cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/OccurrenceServiceTest.java

   1 // $Id$
   2 /**
   3 * Copyright (C) 2014 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 package eu.etaxonomy.cdm.api.service;
  11
  12 import static org.junit.Assert.assertEquals;
  13 import static org.junit.Assert.assertFalse;
  14 import static org.junit.Assert.assertNotEquals;
  15 import static org.junit.Assert.assertTrue;
  16
  17 import java.io.FileNotFoundException;
  18 import java.util.Set;
  19 import java.util.UUID;
  20
  21 import org.apache.log4j.Logger;
  22 import org.junit.Ignore;
  23 import org.junit.Test;
  24 import org.unitils.dbunit.annotation.DataSet;
  25 import org.unitils.spring.annotation.SpringBeanByType;
  26
  27 import eu.etaxonomy.cdm.api.service.config.SpecimenDeleteConfigurator;
  28 import eu.etaxonomy.cdm.api.service.molecular.ISequenceService;
  29 import eu.etaxonomy.cdm.model.agent.Institution;
  30 import eu.etaxonomy.cdm.model.agent.Person;
  31 import eu.etaxonomy.cdm.model.common.CdmBase;
  32 import eu.etaxonomy.cdm.model.common.DefinedTerm;
  33 import eu.etaxonomy.cdm.model.common.IdentifiableSource;
  34 import eu.etaxonomy.cdm.model.common.Language;
  35 import eu.etaxonomy.cdm.model.common.TimePeriod;
  36 import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
  37 import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
  38 import eu.etaxonomy.cdm.model.description.SpecimenDescription;
  39 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  40 import eu.etaxonomy.cdm.model.location.Country;
  41 import eu.etaxonomy.cdm.model.location.NamedArea;
  42 import eu.etaxonomy.cdm.model.location.Point;
  43 import eu.etaxonomy.cdm.model.location.ReferenceSystem;
  44 import eu.etaxonomy.cdm.model.molecular.Amplification;
  45 import eu.etaxonomy.cdm.model.molecular.DnaSample;
  46 import eu.etaxonomy.cdm.model.molecular.Sequence;
  47 import eu.etaxonomy.cdm.model.molecular.SingleRead;
  48 import eu.etaxonomy.cdm.model.name.BotanicalName;
  49 import eu.etaxonomy.cdm.model.name.Rank;
  50 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
  51 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  52 import eu.etaxonomy.cdm.model.name.TypeDesignationBase;
  53 import eu.etaxonomy.cdm.model.occurrence.Collection;
  54 import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
  55 import eu.etaxonomy.cdm.model.occurrence.DerivationEventType;
  56 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  57 import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
  58 import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
  59 import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
  60 import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen;
  61 import eu.etaxonomy.cdm.model.occurrence.PreservationMethod;
  62 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  63 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
  64 import eu.etaxonomy.cdm.model.reference.Reference;
  65 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  66 import eu.etaxonomy.cdm.model.taxon.Taxon;
  67 import eu.etaxonomy.cdm.test.integration.CdmTransactionalIntegrationTest;
  68 import eu.etaxonomy.cdm.test.unitils.CleanSweepInsertLoadStrategy;
  69
  70 /**
  71  * @author pplitzner
  72  * @date 31.03.2014
  73  *
  74  */
  75 public class OccurrenceServiceTest extends CdmTransactionalIntegrationTest {
  76     @SuppressWarnings("unused")
  77     private static final Logger logger = Logger.getLogger(OccurrenceServiceTest.class);
  78
  79     @SpringBeanByType
  80     private IOccurrenceService occurrenceService;
  81
  82     @SpringBeanByType
  83     private ISequenceService sequenceService;
  84
  85     @SpringBeanByType
  86     private ITaxonService taxonService;
  87
  88     @SpringBeanByType
  89     private INameService nameService;
  90
  91     @SpringBeanByType
  92     private IDescriptionService descriptionService;
  93
  94     @Test
  95     public void testGetNonCascadedAssociatedElements(){
  96         //Collection
  97         Collection collection = Collection.NewInstance();
  98         Collection subCollection = Collection.NewInstance();
  99         subCollection.setSuperCollection(collection);
