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.util.ArrayList;
  15 import java.util.Arrays;
  16 import java.util.Collection;
  17 import java.util.HashMap;
  18 import java.util.HashSet;
  19 import java.util.List;
  20 import java.util.Map;
  21 import java.util.Set;
  22 import java.util.UUID;
  23
  24 import org.apache.log4j.Logger;
  25 import org.apache.lucene.index.CorruptIndexException;
  26 import org.apache.lucene.queryParser.ParseException;
  27 import org.apache.lucene.search.BooleanClause.Occur;
  28 import org.apache.lucene.search.BooleanQuery;
  29 import org.apache.lucene.search.SortField;
  30 import org.hibernate.TransientObjectException;
  31 import org.hibernate.search.spatial.impl.Rectangle;
  32 import org.springframework.beans.factory.annotation.Autowired;
  33 import org.springframework.stereotype.Service;
  34 import org.springframework.transaction.annotation.Transactional;
  35
  36 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
  37 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeConfigurator;
  38 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeNotSupportedException;
  39 import eu.etaxonomy.cdm.api.service.molecular.ISequenceService;
  40 import eu.etaxonomy.cdm.api.service.pager.Pager;
  41 import eu.etaxonomy.cdm.api.service.pager.impl.DefaultPagerImpl;
  42 import eu.etaxonomy.cdm.api.service.search.ILuceneIndexToolProvider;
  43 import eu.etaxonomy.cdm.api.service.search.ISearchResultBuilder;
  44 import eu.etaxonomy.cdm.api.service.search.LuceneSearch;
  45 import eu.etaxonomy.cdm.api.service.search.LuceneSearch.TopGroupsWithMaxScore;
  46 import eu.etaxonomy.cdm.api.service.search.QueryFactory;
  47 import eu.etaxonomy.cdm.api.service.search.SearchResult;
  48 import eu.etaxonomy.cdm.api.service.search.SearchResultBuilder;
  49 import eu.etaxonomy.cdm.api.service.util.TaxonRelationshipEdge;
  50 import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
  51 import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
  52 import eu.etaxonomy.cdm.model.CdmBaseType;
  53 import eu.etaxonomy.cdm.model.common.DefinedTerm;
  54 import eu.etaxonomy.cdm.model.common.DefinedTermBase;
  55 import eu.etaxonomy.cdm.model.common.ICdmBase;
  56 import eu.etaxonomy.cdm.model.common.Language;
  57 import eu.etaxonomy.cdm.model.common.UuidAndTitleCache;
  58 import eu.etaxonomy.cdm.model.description.DescriptionBase;
  59 import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
  60 import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
  61 import eu.etaxonomy.cdm.model.location.Country;
  62 import eu.etaxonomy.cdm.model.location.NamedArea;
  63 import eu.etaxonomy.cdm.model.media.Media;
  64 import eu.etaxonomy.cdm.model.molecular.DnaSample;
  65 import eu.etaxonomy.cdm.model.molecular.Sequence;
  66 import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
  67 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  68 import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
  69 import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
  70 import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
  71 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  72 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
  73 import eu.etaxonomy.cdm.model.taxon.Taxon;
  74 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  75 import eu.etaxonomy.cdm.persistence.dao.common.IDefinedTermDao;
  76 import eu.etaxonomy.cdm.persistence.dao.initializer.AbstractBeanInitializer;
  77 import eu.etaxonomy.cdm.persistence.dao.occurrence.IOccurrenceDao;
  78 import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao;
  79 import eu.etaxonomy.cdm.persistence.query.OrderHint;
  80 import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
  81
  82 /**
  83  * @author a.babadshanjan
  84  * @created 01.09.2008
  85  */
  86 @Service
  87 @Transactional(readOnly = true)
  88 public class OccurrenceServiceImpl extends IdentifiableServiceBase<SpecimenOrObservationBase,IOccurrenceDao> implements IOccurrenceService {
  89
  90     static private final Logger logger = Logger.getLogger(OccurrenceServiceImpl.class);
  91
  92     @Autowired
  93     private IDefinedTermDao definedTermDao;
  94
  95     @Autowired
  96     private IDescriptionService descriptionService;
  97
  98     @Autowired
  99     private ITaxonService taxonService;
 100
 101     @Autowired
 102     private ITermService termService;
 103
 104     @Autowired
 105     private INameService nameService;
 106
 107     @Autowired
 108     private ISequenceService sequenceService;
