaths);
 568             for (SpecimenOrObservationBase o : perTaxonOccurrences) {
 569                 occurrenceIds.add(o.getId());
 570             }
 571         }
 572         occurrences = (List<T>) dao.listByIds(occurrenceIds, pageSize, pageNumber, orderHints, propertyPaths);
 573
 574         return new DefaultPagerImpl<T>(pageNumber, occurrenceIds.size(), pageSize, occurrences);
 575
 576     }
 577
 578     /* (non-Javadoc)
 579      * @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)
 580      */
 581     @SuppressWarnings("unchecked")
 582     @Override
 583     public <T extends SpecimenOrObservationBase> Pager<T> pageByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
 584             String taxonUUID, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 585
 586         UUID uuid = UUID.fromString(taxonUUID);
 587         Taxon tax = (Taxon) taxonService.load(uuid);
 588        //TODO REMOVE NULL STATEMENT
 589 type=null;
 590         return pageByAssociatedTaxon( type,includeRelationships,tax, maxDepth, pageSize, pageNumber, orderHints, propertyPaths );
 591
 592     }
 593
 594
 595     @Override
 596     public Pager<SearchResult<SpecimenOrObservationBase>> findByFullText(
 597             Class<? extends SpecimenOrObservationBase> clazz, String queryString, Rectangle boundingBox, List<Language> languages,
 598             boolean highlightFragments, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
 599             List<String> propertyPaths) throws CorruptIndexException, IOException, ParseException {
 600
 601         LuceneSearch luceneSearch = prepareByFullTextSearch(clazz, queryString, boundingBox, languages, highlightFragments);
 602
 603         // --- execute search
 604         TopGroupsWithMaxScore topDocsResultSet = luceneSearch.executeSearch(pageSize, pageNumber);
 605
 606         Map<CdmBaseType, String> idFieldMap = new HashMap<CdmBaseType, String>();
 607         idFieldMap.put(CdmBaseType.SPECIMEN_OR_OBSERVATIONBASE, "id");
 608
 609         // --- initialize taxa, highlight matches ....
 610         ISearchResultBuilder searchResultBuilder = new SearchResultBuilder(luceneSearch, luceneSearch.getQuery());
 611         @SuppressWarnings("rawtypes")
 612         List<SearchResult<SpecimenOrObservationBase>> searchResults = searchResultBuilder.createResultSet(
 613                 topDocsResultSet, luceneSearch.getHighlightFields(), dao, idFieldMap, propertyPaths);
 614
 615         int totalHits = topDocsResultSet != null ? topDocsResultSet.topGroups.totalGroupCount : 0;
 616
 617         return new DefaultPagerImpl<SearchResult<SpecimenOrObservationBase>>(pageNumber, totalHits, pageSize,
 618                 searchResults);
 619
 620     }
 621
 622
 623     /**
 624      * @param clazz
 625      * @param queryString
 626      * @param languages
 627      * @param highlightFragments
 628      * @return
 629      */
 630     private LuceneSearch prepareByFullTextSearch(Class<? extends SpecimenOrObservationBase> clazz, String queryString, Rectangle bbox,
 631             List<Language> languages, boolean highlightFragments) {
 632
 633         BooleanQuery finalQuery = new BooleanQuery();
 634         BooleanQuery textQuery = new BooleanQuery();
 635
 636         LuceneSearch luceneSearch = new LuceneSearch(luceneIndexToolProvider, FieldUnit.class);
 637         QueryFactory queryFactory = luceneIndexToolProvider.newQueryFactoryFor(FieldUnit.class);
 638
 639         // --- criteria
 640         luceneSearch.setCdmTypRestriction(clazz);
 641         if(queryString != null){
 642             textQuery.add(queryFactory.newTermQuery("titleCache", queryString), Occur.SHOULD);
 643             finalQuery.add(textQuery, Occur.MUST);
 644         }
 645
 646         // --- spacial query
 647         if(bbox != null){
 648             finalQuery.add(QueryFactory.buildSpatialQueryByRange(bbox, "gatheringEvent.exactLocation.point"), Occur.MUST);
 649         }
 650
 651         luceneSearch.setQuery(finalQuery);
 652
 653         // --- sorting
 654         SortField[] sortFields = new  SortField[]{SortField.FIELD_SCORE, new SortField("titleCache__sort", SortField.STRING, false)};
 655         luceneSearch.setSortFields(sortFields);
 656
 657         if(highlightFragments){
 658             luceneSearch.setHighlightFields(queryFactory.getTextFieldNamesAsArray());
 659         }
 660         return luceneSearch;
 661     }
 662
 663
 664     /* (non-Javadoc)
 665      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getFieldUnits(eu.etaxonomy.cdm.model.occurrence.DerivedUnit)
 666      */
 667     @Override
 668     public Collection<FieldUnit> getFieldUnits(UUID derivedUnitUuid) {
 669         //It will search recursively over all {@link DerivationEvent}s and get the "originals" ({@link SpecimenOrObservationBase})
 670         //from which this DerivedUnit was derived until all FieldUnits are found.