 100
 101         Institution institution = Institution.NewInstance();
 102         institution.addType(DefinedTerm.NewInstitutionTypeInstance("Research and teaching", "botanical garden", "BGBM"));
 103         collection.setInstitute(institution);
 104
 105         //Source
 106         Reference<?> article = ReferenceFactory.newArticle(getReference(), Person.NewInstance(), "title", "pages", "series", "volume", TimePeriod.NewInstance(2014));
 107         IdentifiableSource source = IdentifiableSource.NewPrimarySourceInstance(article, "microCitation");
 108
 109         //FieldUnit
 110         FieldUnit fieldUnit = FieldUnit.NewInstance();
 111         Person primaryCollector = Person.NewInstance();
 112         primaryCollector.setLifespan(TimePeriod.NewInstance(2014));
 113         fieldUnit.setPrimaryCollector(primaryCollector);
 114         fieldUnit.addSource(source);
 115
 116         //GatheringEvent
 117         GatheringEvent gatheringEvent = GatheringEvent.NewInstance();
 118         fieldUnit.setGatheringEvent(gatheringEvent);
 119         gatheringEvent.putLocality(Language.ENGLISH(), "locality");
 120         gatheringEvent.setExactLocation(Point.NewInstance(22.4, -34.2,
 121                 ReferenceSystem.NewInstance("MyReferenceSystem", "label", "labelAbbrev"), 33));
 122         gatheringEvent.setCountry(Country.GERMANY());
 123         gatheringEvent.addCollectingArea(NamedArea.EUROPE());
 124
 125         //Derived Unit
 126         MediaSpecimen mediaSpecimen = MediaSpecimen.NewInstance(SpecimenOrObservationType.StillImage);
 127         mediaSpecimen.setCollection(collection);
 128         BotanicalName storedUnder = BotanicalName.NewInstance(Rank.SPECIES());
 129         mediaSpecimen.setStoredUnder(storedUnder);
 130         PreservationMethod preservation = PreservationMethod.NewInstance(null, "My preservation");
 131         preservation.setMedium(DefinedTerm.NewDnaMarkerInstance("medium", "medium", "medium"));//dummy defined term
 132         mediaSpecimen.setPreservation(preservation);
 133
 134         //DerivationEvent
 135         DerivationEvent event = DerivationEvent.NewInstance(DerivationEventType.ACCESSIONING());
 136         event.addOriginal(fieldUnit);
 137         event.addDerivative(mediaSpecimen);
 138
 139         //SpecOrObservationBase
 140         fieldUnit.setSex(DefinedTerm.SEX_FEMALE());
 141         fieldUnit.setLifeStage(DefinedTerm.NewStageInstance("Live stage", "stage", null));
 142         fieldUnit.setKindOfUnit(DefinedTerm.NewKindOfUnitInstance("Kind of unit", "Kind of unit", null));
 143         fieldUnit.putDefinition(Language.ENGLISH(), "definition");
 144
 145         //Determination
 146         DeterminationEvent determinationEvent = DeterminationEvent.NewInstance(getTaxon(), mediaSpecimen);
 147         determinationEvent.setModifier(DefinedTerm.NewModifierInstance("modifierDescription", "modifierLabel", "mofifierLabelAbbrev"));
 148         determinationEvent.setPreferredFlag(true);
 149         Reference<?> reference = getReference();
 150         determinationEvent.addReference(reference);
 151
 152         /*NonCascaded
 153          * SOOB
 154          *  - sex (FEMALE)
 155          *  - stage (Live stage)
 156          *  - kindOfUnit (Kind of unit)
 157          * GatheringEvent
 158          *  - country (GERMANY)
 159          *  - collectingArea (EUROPE)
 160          *  DerivedUnit
 161          *  - storedUnder (botanical name)
 162          *  DerivedUnit-> Collection -> institiute
 163          *  - type (botanical garden)
 164          *
 165          * */
 166
 167         assertEquals("Incorrect number of non cascaded CDM entities", 9, occurrenceService.getNonCascadedAssociatedElements(fieldUnit).size());
 168         assertEquals("Incorrect number of non cascaded CDM entities", 9, occurrenceService.getNonCascadedAssociatedElements(mediaSpecimen).size());
 169
 170     }
 171     private Reference<?> getReference() {
 172         Reference<?> result = ReferenceFactory.newGeneric();
 173         result.setTitle("some generic reference");
 174         return result;
 175    }
 176    private Taxon getTaxon() {
 177        Reference<?> sec = getReference();