 109
 110     @Autowired
 111     private AbstractBeanInitializer beanInitializer;
 112
 113     @Autowired
 114     private ITaxonDao taxonDao;
 115
 116     @Autowired
 117     private ILuceneIndexToolProvider luceneIndexToolProvider;
 118
 119
 120     public OccurrenceServiceImpl() {
 121         logger.debug("Load OccurrenceService Bean");
 122     }
 123
 124
 125     /* (non-Javadoc)
 126      * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#updateTitleCache(java.lang.Integer, eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy)
 127      */
 128     @Override
 129     @Transactional(readOnly = false)
 130     public void updateTitleCache(Class<? extends SpecimenOrObservationBase> clazz, Integer stepSize, IIdentifiableEntityCacheStrategy<SpecimenOrObservationBase> cacheStrategy, IProgressMonitor monitor) {
 131         if (clazz == null){
 132             clazz = SpecimenOrObservationBase.class;
 133         }
 134         super.updateTitleCacheImpl(clazz, stepSize, cacheStrategy, monitor);
 135     }
 136
 137
 138     /**
 139      * FIXME Candidate for harmonization
 140      * move to termService
 141      */
 142     @Override
 143     public Country getCountryByIso(String iso639) {
 144         return this.definedTermDao.getCountryByIso(iso639);
 145
 146     }
 147
 148     /**
 149      * FIXME Candidate for harmonization
 150      * move to termService
 151      */
 152     @Override
 153     public List<Country> getCountryByName(String name) {
 154         List<? extends DefinedTermBase> terms = this.definedTermDao.findByTitle(Country.class, name, null, null, null, null, null, null) ;
 155         List<Country> countries = new ArrayList<Country>();
 156         for (int i=0;i<terms.size();i++){
 157             countries.add((Country)terms.get(i));
 158         }
 159         return countries;
 160     }
 161
 162     @Override
 163     @Autowired
 164     protected void setDao(IOccurrenceDao dao) {
 165         this.dao = dao;
 166     }
 167
 168     @Override
 169     public Pager<DerivationEvent> getDerivationEvents(SpecimenOrObservationBase occurence, Integer pageSize,Integer pageNumber, List<String> propertyPaths) {
 170         Integer numberOfResults = dao.countDerivationEvents(occurence);
 171
 172         List<DerivationEvent> results = new ArrayList<DerivationEvent>();
 173         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 174             results = dao.getDerivationEvents(occurence, pageSize, pageNumber,propertyPaths);
 175         }
 176
 177         return new DefaultPagerImpl<DerivationEvent>(pageNumber, numberOfResults, pageSize, results);
 178     }
 179
 180     /* (non-Javadoc)
 181      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#countDeterminations(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase, eu.etaxonomy.cdm.model.taxon.TaxonBase)
 182      */
 183     @Override
 184     public int countDeterminations(SpecimenOrObservationBase occurence, TaxonBase taxonbase) {
 185         return dao.countDeterminations(occurence, taxonbase);
 186     }
 187
 188     @Override
 189     public Pager<DeterminationEvent> getDeterminations(SpecimenOrObservationBase occurrence, TaxonBase taxonBase, Integer pageSize,Integer pageNumber, List<String> propertyPaths) {
 190         Integer numberOfResults = dao.countDeterminations(occurrence, taxonBase);
 191
 192         List<DeterminationEvent> results = new ArrayList<DeterminationEvent>();
 193         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 194             results = dao.getDeterminations(occurrence,taxonBase, pageSize, pageNumber, propertyPaths);
 195         }
 196
 197         return new DefaultPagerImpl<DeterminationEvent>(pageNumber, numberOfResults, pageSize, results);
 198     }
 199
 200     @Override
 201     public Pager<Media> getMedia(SpecimenOrObservationBase occurence,Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
 202         Integer numberOfResults = dao.countMedia(occurence);
 203
 204         List<Media> results = new ArrayList<Media>();
 205         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 206             results = dao.getMedia(occurence, pageSize, pageNumber, propertyPaths);
 207         }
 208
 209         return new DefaultPagerImpl<Media>(pageNumber, numberOfResults, pageSize, results);
 210     }
 211
 212     /* (non-Javadoc)
 213      * @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)
 214      */
 215     @Override