 671
 672         //FIXME: use HQL queries to increase performance
 673         SpecimenOrObservationBase<?> specimen = load(derivedUnitUuid);
 674 //        specimen = HibernateProxyHelper.deproxy(specimen, SpecimenOrObservationBase.class);
 675         Collection<FieldUnit> fieldUnits = new ArrayList<FieldUnit>();
 676
 677         if(specimen instanceof FieldUnit){
 678             fieldUnits.add((FieldUnit) specimen);
 679         }
 680         else if(specimen instanceof DerivedUnit){
 681             getFieldUnits((DerivedUnit) specimen, fieldUnits);
 682         }
 683         return fieldUnits;
 684     }
 685
 686
 687     /**
 688      * @param original
 689      * @param fieldUnits
 690      */
 691     private void getFieldUnits(DerivedUnit derivedUnit, Collection<FieldUnit> fieldUnits) {
 692         Set<SpecimenOrObservationBase> originals = derivedUnit.getOriginals();
 693         if(originals!=null && !originals.isEmpty()){
 694             for(SpecimenOrObservationBase<?> original:originals){
 695                 if(original instanceof FieldUnit){
 696                     fieldUnits.add((FieldUnit) original);
 697                 }
 698                 else if(original instanceof DerivedUnit){
 699                     getFieldUnits((DerivedUnit) original, fieldUnits);
 700                 }
 701             }
 702         }
 703     }
 704
 705     /* (non-Javadoc)
 706      * @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)
 707      */
 708     @Override
 709     public boolean moveSequence(DnaSample from, DnaSample to, Sequence sequence) {
 710         //reload specimens to avoid session conflicts
 711         from = (DnaSample) load(from.getUuid());
 712         to = (DnaSample) load(to.getUuid());
 713         sequence = sequenceService.load(sequence.getUuid());
 714
 715         if(from==null || to==null || sequence==null){
 716             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" +
 717                     "Operation was move "+sequence+ " from "+from+" to "+to);
 718         }
 719         from.removeSequence(sequence);
 720         saveOrUpdate(from);
 721         to.addSequence(sequence);
 722         saveOrUpdate(to);
 723         return true;
 724     }
 725
 726     /* (non-Javadoc)
 727      * @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)
 728      */
 729     @Override
 730     public boolean moveDerivate(SpecimenOrObservationBase<?> from, SpecimenOrObservationBase<?> to, DerivedUnit derivate) {
 731         //reload specimens to avoid session conflicts
 732         from = load(from.getUuid());
 733         to = load(to.getUuid());
 734         derivate = (DerivedUnit) load(derivate.getUuid());
 735
 736         if(from==null || to==null || derivate==null){
 737             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" +
 738                         "Operation was move "+derivate+ " from "+from+" to "+to);
 739         }
 740
 741         SpecimenOrObservationType derivateType = derivate.getRecordBasis();
 742         SpecimenOrObservationType toType = to.getRecordBasis();
 743         //check if type is a sub derivate type
 744         if(toType==SpecimenOrObservationType.FieldUnit //moving to FieldUnit always works
 745                 || derivateType==SpecimenOrObservationType.Media //moving media always works
 746                 || (derivateType.isKindOf(toType) && toType!=derivateType)){ //moving only to parent derivate type
 747             //remove derivation event from parent specimen of dragged object
 748             DerivationEvent eventToRemove = null;
 749             for(DerivationEvent event:from.getDerivationEvents()){
 750                 if(event.getDerivatives().contains(derivate)){
 751                     eventToRemove = event;
 752                     break;
 753                 }
 754             }
 755             from.removeDerivationEvent(eventToRemove);
 756             saveOrUpdate(from);
 757             //add new derivation event to target
 758             to.addDerivationEvent(DerivationEvent.NewSimpleInstance(to, derivate, eventToRemove==null?null:eventToRemove.getType()));
 759             saveOrUpdate(to);
 760             return true;
 761         }
 762         return false;
 763     }
 764
 765     @Override
 766     public Collection<ICdmBase> getNonCascadedAssociatedElements(SpecimenOrObservationBase<?> specimen){
 767         //potential fields that are not persisted cascadingly
 768         /*
 769          * SOOB
 770         -DescriptionBase
 771         -determinations
 772         --modifier TERM
 773         -kindOfUnit TERM
 774         -lifeStage TERM
 775         -sex TERM
 776
 777         FieldUnit
 778         -GatheringEvent
 779         --Country TERM
 780         --CollectingAreas TERM
 781
 782         DerivedUnit
 783         -collection
 784         --institute
 785         ---types TERM
 786         -preservationMethod
