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.util.ArrayList;
  16 import java.util.Arrays;
  17 import java.util.Collection;
  18 import java.util.HashMap;
  19 import java.util.HashSet;
  20 import java.util.List;
  21 import java.util.Map;
  22 import java.util.Map.Entry;
  23 import java.util.Set;
  24 import java.util.UUID;
  25
  26 import org.apache.log4j.Logger;
  27 import org.apache.lucene.index.CorruptIndexException;
  28 import org.apache.lucene.queryParser.ParseException;
  29 import org.apache.lucene.search.BooleanClause.Occur;
  30 import org.apache.lucene.search.BooleanQuery;
  31 import org.apache.lucene.search.SortField;
  32 import org.hibernate.TransientObjectException;
  33 import org.hibernate.search.spatial.impl.Rectangle;
  34 import org.joda.time.Partial;
  35 import org.springframework.beans.factory.annotation.Autowired;
  36 import org.springframework.stereotype.Service;
  37 import org.springframework.transaction.annotation.Transactional;
  38
  39 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
  40 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeConfigurator;
  41 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeNotSupportedException;
  42 import eu.etaxonomy.cdm.api.service.dto.DerivateHierarchyDTO;
  43 import eu.etaxonomy.cdm.api.service.molecular.ISequenceService;
  44 import eu.etaxonomy.cdm.api.service.pager.Pager;
  45 import eu.etaxonomy.cdm.api.service.pager.impl.DefaultPagerImpl;
  46 import eu.etaxonomy.cdm.api.service.search.ILuceneIndexToolProvider;
  47 import eu.etaxonomy.cdm.api.service.search.ISearchResultBuilder;
  48 import eu.etaxonomy.cdm.api.service.search.LuceneSearch;
  49 import eu.etaxonomy.cdm.api.service.search.LuceneSearch.TopGroupsWithMaxScore;
  50 import eu.etaxonomy.cdm.api.service.search.QueryFactory;
  51 import eu.etaxonomy.cdm.api.service.search.SearchResult;
  52 import eu.etaxonomy.cdm.api.service.search.SearchResultBuilder;
  53 import eu.etaxonomy.cdm.api.service.util.TaxonRelationshipEdge;
  54 import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
  55 import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
  56 import eu.etaxonomy.cdm.model.CdmBaseType;
  57 import eu.etaxonomy.cdm.model.agent.AgentBase;
  58 import eu.etaxonomy.cdm.model.common.DefinedTerm;
  59 import eu.etaxonomy.cdm.model.common.DefinedTermBase;
  60 import eu.etaxonomy.cdm.model.common.ICdmBase;
  61 import eu.etaxonomy.cdm.model.common.Language;
  62 import eu.etaxonomy.cdm.model.common.UuidAndTitleCache;
  63 import eu.etaxonomy.cdm.model.description.DescriptionBase;
  64 import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
  65 import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
  66 import eu.etaxonomy.cdm.model.location.Country;
  67 import eu.etaxonomy.cdm.model.location.NamedArea;
  68 import eu.etaxonomy.cdm.model.media.Media;
  69 import eu.etaxonomy.cdm.model.media.MediaRepresentation;
  70 import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;
  71 import eu.etaxonomy.cdm.model.molecular.DnaSample;
  72 import eu.etaxonomy.cdm.model.molecular.Sequence;
  73 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
  74 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  75 import eu.etaxonomy.cdm.model.name.TypeDesignationStatusBase;
  76 import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
  77 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  78 import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
  79 import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
  80 import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
  81 import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen;
  82 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  83 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
  84 import eu.etaxonomy.cdm.model.taxon.Taxon;
  85 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  86 import eu.etaxonomy.cdm.persistence.dao.common.IDefinedTermDao;
  87 import eu.etaxonomy.cdm.persistence.dao.initializer.AbstractBeanInitializer;
  88 import eu.etaxonomy.cdm.persistence.dao.occurrence.IOccurrenceDao;
  89 import eu.etaxonomy.cdm.persistence.query.OrderHint;
  90 import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
  91
  92 /**
  93  * @author a.babadshanjan
  94  * @created 01.09.2008
  95  */
  96 @Service
  97 @Transactional(readOnly = true)
  98 public class OccurrenceServiceImpl extends IdentifiableServiceBase<SpecimenOrObservationBase,IOccurrenceDao> implements IOccurrenceService {
  99
 100     static private final Logger logger = Logger.getLogger(OccurrenceServiceImpl.class);
 101
 102     @Autowired
 103     private IDefinedTermDao definedTermDao;
 104
 105     @Autowired
 106     private IDescriptionService descriptionService;
 107
 108     @Autowired
 109     private ITaxonService taxonService;
 110
 111     @Autowired
 112     private ITermService termService;
 113
 114     @Autowired
 115     private INameService nameService;
 116
 117     @Autowired
 118     private ISequenceService sequenceService;
 119
 120     @Autowired
 121     private AbstractBeanInitializer beanInitializer;
 122
 123     @Autowired
 124     private ILuceneIndexToolProvider luceneIndexToolProvider;
 125
 126
 127     public OccurrenceServiceImpl() {
 128         logger.debug("Load OccurrenceService Bean");