 216     public Pager<SpecimenOrObservationBase> list(Class<? extends SpecimenOrObservationBase> type, TaxonBase determinedAs, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 217         Integer numberOfResults = dao.count(type,determinedAs);
 218         List<SpecimenOrObservationBase> results = new ArrayList<SpecimenOrObservationBase>();
 219         pageNumber = pageNumber == null ? 0 : pageNumber;
 220         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 221             Integer start = pageSize == null ? 0 : pageSize * pageNumber;
 222             results = dao.list(type,determinedAs, pageSize, start, orderHints,propertyPaths);
 223         }
 224         return new DefaultPagerImpl<SpecimenOrObservationBase>(pageNumber, numberOfResults, pageSize, results);
 225     }
 226
 227     @Override
 228     public List<UuidAndTitleCache<DerivedUnit>> getDerivedUnitUuidAndTitleCache() {
 229         return dao.getDerivedUnitUuidAndTitleCache();
 230     }
 231
 232     @Override
 233     public List<UuidAndTitleCache<FieldUnit>> getFieldUnitUuidAndTitleCache() {
 234         return dao.getFieldUnitUuidAndTitleCache();
 235     }
 236
 237     /* (non-Javadoc)
 238      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getDerivedUnitFacade(eu.etaxonomy.cdm.model.occurrence.DerivedUnit)
 239      */
 240     @Override
 241     public DerivedUnitFacade getDerivedUnitFacade(DerivedUnit derivedUnit, List<String> propertyPaths) throws DerivedUnitFacadeNotSupportedException {
 242         derivedUnit = (DerivedUnit)dao.load(derivedUnit.getUuid(), null);
 243         DerivedUnitFacadeConfigurator config = DerivedUnitFacadeConfigurator.NewInstance();
 244         config.setThrowExceptionForNonSpecimenPreservationMethodRequest(false);
 245         DerivedUnitFacade derivedUnitFacade = DerivedUnitFacade.NewInstance(derivedUnit, config);
 246         beanInitializer.initialize(derivedUnitFacade, propertyPaths);
 247         return derivedUnitFacade;
 248     }
 249
 250     /* (non-Javadoc)
 251      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#listDerivedUnitFacades(eu.etaxonomy.cdm.model.description.DescriptionBase, java.util.List)
 252      */
 253     @Override
 254     public List<DerivedUnitFacade> listDerivedUnitFacades(
 255             DescriptionBase description, List<String> propertyPaths) {
 256
 257         List<DerivedUnitFacade> derivedUnitFacadeList = new ArrayList<DerivedUnitFacade>();
 258         IndividualsAssociation tempIndividualsAssociation;
 259         SpecimenOrObservationBase tempSpecimenOrObservationBase;
 260         List<DescriptionElementBase> elements = descriptionService.listDescriptionElements(description, null, IndividualsAssociation.class, null, 0, Arrays.asList(new String []{"associatedSpecimenOrObservation"}));
 261         for(DescriptionElementBase element : elements){
 262             if(element instanceof IndividualsAssociation){
 263                 tempIndividualsAssociation = (IndividualsAssociation)element;
 264                 if(tempIndividualsAssociation.getAssociatedSpecimenOrObservation() != null){
 265                     tempSpecimenOrObservationBase = HibernateProxyHelper.deproxy(tempIndividualsAssociation.getAssociatedSpecimenOrObservation(), SpecimenOrObservationBase.class);
 266                     if(tempSpecimenOrObservationBase instanceof DerivedUnit){
 267                         try {
 268                             derivedUnitFacadeList.add(DerivedUnitFacade.NewInstance((DerivedUnit)tempSpecimenOrObservationBase));
 269                         } catch (DerivedUnitFacadeNotSupportedException e) {
 270                             logger.warn(tempIndividualsAssociation.getAssociatedSpecimenOrObservation().getTitleCache() + " : " +e.getMessage());
 271                         }
 272                     }
 273                 }
 274
 275             }
 276         }
 277
 278         beanInitializer.initializeAll(derivedUnitFacadeList, propertyPaths);
 279
 280         return derivedUnitFacadeList;
 281     }
 282
 283
 284     /* (non-Javadoc)
 285      * @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)
 286      */
 287     @Override
 288     public <T extends SpecimenOrObservationBase> List<T> listByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
 289             Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 290
 291         return pageByAssociatedTaxon(type, includeRelationships, associatedTaxon, maxDepth, pageSize, pageNumber, orderHints, propertyPaths).getRecords();
 292     }
 293
 294
 295     /* (non-Javadoc)