 787         --medium TERM
 788         -storedUnder CDM TaxonNameBase
 789         */
 790
 791         Collection<ICdmBase> nonCascadedCdmEntities = new HashSet<ICdmBase>();
 792
 793         //Choose the correct entry point to traverse the graph (FieldUnit or DerivedUnit)
 794
 795         //FieldUnit
 796         if(specimen instanceof FieldUnit){
 797             nonCascadedCdmEntities.addAll(getFieldUnitNonCascadedAssociatedElements((FieldUnit)specimen));
 798         }
 799         //DerivedUnit
 800         else if(specimen instanceof DerivedUnit){
 801             DerivedUnit derivedUnit = (DerivedUnit)specimen;
 802             if(derivedUnit.getDerivedFrom()!=null){
 803                 Collection<FieldUnit> fieldUnits = new ArrayList<FieldUnit>();
 804                 getFieldUnits(derivedUnit, fieldUnits);
 805                 for(FieldUnit fieldUnit:fieldUnits){
 806                     nonCascadedCdmEntities.addAll(getFieldUnitNonCascadedAssociatedElements(fieldUnit));
 807                 }
 808             }
 809         }
 810         return nonCascadedCdmEntities;
 811     }
 812
 813     private Collection<ICdmBase> getFieldUnitNonCascadedAssociatedElements(FieldUnit fieldUnit){
 814         //get non cascaded element on SpecimenOrObservationBase level
 815         Collection<ICdmBase> nonCascadedCdmEntities = getSpecimenOrObservationNonCascadedAssociatedElements(fieldUnit);
 816
 817         //get FieldUnit specific elements
 818         GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
 819         if(gatheringEvent!=null){
 820             //country
 821             if(gatheringEvent.getCountry()!=null){
 822                 nonCascadedCdmEntities.add(gatheringEvent.getCountry());
 823             }
 824             //collecting areas
 825             for (NamedArea namedArea : gatheringEvent.getCollectingAreas()) {
 826                 nonCascadedCdmEntities.add(namedArea);
 827             }
 828         }
 829         for (DerivationEvent derivationEvent : fieldUnit.getDerivationEvents()) {
 830             for (DerivedUnit derivedUnit : derivationEvent.getDerivatives()) {
 831                 nonCascadedCdmEntities.addAll(getDerivedUnitNonCascadedAssociatedElements(derivedUnit));
 832             }
 833         }
 834         return nonCascadedCdmEntities;
 835     }
 836
 837     private Collection<ICdmBase> getDerivedUnitNonCascadedAssociatedElements(DerivedUnit derivedUnit){
 838         //get non cascaded element on SpecimenOrObservationBase level
 839         Collection<ICdmBase> nonCascadedCdmEntities = getSpecimenOrObservationNonCascadedAssociatedElements(derivedUnit);
 840
 841         //get DerivedUnit specific elements
 842         if(derivedUnit.getCollection()!=null && derivedUnit.getCollection().getInstitute()!=null){
 843             for (DefinedTerm type : derivedUnit.getCollection().getInstitute().getTypes()) {
 844                 nonCascadedCdmEntities.add(type);
 845             }
 846         }
 847         if(derivedUnit.getPreservation()!=null && derivedUnit.getPreservation().getMedium()!=null){
 848             nonCascadedCdmEntities.add(derivedUnit.getPreservation().getMedium());
 849         }
 850         if(derivedUnit.getStoredUnder()!=null){
 851             nonCascadedCdmEntities.add(derivedUnit.getStoredUnder());
 852         }
 853         return nonCascadedCdmEntities;
 854     }
 855
 856     /**
 857      * @param specimen
 858      * @return
 859      */
 860     private Collection<ICdmBase> getSpecimenOrObservationNonCascadedAssociatedElements(
 861             SpecimenOrObservationBase<?> specimen) {
 862         Collection<ICdmBase> nonCascadedCdmEntities = new HashSet<ICdmBase>();
 863         //scan SpecimenOrObservationBase
 864         for(DeterminationEvent determinationEvent:specimen.getDeterminations()){
 865             //modifier
 866             if(determinationEvent.getModifier()!=null){
 867                 nonCascadedCdmEntities.add(determinationEvent.getModifier());
 868             }
 869         }
 870         //kindOfUnit
 871         if(specimen.getKindOfUnit()!=null){
 872             nonCascadedCdmEntities.add(specimen.getKindOfUnit());
 873         }
 874         //lifeStage
 875         if(specimen.getLifeStage()!=null){
 876             nonCascadedCdmEntities.add(specimen.getLifeStage());
 877         }
 878         //sex
 879         if(specimen.getSex()!=null){
 880             nonCascadedCdmEntities.add(specimen.getSex());
 881         }
 882         return nonCascadedCdmEntities;
 883     }
 884
 885     /* (non-Javadoc)
 886      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#deleteDerivateHierarchy(eu.etaxonomy.cdm.model.common.ICdmBase)
 887      */
 888     @Override
 889     public DeleteResult deleteDerivateHierarchy(ICdmBase from) {
 890         DeleteResult deleteResult = new DeleteResult();
 891         return deleteResult;
 892     }
 893
 894 }