 129     }
 130
 131
 132     /* (non-Javadoc)
 133      * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#updateTitleCache(java.lang.Integer, eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy)
 134      */
 135     @Override
 136     @Transactional(readOnly = false)
 137     public void updateTitleCache(Class<? extends SpecimenOrObservationBase> clazz, Integer stepSize, IIdentifiableEntityCacheStrategy<SpecimenOrObservationBase> cacheStrategy, IProgressMonitor monitor) {
 138         if (clazz == null){
 139             clazz = SpecimenOrObservationBase.class;
 140         }
 141         super.updateTitleCacheImpl(clazz, stepSize, cacheStrategy, monitor);
 142     }
 143
 144
 145     /**
 146      * FIXME Candidate for harmonization
 147      * move to termService
 148      */
 149     @Override
 150     public Country getCountryByIso(String iso639) {
 151         return this.definedTermDao.getCountryByIso(iso639);
 152
 153     }
 154
 155     /**
 156      * FIXME Candidate for harmonization
 157      * move to termService
 158      */
 159     @Override
 160     public List<Country> getCountryByName(String name) {
 161         List<? extends DefinedTermBase> terms = this.definedTermDao.findByTitle(Country.class, name, null, null, null, null, null, null) ;
 162         List<Country> countries = new ArrayList<Country>();
 163         for (int i=0;i<terms.size();i++){
 164             countries.add((Country)terms.get(i));
 165         }
 166         return countries;
 167     }
 168
 169     @Override
 170     @Autowired
 171     protected void setDao(IOccurrenceDao dao) {
 172         this.dao = dao;
 173     }
 174
 175     @Override
 176     public Pager<DerivationEvent> getDerivationEvents(SpecimenOrObservationBase occurence, Integer pageSize,Integer pageNumber, List<String> propertyPaths) {
 177         Integer numberOfResults = dao.countDerivationEvents(occurence);
 178
 179         List<DerivationEvent> results = new ArrayList<DerivationEvent>();
 180         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 181             results = dao.getDerivationEvents(occurence, pageSize, pageNumber,propertyPaths);
 182         }
 183
 184         return new DefaultPagerImpl<DerivationEvent>(pageNumber, numberOfResults, pageSize, results);
 185     }
 186
 187     /* (non-Javadoc)
 188      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#countDeterminations(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase, eu.etaxonomy.cdm.model.taxon.TaxonBase)
 189      */
 190     @Override
 191     public int countDeterminations(SpecimenOrObservationBase occurence, TaxonBase taxonbase) {
 192         return dao.countDeterminations(occurence, taxonbase);
 193     }
 194
 195     @Override
 196     public Pager<DeterminationEvent> getDeterminations(SpecimenOrObservationBase occurrence, TaxonBase taxonBase, Integer pageSize,Integer pageNumber, List<String> propertyPaths) {
 197         Integer numberOfResults = dao.countDeterminations(occurrence, taxonBase);
 198
 199         List<DeterminationEvent> results = new ArrayList<DeterminationEvent>();
 200         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 201             results = dao.getDeterminations(occurrence,taxonBase, pageSize, pageNumber, propertyPaths);
 202         }
 203
 204         return new DefaultPagerImpl<DeterminationEvent>(pageNumber, numberOfResults, pageSize, results);
 205     }
 206
 207     @Override
 208     public Pager<Media> getMedia(SpecimenOrObservationBase occurence,Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
 209         Integer numberOfResults = dao.countMedia(occurence);
 210
 211         List<Media> results = new ArrayList<Media>();
 212         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 213             results = dao.getMedia(occurence, pageSize, pageNumber, propertyPaths);
 214         }
 215
 216         return new DefaultPagerImpl<Media>(pageNumber, numberOfResults, pageSize, results);
 217     }
 218
 219     /* (non-Javadoc)
 220      * @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)
 221      */
 222     @Override
 223     public Pager<SpecimenOrObservationBase> list(Class<? extends SpecimenOrObservationBase> type, TaxonBase determinedAs, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 224         Integer numberOfResults = dao.count(type,determinedAs);
 225         List<SpecimenOrObservationBase> results = new ArrayList<SpecimenOrObservationBase>();
 226         pageNumber = pageNumber == null ? 0 : pageNumber;
 227         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 228             Integer start = pageSize == null ? 0 : pageSize * pageNumber;
 229             results = dao.list(type,determinedAs, pageSize, start, orderHints,propertyPaths);
 230         }
 231         return new DefaultPagerImpl<SpecimenOrObservationBase>(pageNumber, numberOfResults, pageSize, results);
 232     }
 233
 234     @Override
 235     public List<UuidAndTitleCache<DerivedUnit>> getDerivedUnitUuidAndTitleCache() {
 236         return dao.getDerivedUnitUuidAndTitleCache();
 237     }
 238
 239     @Override
 240     public List<UuidAndTitleCache<FieldUnit>> getFieldUnitUuidAndTitleCache() {
 241         return dao.getFieldUnitUuidAndTitleCache();
 242     }
 243
 244     /* (non-Javadoc)