 296      * @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)
 297      */
 298     @SuppressWarnings("unchecked")
 299     @Override
 300     public <T extends SpecimenOrObservationBase> Pager<T> pageByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
 301             Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 302
 303         Set<Taxon> taxa = new HashSet<Taxon>();
 304         Set<Integer> occurrenceIds = new HashSet<Integer>();
 305         List<T> occurrences = new ArrayList<T>();
 306
 307 //        Integer limit = PagerUtils.limitFor(pageSize);
 308 //        Integer start = PagerUtils.startFor(pageSize, pageNumber);
 309
 310         associatedTaxon = (Taxon) taxonDao.load(associatedTaxon.getUuid());
 311
 312         if(includeRelationships != null) {
 313             taxa = taxonService.listRelatedTaxa(associatedTaxon, includeRelationships, maxDepth, null, null, propertyPaths);
 314         }
 315
 316         taxa.add(associatedTaxon);
 317
 318         for (Taxon taxon : taxa) {
 319             List<T> perTaxonOccurrences = dao.listByAssociatedTaxon(type, taxon, null, null, orderHints, propertyPaths);
 320             for (SpecimenOrObservationBase o : perTaxonOccurrences) {
 321                 occurrenceIds.add(o.getId());
 322             }
 323         }
 324         occurrences = (List<T>) dao.listByIds(occurrenceIds, pageSize, pageNumber, orderHints, propertyPaths);
 325
 326         return new DefaultPagerImpl<T>(pageNumber, occurrenceIds.size(), pageSize, occurrences);
 327
 328     }
 329
 330     /* (non-Javadoc)
 331      * @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)
 332      */
 333     @SuppressWarnings("unchecked")
 334     @Override
 335     public <T extends SpecimenOrObservationBase> Pager<T> pageByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
 336             String taxonUUID, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 337
 338         UUID uuid = UUID.fromString(taxonUUID);
 339         Taxon tax = (Taxon) taxonDao.load(uuid);
 340        //TODO REMOVE NULL STATEMENT
 341 type=null;
 342         return pageByAssociatedTaxon( type,includeRelationships,tax, maxDepth, pageSize, pageNumber, orderHints, propertyPaths );
 343
 344     }
 345
 346
 347     @Override
 348     public Pager<SearchResult<SpecimenOrObservationBase>> findByFullText(
 349             Class<? extends SpecimenOrObservationBase> clazz, String queryString, Rectangle boundingBox, List<Language> languages,
 350             boolean highlightFragments, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
 351             List<String> propertyPaths) throws CorruptIndexException, IOException, ParseException {
 352
 353         LuceneSearch luceneSearch = prepareByFullTextSearch(clazz, queryString, boundingBox, languages, highlightFragments);
 354
 355         // --- execute search
 356         TopGroupsWithMaxScore topDocsResultSet = luceneSearch.executeSearch(pageSize, pageNumber);
 357
 358         Map<CdmBaseType, String> idFieldMap = new HashMap<CdmBaseType, String>();
 359         idFieldMap.put(CdmBaseType.SPECIMEN_OR_OBSERVATIONBASE, "id");
 360
 361         // --- initialize taxa, highlight matches ....
 362         ISearchResultBuilder searchResultBuilder = new SearchResultBuilder(luceneSearch, luceneSearch.getQuery());
 363         @SuppressWarnings("rawtypes")
 364         List<SearchResult<SpecimenOrObservationBase>> searchResults = searchResultBuilder.createResultSet(
 365                 topDocsResultSet, luceneSearch.getHighlightFields(), dao, idFieldMap, propertyPaths);
 366
 367         int totalHits = topDocsResultSet != null ? topDocsResultSet.topGroups.totalGroupCount : 0;
 368
 369         return new DefaultPagerImpl<SearchResult<SpecimenOrObservationBase>>(pageNumber, totalHits, pageSize,
 370                 searchResults);
 371
 372     }
 373
 374
 375     /**
 376      * @param clazz
 377      * @param queryString
 378      * @param languages
 379      * @param highlightFragments
 380      * @return
 381      */
 382     private LuceneSearch prepareByFullTextSearch(Class<? extends SpecimenOrObservationBase> clazz, String queryString, Rectangle bbox,
 383             List<Language> languages, boolean highlightFragments) {
 384
 385         BooleanQuery finalQuery = new BooleanQuery();
 386         BooleanQuery textQuery = new BooleanQuery();
 387
 388         LuceneSearch luceneSearch = new LuceneSearch(luceneIndexToolProvider, FieldUnit.class);
 389         QueryFactory queryFactory = luceneIndexToolProvider.newQueryFactoryFor(FieldUnit.class);