 178        TaxonNameBase<?,?> name = BotanicalName.NewInstance(Rank.GENUS());
 179        Taxon taxon = Taxon.NewInstance(name, sec);
 180        return taxon;
 181
 182    }
 183
 184     @Test
 185     @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="OccurenceServiceTest.move.xml")
 186     public void testMoveDerivate(){
 187         DerivedUnit specimenA = (DerivedUnit) occurrenceService.load(UUID.fromString("35cfb0b3-588d-4eee-9db6-ac9caa44e39a"));
 188         DerivedUnit specimenB = (DerivedUnit) occurrenceService.load(UUID.fromString("09496534-efd0-44c8-b1ce-01a34a8a0229"));
 189         DerivedUnit dnaSample = (DnaSample) occurrenceService.load(UUID.fromString("5995f852-0e78-405c-b849-d923bd6781d9"));
 190
 191
 192         occurrenceService.saveOrUpdate(specimenA);
 193         occurrenceService.saveOrUpdate(specimenB);
 194         occurrenceService.saveOrUpdate(dnaSample);
 195
 196         DerivationEvent originalDerivedFromEvent = DerivationEvent.NewSimpleInstance(specimenA, dnaSample, DerivationEventType.DNA_EXTRACTION());
 197
 198         occurrenceService.moveDerivate(specimenA, specimenB, dnaSample);
 199         assertTrue("DerivationEvent not removed from source!", specimenA.getDerivationEvents().isEmpty());
 200         assertEquals("DerivationEvent not moved to source!", 1, specimenB.getDerivationEvents().size());
 201         DerivationEvent derivationEvent = specimenB.getDerivationEvents().iterator().next();
 202         assertEquals("Moved DerivationEvent not of same type!", DerivationEventType.DNA_EXTRACTION(), derivationEvent.getType());
 203         assertEquals("Wrong number of derivation originals!", 1, derivationEvent.getOriginals().size());
 204         SpecimenOrObservationBase<?> newOriginal = derivationEvent.getOriginals().iterator().next();
 205         assertEquals("Origin of moved object not correct", specimenB, newOriginal);
 206         assertEquals("Wrong number of derivatives!", 1, derivationEvent.getDerivatives().size());
 207         DerivedUnit movedDerivate = derivationEvent.getDerivatives().iterator().next();
 208         assertEquals("Moved derivate has wrong type", SpecimenOrObservationType.DnaSample, movedDerivate.getRecordBasis());
 209         assertNotEquals("DerivationEvent 'derivedFrom' has not been changed after moving", originalDerivedFromEvent, movedDerivate.getDerivedFrom());
 210
 211     }
 212
 213     @Test
 214     @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="OccurenceServiceTest.move.xml")
 215     public void testMoveSequence(){
 216         DnaSample dnaSampleA = (DnaSample) occurrenceService.load(UUID.fromString("5995f852-0e78-405c-b849-d923bd6781d9"));
 217         DnaSample dnaSampleB = (DnaSample) occurrenceService.load(UUID.fromString("85fccc2f-c796-46b3-b2fc-6c9a4d68cfda"));
 218         String consensusSequence = "ATTCG";
 219         Sequence sequence = sequenceService.load(UUID.fromString("6da4f378-9861-4338-861b-7b8073763e7a"));
 220
 221         occurrenceService.saveOrUpdate(dnaSampleA);
 222         occurrenceService.saveOrUpdate(dnaSampleB);
 223         sequenceService.saveOrUpdate(sequence);
 224
 225         dnaSampleA.addSequence(sequence);
 226
 227         occurrenceService.moveSequence(dnaSampleA, dnaSampleB, sequence);
 228         assertEquals("Number of sequences is wrong", 0, dnaSampleA.getSequences().size());
 229         assertEquals("Number of sequences is wrong", 1, dnaSampleB.getSequences().size());
 230         Sequence next = dnaSampleB.getSequences().iterator().next();
 231         assertEquals("Sequences are not equals", sequence, next);
 232         assertEquals("Sequences are not equals", consensusSequence, next.getSequenceString());
 233     }
 234
 235 //    @Test
 236 //    public void testDeleteDerivateHierarchy_FieldUnit(){
 237 //        String assertMessage = "Incorrect number of specimens after deletion.";
 238 //
 239 //        FieldUnit fieldUnit = initDerivateHierarchy();
 240 //
 241 //        //delete field unit
 242 //        occurrenceService.deleteDerivateHierarchy(fieldUnit);
 243 //        commit();
 244 //        assertEquals(assertMessage, 0, occurrenceService.count(SpecimenOrObservationBase.class));
 245 //        assertEquals(assertMessage, 0, occurrenceService.count(FieldUnit.class));