 245      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getDerivedUnitFacade(eu.etaxonomy.cdm.model.occurrence.DerivedUnit)
 246      */
 247     @Override
 248     public DerivedUnitFacade getDerivedUnitFacade(DerivedUnit derivedUnit, List<String> propertyPaths) throws DerivedUnitFacadeNotSupportedException {
 249         derivedUnit = (DerivedUnit)dao.load(derivedUnit.getUuid(), null);
 250         DerivedUnitFacadeConfigurator config = DerivedUnitFacadeConfigurator.NewInstance();
 251         config.setThrowExceptionForNonSpecimenPreservationMethodRequest(false);
 252         DerivedUnitFacade derivedUnitFacade = DerivedUnitFacade.NewInstance(derivedUnit, config);
 253         beanInitializer.initialize(derivedUnitFacade, propertyPaths);
 254         return derivedUnitFacade;
 255     }
 256
 257     /* (non-Javadoc)
 258      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#listDerivedUnitFacades(eu.etaxonomy.cdm.model.description.DescriptionBase, java.util.List)
 259      */
 260     @Override
 261     public List<DerivedUnitFacade> listDerivedUnitFacades(
 262             DescriptionBase description, List<String> propertyPaths) {
 263
 264         List<DerivedUnitFacade> derivedUnitFacadeList = new ArrayList<DerivedUnitFacade>();
 265         IndividualsAssociation tempIndividualsAssociation;
 266         SpecimenOrObservationBase tempSpecimenOrObservationBase;
 267         List<DescriptionElementBase> elements = descriptionService.listDescriptionElements(description, null, IndividualsAssociation.class, null, 0, Arrays.asList(new String []{"associatedSpecimenOrObservation"}));
 268         for(DescriptionElementBase element : elements){
 269             if(element instanceof IndividualsAssociation){
 270                 tempIndividualsAssociation = (IndividualsAssociation)element;
 271                 if(tempIndividualsAssociation.getAssociatedSpecimenOrObservation() != null){
 272                     tempSpecimenOrObservationBase = HibernateProxyHelper.deproxy(tempIndividualsAssociation.getAssociatedSpecimenOrObservation(), SpecimenOrObservationBase.class);
 273                     if(tempSpecimenOrObservationBase instanceof DerivedUnit){
 274                         try {
 275                             derivedUnitFacadeList.add(DerivedUnitFacade.NewInstance((DerivedUnit)tempSpecimenOrObservationBase));
 276                         } catch (DerivedUnitFacadeNotSupportedException e) {
 277                             logger.warn(tempIndividualsAssociation.getAssociatedSpecimenOrObservation().getTitleCache() + " : " +e.getMessage());
 278                         }
 279                     }
 280                 }
 281
 282             }
 283         }
 284
 285         beanInitializer.initializeAll(derivedUnitFacadeList, propertyPaths);
 286
 287         return derivedUnitFacadeList;
 288     }
 289
 290
 291     /* (non-Javadoc)
 292      * @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)
 293      */
 294     @Override
 295     public <T extends SpecimenOrObservationBase> List<T> listByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
 296             Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 297
 298         return pageByAssociatedTaxon(type, includeRelationships, associatedTaxon, maxDepth, pageSize, pageNumber, orderHints, propertyPaths).getRecords();
 299     }
 300
 301     /* (non-Javadoc)
 302      * @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)
 303      */
 304     @Override
 305     public Collection<FieldUnit> listFieldUnitsByAssociatedTaxon(Set<TaxonRelationshipEdge> includeRelationships,
 306             Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 307
 308         if(!getSession().contains(associatedTaxon)){
 309             associatedTaxon = (Taxon) taxonService.load(associatedTaxon.getUuid());
 310         }
 311
 312         Set<FieldUnit> fieldUnits = new HashSet<FieldUnit>();
 313
 314         List<SpecimenOrObservationBase> records = pageByAssociatedTaxon(null, includeRelationships, associatedTaxon, maxDepth, pageSize, pageNumber, orderHints, propertyPaths).getRecords();
 315         for(SpecimenOrObservationBase<?> specimen:records){
 316             fieldUnits.addAll(getFieldUnits(specimen.getUuid()));
 317         }
 318         return fieldUnits;
 319     }
 320
 321     @Override
 322     public DerivateHierarchyDTO assembleDerivateHierarchyDTO(FieldUnit fieldUnit, UUID associatedTaxonUuid){
 323
 324         if(!getSession().contains(fieldUnit)){
 325             fieldUnit = (FieldUnit) load(fieldUnit.getUuid());
 326         }
 327         TaxonBase associatedTaxon = taxonService.load(associatedTaxonUuid);
 328
 329         DerivateHierarchyDTO dto = new DerivateHierarchyDTO();
 330         Map<UUID, TypeDesignationStatusBase> typeSpecimenUUIDtoTypeDesignationStatus = new HashMap<UUID, TypeDesignationStatusBase>();
 331
 332         //gather types for this taxon name
 333         TaxonNameBase<?,?> name = associatedTaxon.getName();
 334         Set<?> typeDesignations = name.getSpecimenTypeDesignations();
 335         for (Object object : typeDesignations) {
 336             if(object instanceof SpecimenTypeDesignation){
 337                 SpecimenTypeDesignation specimenTypeDesignation = (SpecimenTypeDesignation)object;
 338                 DerivedUnit typeSpecimen = specimenTypeDesignation.getTypeSpecimen();