 390
 391         // --- criteria
 392         luceneSearch.setCdmTypRestriction(clazz);
 393         if(queryString != null){
 394             textQuery.add(queryFactory.newTermQuery("titleCache", queryString), Occur.SHOULD);
 395             finalQuery.add(textQuery, Occur.MUST);
 396         }
 397
 398         // --- spacial query
 399         if(bbox != null){
 400             finalQuery.add(QueryFactory.buildSpatialQueryByRange(bbox, "gatheringEvent.exactLocation.point"), Occur.MUST);
 401         }
 402
 403         luceneSearch.setQuery(finalQuery);
 404
 405         // --- sorting
 406         SortField[] sortFields = new  SortField[]{SortField.FIELD_SCORE, new SortField("titleCache__sort", SortField.STRING, false)};
 407         luceneSearch.setSortFields(sortFields);
 408
 409         if(highlightFragments){
 410             luceneSearch.setHighlightFields(queryFactory.getTextFieldNamesAsArray());
 411         }
 412         return luceneSearch;
 413     }
 414
 415
 416     /* (non-Javadoc)
 417      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getFieldUnits(eu.etaxonomy.cdm.model.occurrence.DerivedUnit)
 418      */
 419     @Override
 420     public Collection<FieldUnit> getFieldUnits(UUID derivedUnitUuid) {
 421         //It will search recursively over all {@link DerivationEvent}s and get the "originals" ({@link SpecimenOrObservationBase})
 422         //from which this DerivedUnit was derived until all FieldUnits are found.
 423
 424         //FIXME: use HQL queries to increase performance
 425         Collection<FieldUnit> fieldUnits = new ArrayList<FieldUnit>();
 426         SpecimenOrObservationBase derivedUnit = load(derivedUnitUuid);
 427         if(derivedUnit instanceof DerivedUnit){
 428             getFieldUnits((DerivedUnit) derivedUnit, fieldUnits);
 429         }
 430         return fieldUnits;
 431     }
 432
 433
 434     /**
 435      * @param original
 436      * @param fieldUnits
 437      */
 438     private void getFieldUnits(DerivedUnit derivedUnit, Collection<FieldUnit> fieldUnits) {
 439         Set<SpecimenOrObservationBase> originals = derivedUnit.getOriginals();
 440         if(originals!=null && !originals.isEmpty()){
 441             for(SpecimenOrObservationBase<?> original:originals){
 442                 if(original instanceof FieldUnit){
 443                     fieldUnits.add((FieldUnit) original);
 444                 }
 445                 else if(original instanceof DerivedUnit){
 446                     getFieldUnits((DerivedUnit) original, fieldUnits);
 447                 }
 448             }
 449         }
 450     }
 451
 452     /* (non-Javadoc)
 453      * @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)
 454      */
 455     @Override
 456     public boolean moveSequence(DnaSample from, DnaSample to, Sequence sequence) {
 457         //reload specimens to avoid session conflicts
 458         from = (DnaSample) load(from.getUuid());
 459         to = (DnaSample) load(to.getUuid());
 460         sequence = sequenceService.load(sequence.getUuid());
 461
 462         if(from==null || to==null || sequence==null){
 463             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" +
 464                     "Operation was move "+sequence+ " from "+from+" to "+to);
 465         }
 466         from.removeSequence(sequence);
 467         saveOrUpdate(from);
 468         to.addSequence(sequence);
 469         saveOrUpdate(to);
 470         return true;
 471     }
 472
 473     /* (non-Javadoc)
 474      * @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)
 475      */
 476     @Override
 477     public boolean moveDerivate(SpecimenOrObservationBase<?> from, SpecimenOrObservationBase<?> to, DerivedUnit derivate) {
 478         //reload specimens to avoid session conflicts
 479         from = load(from.getUuid());
 480         to = load(to.getUuid());
 481         derivate = (DerivedUnit) load(derivate.getUuid());
 482
 483         if(from==null || to==null || derivate==null){
 484             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" +
 485                         "Operation was move "+derivate+ " from "+from+" to "+to);
 486         }
 487
 488         SpecimenOrObservationType derivateType = derivate.getRecordBasis();
 489         SpecimenOrObservationType toType = to.getRecordBasis();
 490         //check if type is a sub derivate type
 491         if(toType==SpecimenOrObservationType.FieldUnit //moving to FieldUnit always works
 492                 || derivateType==SpecimenOrObservationType.Media //moving media always works