 246 //        assertEquals(assertMessage, 0, occurrenceService.count(DerivedUnit.class));
 247 //        assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
 248 //    }
 249
 250 //    @Test
 251 //    public void testDeleteDerivateHierarchy_DerivedUnit(){
 252 //        String assertMessage = "Incorrect number of specimens after deletion.";
 253 //
 254 //        FieldUnit fieldUnit = initDerivateHierarchy();
 255 //
 256 //        //delete derived unit
 257 //        DerivedUnit derivedUnit = fieldUnit.getDerivationEvents().iterator().next().getDerivatives().iterator().next();
 258 //        occurrenceService.deleteDerivateHierarchy(derivedUnit);
 259 //        commit();
 260 //        assertEquals(assertMessage, 1, occurrenceService.count(SpecimenOrObservationBase.class));
 261 //        assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
 262 //        assertEquals(assertMessage, 0, occurrenceService.count(DerivedUnit.class));
 263 //        assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
 264 //    }
 265
 266     @Test
 267     @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class) //loads OccurrenceServiceTest.xml as base DB
 268     public void testDeleteIndividualAssociatedAndTypeSpecimen(){
 269         FieldUnit associatedFieldUnit = (FieldUnit) occurrenceService.load(UUID.fromString("afbe6682-2bd6-4f9e-ae24-b7479e0e585f"));
 270         DerivedUnit typeSpecimen = (DerivedUnit) occurrenceService.load(UUID.fromString("3699806e-8d2b-4ae6-b96e-d065525b654a"));
 271         BotanicalName name = (BotanicalName) nameService.load(UUID.fromString("da487692-6b8e-4e88-bda8-4afc93ff6461"));
 272         TaxonDescription taxonDescription = (TaxonDescription) descriptionService.load(UUID.fromString("6ef35ede-4906-4f9c-893a-e4186f84dfc4"));
 273         //check initial state (IndividualsAssociation)
 274         Set<DescriptionElementBase> elements = taxonDescription.getElements();
 275         DescriptionElementBase descriptionElement = elements.iterator().next();
 276         assertTrue("wrong type of description element", descriptionElement instanceof IndividualsAssociation);
 277         assertEquals("associated specimen is incorrect", associatedFieldUnit, ((IndividualsAssociation)descriptionElement).getAssociatedSpecimenOrObservation());
 278         //check initial state (Type Designation)
 279         Set<TypeDesignationBase> typeDesignations = name.getTypeDesignations();
 280         TypeDesignationBase typeDesignation = typeDesignations.iterator().next();
 281         assertTrue("wrong type of type designation", typeDesignation instanceof SpecimenTypeDesignation);
 282         assertEquals("type specimen is incorrect", typeSpecimen, ((SpecimenTypeDesignation)typeDesignation).getTypeSpecimen());
 283
 284         SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
 285         config.setDeleteChildren(false);
 286         //delete associated field unit from IndividualsAssociation
 287         config.setDeleteFromIndividualsAssociation(true);
 288         occurrenceService.delete(associatedFieldUnit, config);
 289         assertTrue(((IndividualsAssociation)descriptionElement).getAssociatedSpecimenOrObservation()==null);
 290         //delete type specimen from type designation
 291         config.setDeleteFromTypeDesignation(true);
 292         occurrenceService.delete(typeSpecimen, config);
 293         assertTrue(((SpecimenTypeDesignation)typeDesignation).getTypeSpecimen()==null);
 294
 295     }
 296
 297     @Test
 298     @DataSet(value="OccurrenceService.loadData.xml")
 299     public void testLoadData() {
 300         String fieldUnitUuid = "5a31df5a-2e4d-40b1-8d4e-5754736ae7ef";
 301         String derivedUnitUuid = "18f70977-5d9c-400a-96c4-0cb7a2cd287e";
 302
 303         FieldUnit fieldUnit = (FieldUnit) occurrenceService.load(UUID.fromString(fieldUnitUuid));
 304         DerivedUnit derivedUnit = (DerivedUnit) occurrenceService.load(UUID.fromString(derivedUnitUuid));
 305
 306         assertFalse(fieldUnit.getDerivationEvents().iterator().next().getDerivatives().isEmpty());
 307         assertTrue(derivedUnit.getDerivedFrom()!=null);
 308     }
 309
 310     @Test