 339                 final TypeDesignationStatusBase typeStatus = specimenTypeDesignation.getTypeStatus();
 340                 typeSpecimenUUIDtoTypeDesignationStatus.put(typeSpecimen.getUuid(), typeStatus);
 341             }
 342         }
 343
 344         if(fieldUnit.getGatheringEvent()!=null){
 345             GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
 346             //Country
 347             final NamedArea country = gatheringEvent.getCountry();
 348             dto.setCountry(country!=null?country.getDescription():"");
 349             //Collection
 350             final AgentBase collector = gatheringEvent.getCollector();
 351             final String fieldNumber = fieldUnit.getFieldNumber();
 352             dto.setCollection(((collector!=null?collector:"") + " " + (fieldNumber!=null?fieldNumber:"")).trim());
 353             //Date
 354             final Partial gatheringDate = gatheringEvent.getGatheringDate();
 355             dto.setDate(gatheringDate!=null?gatheringDate.toString():"");
 356         }
 357
 358         //Taxon Name
 359         dto.setTaxonName(associatedTaxon.getName().getFullTitleCache());
 360
 361
 362         Collection<DerivedUnit> derivedUnits = new ArrayList<DerivedUnit>();
 363         getDerivedUnitsFor(fieldUnit, derivedUnits);
 364
 365         //Herbaria map
 366         Map<eu.etaxonomy.cdm.model.occurrence.Collection, Integer> collectionToCountMap = new HashMap<eu.etaxonomy.cdm.model.occurrence.Collection, Integer>();
 367         //List of accession numbers for citation
 368         List<String> preservedSpecimenAccessionNumbers = new ArrayList<String>();
 369
 370         //iterate over sub derivates
 371         for (DerivedUnit derivedUnit : derivedUnits) {
 372             //current accession number
 373             String currentAccessionNumber = derivedUnit.getAccessionNumber()!=null?derivedUnit.getAccessionNumber():"";
 374             //current herbarium
 375             String currentHerbarium = "";
 376             eu.etaxonomy.cdm.model.occurrence.Collection collection = derivedUnit.getCollection();
 377             if(collection!=null){
 378                 currentHerbarium = collection.getCode()!=null?collection.getCode():"";
 379                 //count herbaria
 380                 Integer count = collectionToCountMap.get(collection);
 381                 if(count==null){
 382                     count = 1;
 383                 }
 384                 else{
 385                     count++;
 386                 }
 387                 collectionToCountMap.put(collection, count);
 388             }
 389             //check if derived unit is a type
 390             if(typeSpecimenUUIDtoTypeDesignationStatus.keySet().contains(derivedUnit.getUuid())){
 391                 dto.setHasType(true);
 392                 TypeDesignationStatusBase typeDesignationStatus = typeSpecimenUUIDtoTypeDesignationStatus.get(derivedUnit.getUuid());
 393                 String typeStatus = typeDesignationStatus.getLabel();
 394                 dto.addTypes(typeStatus, currentAccessionNumber);
 395             }
 396             //assemble molecular data
 397             if(derivedUnit instanceof DnaSample){//.getRecordBasis()==SpecimenOrObservationType.DnaSample){
 398                 dto.setHasDna(true);
 399
 400                 DnaSample dna = (DnaSample)derivedUnit;
 401                 for(Sequence sequence:dna.getSequences()){
 402                     final URI boldUri = sequence.getBoldUri();
 403                     final DefinedTerm dnaMarker = sequence.getDnaMarker();
 404                     dto.addMolecularData(boldUri!=null?boldUri.toString():"", dnaMarker!=null?dnaMarker.getLabel():"[no marker]");
 405                 }
 406             }
 407             //assemble media data
 408             else if(derivedUnit instanceof MediaSpecimen){
 409
 410                 MediaSpecimen media = (MediaSpecimen)derivedUnit;
 411                 String mediaUriString = getMediaUriString(media);
 412                 if(media.getKindOfUnit()!=null){
 413                     if(media.getKindOfUnit().getUuid().equals(UUID.fromString("acda15be-c0e2-4ea8-8783-b9b0c4ad7f03"))){
 414                         dto.setHasSpecimenScan(true);
 415                         if(mediaUriString!=null){
 416                             final String imageLinkText = currentHerbarium+" "+currentAccessionNumber;
 417                             dto.addSpecimenScan(mediaUriString, !imageLinkText.equals(" ")?imageLinkText:"[no accession]");
 418                         }
 419                     }
 420                     else if(media.getKindOfUnit().getUuid().equals(UUID.fromString("31eb8d02-bf5d-437c-bcc6-87a626445f34"))){
 421                         dto.setHasDetailImage(true);
 422                         if(mediaUriString!=null){
 423                             String motif = "";
 424                             if(media.getMediaSpecimen()!=null && media.getMediaSpecimen().getTitle()!=null){
 425                                 motif = media.getMediaSpecimen().getTitle().getText();
 426                             }
 427                             dto.addDetailImage(mediaUriString, motif!=null?motif:"[no motif]");
 428                         }
 429                     }