 493                 || (derivateType.isKindOf(toType) && toType!=derivateType)){ //moving only to parent derivate type
 494             //remove derivation event from parent specimen of dragged object
 495             DerivationEvent eventToRemove = null;
 496             for(DerivationEvent event:from.getDerivationEvents()){
 497                 if(event.getDerivatives().contains(derivate)){
 498                     eventToRemove = event;
 499                     break;
 500                 }
 501             }
 502             from.removeDerivationEvent(eventToRemove);
 503             saveOrUpdate(from);
 504             //add new derivation event to target
 505             to.addDerivationEvent(DerivationEvent.NewSimpleInstance(to, derivate, eventToRemove==null?null:eventToRemove.getType()));
 506             saveOrUpdate(to);
 507             return true;
 508         }
 509         return false;
 510     }
 511
 512     @Override
 513     public Collection<ICdmBase> getNonCascadedAssociatedElements(SpecimenOrObservationBase<?> specimen){
 514         //potential fields that are not persisted cascadingly
 515         /*
 516          * SOOB
 517         -DescriptionBase
 518         -determinations
 519         --modifier TERM
 520         -kindOfUnit TERM
 521         -lifeStage TERM
 522         -sex TERM
 523
 524         FieldUnit
 525         -GatheringEvent
 526         --Country TERM
 527         --CollectingAreas TERM
 528
 529         DerivedUnit
 530         -collection
 531         --institute
 532         ---types TERM
 533         -preservationMethod
 534         --medium TERM
 535         -storedUnder CDM TaxonNameBase
 536         */
 537
 538         Collection<ICdmBase> nonCascadedCdmEntities = new HashSet<ICdmBase>();
 539         //scan SpecimenOrObservationBase
 540         for(DeterminationEvent determinationEvent:specimen.getDeterminations()){
 541             //modifier
 542             if(determinationEvent.getModifier()!=null){
 543                 nonCascadedCdmEntities.add(determinationEvent.getModifier());
 544             }
 545         }
 546         //kindOfUnit
 547         if(specimen.getKindOfUnit()!=null){
 548             nonCascadedCdmEntities.add(specimen.getKindOfUnit());
 549         }
 550         //lifeStage
 551         if(specimen.getLifeStage()!=null){
 552             nonCascadedCdmEntities.add(specimen.getLifeStage());
 553         }
 554         //sex
 555         if(specimen.getSex()!=null){
 556             nonCascadedCdmEntities.add(specimen.getSex());
 557         }
 558
 559         //FieldUnit
 560         if(specimen instanceof FieldUnit){
 561             FieldUnit fieldUnit = (FieldUnit)specimen;
 562             GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
 563             if(gatheringEvent!=null){
 564                 //country
 565                 if(gatheringEvent.getCountry()!=null){
 566                     nonCascadedCdmEntities.add(gatheringEvent.getCountry());
 567                 }
 568                 //collecting areas
 569                 for (NamedArea namedArea : gatheringEvent.getCollectingAreas()) {
 570                     nonCascadedCdmEntities.add(namedArea);
 571                 }
 572             }
 573             for (DerivationEvent derivationEvent : fieldUnit.getDerivationEvents()) {
 574                 for (DerivedUnit derivedUnit : derivationEvent.getDerivatives()) {
 575                     nonCascadedCdmEntities.addAll(getNonCascadedAssociatedElements(derivedUnit));
 576                 }
 577             }
 578         }
 579
 580         //DerivedUnit
 581         else if(specimen instanceof DerivedUnit){
 582             DerivedUnit derivedUnit = (DerivedUnit)specimen;
 583             if(derivedUnit.getCollection()!=null && derivedUnit.getCollection().getInstitute()!=null){
 584                 for (DefinedTerm type : derivedUnit.getCollection().getInstitute().getTypes()) {
 585                     nonCascadedCdmEntities.add(type);
 586                 }
 587             }
 588             if(derivedUnit.getPreservation()!=null && derivedUnit.getPreservation().getMedium()!=null){
 589                 nonCascadedCdmEntities.add(derivedUnit.getPreservation().getMedium());
 590             }
 591             if(derivedUnit.getStoredUnder()!=null){
 592                 nonCascadedCdmEntities.add(derivedUnit.getStoredUnder());
 593             }
 594         }
 595         return nonCascadedCdmEntities;
 596     }
 597
 598 }