 430                 }
 431             }
 432             //assemble preserved specimen data
 433             else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.PreservedSpecimen){
 434                 if(!currentAccessionNumber.isEmpty()){
 435                     preservedSpecimenAccessionNumbers.add(currentAccessionNumber);
 436                 }
 437             }
 438         }
 439
 440         final String separator = ", ";
 441         //assemble citation
 442         String citation = "";
 443         citation += !dto.getCountry().isEmpty()?dto.getCountry()+separator:"";
 444         if(fieldUnit.getGatheringEvent()!=null){
 445             if(fieldUnit.getGatheringEvent().getLocality()!=null){
 446                 citation += fieldUnit.getGatheringEvent().getLocality().getText();
 447                 citation += separator;
 448             }
 449             if(fieldUnit.getGatheringEvent().getExactLocation()!=null
 450                     && fieldUnit.getGatheringEvent().getExactLocation().getLatitude()!=null
 451                     && fieldUnit.getGatheringEvent().getExactLocation().getLongitude()!=null){
 452                 citation += fieldUnit.getGatheringEvent().getExactLocation().getLatitude().toString();
 453                 citation += separator;
 454                 citation += fieldUnit.getGatheringEvent().getExactLocation().getLongitude().toString();
 455                 citation += separator;
 456             }
 457         }
 458         citation += !dto.getCollection().isEmpty()?dto.getCollection()+separator:"";
 459         if(!preservedSpecimenAccessionNumbers.isEmpty()){
 460             citation += "(";
 461             for(String accessionNumber:preservedSpecimenAccessionNumbers){
 462                 if(!accessionNumber.isEmpty()){
 463                     citation += accessionNumber+separator;
 464                 }
 465             }
 466             citation = removeTail(citation, separator);
 467             citation += ")";
 468         }
 469         citation = removeTail(citation, separator);
 470         dto.setCitation(citation);
 471
 472         //assemble herbaria string
 473         String herbariaString = "";
 474         for(Entry<eu.etaxonomy.cdm.model.occurrence.Collection, Integer> e:collectionToCountMap.entrySet()){
 475             eu.etaxonomy.cdm.model.occurrence.Collection collection = e.getKey();
 476             if(collection.getCode()!=null){
 477                 herbariaString += collection.getCode();
 478             }
 479             if(e.getValue()>1){
 480                 herbariaString += "("+e.getValue()+")";
 481             }
 482             herbariaString += separator;
 483         }
 484         herbariaString = removeTail(herbariaString, separator);
 485         dto.setHerbarium(herbariaString);
 486
 487         return dto;
 488     }
 489
 490
 491     /**
 492      * @param string
 493      * @param tail
 494      * @return
 495      */
 496     private String removeTail(String string, final String tail) {
 497         if(string.endsWith(tail)){
 498             string = string.substring(0, string.length()-tail.length());
 499         }
 500         return string;
 501     }
 502
 503     private String getMediaUriString(MediaSpecimen mediaSpecimen){
 504         String mediaUri = null;
 505         Collection<MediaRepresentation> mediaRepresentations = mediaSpecimen.getMediaSpecimen().getRepresentations();
 506         if(mediaRepresentations!=null && !mediaRepresentations.isEmpty()){
 507             Collection<MediaRepresentationPart> mediaRepresentationParts = mediaRepresentations.iterator().next().getParts();
 508             if(mediaRepresentationParts!=null && !mediaRepresentationParts.isEmpty()){
 509                 MediaRepresentationPart part = mediaRepresentationParts.iterator().next();
 510                 if(part.getUri()!=null){
 511                     mediaUri = part.getUri().toASCIIString();
 512                 }
 513             }
 514         }
 515         return mediaUri;
 516     }
 517
 518     private void getDerivedUnitsFor(SpecimenOrObservationBase<?> specimen, Collection<DerivedUnit> derivedUnits){
 519         for(DerivationEvent derivationEvent:specimen.getDerivationEvents()){
 520             for(DerivedUnit derivative:derivationEvent.getDerivatives()){
 521                 derivedUnits.add(derivative);
 522                 getDerivedUnitsFor(derivative, derivedUnits);
 523             }
 524         }
 525     }
 526
 527
 528     /* (non-Javadoc)
 529      * @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)
 530      */
 531     @SuppressWarnings("unchecked")
 532     @Override
 533     public <T extends SpecimenOrObservationBase> Pager<T> pageByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
 534             Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 535
 536         Set<Taxon> taxa = new HashSet<Taxon>();
 537         Set<Integer> occurrenceIds = new HashSet<Integer>();
 538         List<T> occurrences = new ArrayList<T>();
 539
 540 //        Integer limit = PagerUtils.limitFor(pageSize);
 541 //        Integer start = PagerUtils.startFor(pageSize, pageNumber);
 542
 543         if(!getSession().contains(associatedTaxon)){
 544             associatedTaxon = (Taxon) taxonService.load(associatedTaxon.getUuid());
 545         }
 546
 547         if(includeRelationships != null) {
 548             taxa = taxonService.listRelatedTaxa(associatedTaxon, includeRelationships, maxDepth, null, null, propertyPaths);
 549         }
 550
 551         taxa.add(associatedTaxon);
 552
 553         for (Taxon taxon : taxa) {
 554             List<T> perTaxonOccurrences = dao.listByAssociatedTaxon(type, taxon, null, null, orderHints, propertyPaths);
 555             for (SpecimenOrObservationBase o : perTaxonOccurrences) {
 556                 occurrenceIds.add(o.getId());
 557             }
 558         }
 559         occurrences = (List<T>) dao.listByIds(occurrenceIds, pageSize, pageNumber, orderHints, propertyPaths);
 560
 561         return new DefaultPagerImpl<T>(pageNumber, occurrenceIds.size(), pageSize, occurrences);
 562
 563     }
 564
 565     /* (non-Javadoc)
 566      * @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)
 567      */
 568     @SuppressWarnings("unchecked")
 569     @Override
 570     public <T extends SpecimenOrObservationBase> Pager<T> pageByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
 571             String taxonUUID, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 572
 573         UUID uuid = UUID.fromString(taxonUUID);
 574         Taxon tax = (Taxon) taxonService.load(uuid);
 575        //TODO REMOVE NULL STATEMENT
 576 type=null;
 577         return pageByAssociatedTaxon( type,includeRelationships,tax, maxDepth, pageSize, pageNumber, orderHints, propertyPaths );
 578
 579     }
 580
 581
 582     @Override
 583     public Pager<SearchResult<SpecimenOrObservationBase>> findByFullText(
 584             Class<? extends SpecimenOrObservationBase> clazz, String queryString, Rectangle boundingBox, List<Language> languages,
 585             boolean highlightFragments, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
 586             List<String> propertyPaths) throws CorruptIndexException, IOException, ParseException {
 587
 588         LuceneSearch luceneSearch = prepareByFullTextSearch(clazz, queryString, boundingBox, languages, highlightFragments);
 589
 590         // --- execute search
 591         TopGroupsWithMaxScore topDocsResultSet = luceneSearch.executeSearch(pageSize, pageNumber);
 592
 593         Map<CdmBaseType, String> idFieldMap = new HashMap<CdmBaseType, String>();
 594         idFieldMap.put(CdmBaseType.SPECIMEN_OR_OBSERVATIONBASE, "id");
 595
 596         // --- initialize taxa, highlight matches ....
 597         ISearchResultBuilder searchResultBuilder = new SearchResultBuilder(luceneSearch, luceneSearch.getQuery());
 598         @SuppressWarnings("rawtypes")
 599         List<SearchResult<SpecimenOrObservationBase>> searchResults = searchResultBuilder.createResultSet(
 600                 topDocsResultSet, luceneSearch.getHighlightFields(), dao, idFieldMap, propertyPaths);
 601
 602         int totalHits = topDocsResultSet != null ? topDocsResultSet.topGroups.totalGroupCount : 0;
 603
 604         return new DefaultPagerImpl<SearchResult<SpecimenOrObservationBase>>(pageNumber, totalHits, pageSize,
 605                 searchResults);
 606
 607     }
 608
 609
 610     /**
 611      * @param clazz
 612      * @param queryString
 613      * @param languages
 614      * @param highlightFragments
 615      * @return
 616      */
 617     private LuceneSearch prepareByFullTextSearch(Class<? extends SpecimenOrObservationBase> clazz, String queryString, Rectangle bbox,
 618             List<Language> languages, boolean highlightFragments) {
 619
 620         BooleanQuery finalQuery = new BooleanQuery();
 621         BooleanQuery textQuery = new BooleanQuery();
 622
 623         LuceneSearch luceneSearch = new LuceneSearch(luceneIndexToolProvider, FieldUnit.class);
 624         QueryFactory queryFactory = luceneIndexToolProvider.newQueryFactoryFor(FieldUnit.class);
 625
 626         // --- criteria
 627         luceneSearch.setCdmTypRestriction(clazz);
 628         if(queryString != null){
 629             textQuery.add(queryFactory.newTermQuery("titleCache", queryString), Occur.SHOULD);
 630             finalQuery.add(textQuery, Occur.MUST);
 631         }
 632
 633         // --- spacial query
 634         if(bbox != null){
 635             finalQuery.add(QueryFactory.buildSpatialQueryByRange(bbox, "gatheringEvent.exactLocation.point"), Occur.MUST);
 636         }
 637
 638         luceneSearch.setQuery(finalQuery);
 639
 640         // --- sorting
 641         SortField[] sortFields = new  SortField[]{SortField.FIELD_SCORE, new SortField("titleCache__sort", SortField.STRING, false)};
 642         luceneSearch.setSortFields(sortFields);
 643
 644         if(highlightFragments){
 645             luceneSearch.setHighlightFields(queryFactory.getTextFieldNamesAsArray());
 646         }
 647         return luceneSearch;
 648     }
 649
 650
 651     /* (non-Javadoc)
 652      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getFieldUnits(eu.etaxonomy.cdm.model.occurrence.DerivedUnit)
 653      */
 654     @Override
 655     public Collection<FieldUnit> getFieldUnits(UUID derivedUnitUuid) {
 656         //It will search recursively over all {@link DerivationEvent}s and get the "originals" ({@link SpecimenOrObservationBase})
 657         //from which this DerivedUnit was derived until all FieldUnits are found.
 658
 659         //FIXME: use HQL queries to increase performance
 660         SpecimenOrObservationBase<?> specimen = load(derivedUnitUuid);
 661 //        specimen = HibernateProxyHelper.deproxy(specimen, SpecimenOrObservationBase.class);
 662         Collection<FieldUnit> fieldUnits = new ArrayList<FieldUnit>();
 663
 664         if(specimen instanceof FieldUnit){
 665             fieldUnits.add((FieldUnit) specimen);
 666         }
 667         else if(specimen instanceof DerivedUnit){
 668             getFieldUnits((DerivedUnit) specimen, fieldUnits);
 669         }
 670         return fieldUnits;
 671     }
 672
 673
 674     /**
 675      * @param original
 676      * @param fieldUnits
 677      */
 678     private void getFieldUnits(DerivedUnit derivedUnit, Collection<FieldUnit> fieldUnits) {
 679         Set<SpecimenOrObservationBase> originals = derivedUnit.getOriginals();
 680         if(originals!=null && !originals.isEmpty()){
 681             for(SpecimenOrObservationBase<?> original:originals){
 682                 if(original instanceof FieldUnit){
 683                     fieldUnits.add((FieldUnit) original);
 684                 }
 685                 else if(original instanceof DerivedUnit){
 686                     getFieldUnits((DerivedUnit) original, fieldUnits);
 687                 }
 688             }
 689         }
 690     }
 691
 692     /* (non-Javadoc)
 693      * @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)
 694      */
 695     @Override
 696     public boolean moveSequence(DnaSample from, DnaSample to, Sequence sequence) {
 697         //reload specimens to avoid session conflicts
 698         from = (DnaSample) load(from.getUuid());
 699         to = (DnaSample) load(to.getUuid());
 700         sequence = sequenceService.load(sequence.getUuid());
 701
 702         if(from==null || to==null || sequence==null){
 703             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" +
 704                     "Operation was move "+sequence+ " from "+from+" to "+to);
 705         }
 706         from.removeSequence(sequence);
 707         saveOrUpdate(from);
 708         to.addSequence(sequence);
 709         saveOrUpdate(to);
 710         return true;
 711     }
 712
 713     /* (non-Javadoc)
 714      * @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)
 715      */
 716     @Override
 717     public boolean moveDerivate(SpecimenOrObservationBase<?> from, SpecimenOrObservationBase<?> to, DerivedUnit derivate) {
 718         //reload specimens to avoid session conflicts
 719         from = load(from.getUuid());
 720         to = load(to.getUuid());
 721         derivate = (DerivedUnit) load(derivate.getUuid());
 722
 723         if(from==null || to==null || derivate==null){
 724             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" +
 725                         "Operation was move "+derivate+ " from "+from+" to "+to);
 726         }
 727
 728         SpecimenOrObservationType derivateType = derivate.getRecordBasis();
 729         SpecimenOrObservationType toType = to.getRecordBasis();
 730         //check if type is a sub derivate type
 731         if(toType==SpecimenOrObservationType.FieldUnit //moving to FieldUnit always works
 732                 || derivateType==SpecimenOrObservationType.Media //moving media always works
 733                 || (derivateType.isKindOf(toType) && toType!=derivateType)){ //moving only to parent derivate type
 734             //remove derivation event from parent specimen of dragged object
 735             DerivationEvent eventToRemove = null;
 736             for(DerivationEvent event:from.getDerivationEvents()){
 737                 if(event.getDerivatives().contains(derivate)){
 738                     eventToRemove = event;
 739                     break;
 740                 }
 741             }
 742             from.removeDerivationEvent(eventToRemove);
 743             saveOrUpdate(from);
 744             //add new derivation event to target
 745             to.addDerivationEvent(DerivationEvent.NewSimpleInstance(to, derivate, eventToRemove==null?null:eventToRemove.getType()));
 746             saveOrUpdate(to);
 747             return true;
 748         }
 749         return false;
 750     }
 751
 752     @Override
 753     public Collection<ICdmBase> getNonCascadedAssociatedElements(SpecimenOrObservationBase<?> specimen){
 754         //potential fields that are not persisted cascadingly
 755         /*
 756          * SOOB
 757         -DescriptionBase
 758         -determinations
 759         --modifier TERM
 760         -kindOfUnit TERM
 761         -lifeStage TERM
 762         -sex TERM
 763
 764         FieldUnit
 765         -GatheringEvent
 766         --Country TERM
 767         --CollectingAreas TERM
 768
 769         DerivedUnit
 770         -collection
 771         --institute
 772         ---types TERM
 773         -preservationMethod
 774         --medium TERM
 775         -storedUnder CDM TaxonNameBase
 776         */
 777
 778         Collection<ICdmBase> nonCascadedCdmEntities = new HashSet<ICdmBase>();
 779         //scan SpecimenOrObservationBase
 780         for(DeterminationEvent determinationEvent:specimen.getDeterminations()){
 781             //modifier
 782             if(determinationEvent.getModifier()!=null){
 783                 nonCascadedCdmEntities.add(determinationEvent.getModifier());
 784             }
 785         }
 786         //kindOfUnit
 787         if(specimen.getKindOfUnit()!=null){
 788             nonCascadedCdmEntities.add(specimen.getKindOfUnit());
 789         }
 790         //lifeStage
 791         if(specimen.getLifeStage()!=null){
 792             nonCascadedCdmEntities.add(specimen.getLifeStage());
 793         }
 794         //sex
 795         if(specimen.getSex()!=null){
 796             nonCascadedCdmEntities.add(specimen.getSex());
 797         }
 798
 799         //FieldUnit
 800         if(specimen instanceof FieldUnit){
 801             nonCascadedCdmEntities.addAll(getNonCascadedAssociatedElements((FieldUnit)specimen));
 802         }
 803         //DerivedUnit
 804         else if(specimen instanceof DerivedUnit){
 805             DerivedUnit derivedUnit = (DerivedUnit)specimen;
 806             if(derivedUnit.getDerivedFrom()!=null){
 807                 Collection<FieldUnit> fieldUnits = new ArrayList<FieldUnit>();
 808                 getFieldUnits(derivedUnit, fieldUnits);
 809                 for(FieldUnit fieldUnit:fieldUnits){
 810                     nonCascadedCdmEntities.addAll(getNonCascadedAssociatedElements(fieldUnit));
 811                 }
 812             }
 813         }
 814         return nonCascadedCdmEntities;
 815     }
 816
 817     private Collection<ICdmBase> getNonCascadedAssociatedElements(FieldUnit fieldUnit){
 818         Collection<ICdmBase> nonCascadedCdmEntities = new HashSet<ICdmBase>();
 819         GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
 820         if(gatheringEvent!=null){
 821             //country
 822             if(gatheringEvent.getCountry()!=null){
 823                 nonCascadedCdmEntities.add(gatheringEvent.getCountry());
 824             }
 825             //collecting areas
 826             for (NamedArea namedArea : gatheringEvent.getCollectingAreas()) {
 827                 nonCascadedCdmEntities.add(namedArea);
 828             }
 829         }
 830         for (DerivationEvent derivationEvent : fieldUnit.getDerivationEvents()) {
 831             for (DerivedUnit derivedUnit : derivationEvent.getDerivatives()) {
 832                 nonCascadedCdmEntities.addAll(getNonCascadedAssociatedElements(derivedUnit));
 833             }
 834         }
 835         return nonCascadedCdmEntities;
 836     }
 837
 838     private Collection<ICdmBase> getNonCascadedAssociatedElements(DerivedUnit derivedUnit){
 839         Collection<ICdmBase> nonCascadedCdmEntities = new HashSet<ICdmBase>();
 840         if(derivedUnit.getCollection()!=null && derivedUnit.getCollection().getInstitute()!=null){
 841             for (DefinedTerm type : derivedUnit.getCollection().getInstitute().getTypes()) {
 842                 nonCascadedCdmEntities.add(type);
 843             }
 844         }
 845         if(derivedUnit.getPreservation()!=null && derivedUnit.getPreservation().getMedium()!=null){
 846             nonCascadedCdmEntities.add(derivedUnit.getPreservation().getMedium());
 847         }
 848         if(derivedUnit.getStoredUnder()!=null){
 849             nonCascadedCdmEntities.add(derivedUnit.getStoredUnder());
 850         }
 851         return nonCascadedCdmEntities;
 852     }
 853
 854
 855 }