 311     @DataSet//(loadStrategy=CleanSweepInsertLoadStrategy.class) //loads OccurrenceServiceTest.xml as base DB
 312     @Ignore
 313     //FIXME re-generate test XML
 314     public void testDeleteDerivateHierarchy_StepByStep(){
 315         String assertMessage = "Incorrect number of specimens after deletion.";
 316         DeleteResult deleteResult = null;
 317         SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
 318         config.setDeleteChildren(false);
 319
 320         FieldUnit fieldUnit = (FieldUnit) occurrenceService.load(UUID.fromString("afbe6682-2bd6-4f9e-ae24-b7479e0e585f"));
 321         DerivedUnit derivedUnit = (DerivedUnit) occurrenceService.load(UUID.fromString("3699806e-8d2b-4ae6-b96e-d065525b654a"));
 322         DnaSample dnaSample = (DnaSample) occurrenceService.load(UUID.fromString("b62d34ae-5093-43dc-b82e-fe60997feda0"));
 323         Sequence consensusSequence = sequenceService.load(UUID.fromString("adec5a43-1bcb-42dc-ba68-9387a200859a"));
 324
 325         //check initial state
 326         assertEquals(assertMessage, 4, occurrenceService.count(SpecimenOrObservationBase.class));
 327         assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
 328         assertEquals(assertMessage, 3, occurrenceService.count(DerivedUnit.class));
 329         assertEquals(assertMessage, 1, occurrenceService.count(DnaSample.class));
 330         assertEquals("number of sequences incorrect", 1, dnaSample.getSequences().size());
 331
 332         //delete sequence
 333         deleteResult = occurrenceService.deleteDerivateHierarchy(consensusSequence, config);
 334         assertTrue(deleteResult.toString(), DeleteResult.DeleteStatus.OK.equals(deleteResult.getStatus()));
 335         assertEquals("number of sequences incorrect", 0, dnaSample.getSequences().size());
 336
 337
 338         //delete dna sample
 339         deleteResult = occurrenceService.deleteDerivateHierarchy(dnaSample, config);
 340         assertTrue(deleteResult.toString(), DeleteResult.DeleteStatus.OK.equals(deleteResult.getStatus()));
 341         assertEquals(assertMessage, 3, occurrenceService.count(SpecimenOrObservationBase.class));
 342         assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
 343         assertEquals(assertMessage, 2, occurrenceService.count(DerivedUnit.class));
 344         assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
 345
 346         //delete derived unit
 347         deleteResult = occurrenceService.deleteDerivateHierarchy(derivedUnit, config);
 348         //deleting type specimen should fail
 349         assertFalse(deleteResult.toString(), DeleteResult.DeleteStatus.OK.equals(deleteResult.getStatus()));
 350         config.setDeleteFromTypeDesignation(true);
 351         deleteResult = occurrenceService.deleteDerivateHierarchy(derivedUnit, config);
 352         //deleting type specimen should work
 353         assertTrue(deleteResult.toString(), DeleteResult.DeleteStatus.OK.equals(deleteResult.getStatus()));
 354         assertEquals(assertMessage, 2, occurrenceService.count(SpecimenOrObservationBase.class));
 355         assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
 356         assertEquals(assertMessage, 1, occurrenceService.count(DerivedUnit.class));
 357         assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
 358
 359         //delete field unit
 360         deleteResult = occurrenceService.deleteDerivateHierarchy(fieldUnit, config);
 361         //deleting specimen with IndividualsAssociation should fail
 362         assertFalse(deleteResult.toString(), DeleteResult.DeleteStatus.OK.equals(deleteResult.getStatus()));
 363         config.setDeleteFromIndividualsAssociation(true);
 364         deleteResult = occurrenceService.deleteDerivateHierarchy(fieldUnit, config);
 365         //deleting specimen with IndividualsAssociation should work
 366         assertTrue(deleteResult.toString(), DeleteResult.DeleteStatus.OK.equals(deleteResult.getStatus()));
 367         assertEquals(assertMessage, 0, occurrenceService.count(SpecimenOrObservationBase.class));
 368         assertEquals(assertMessage, 0, occurrenceService.count(FieldUnit.class));
 369         assertEquals(assertMessage, 0, occurrenceService.count(DerivedUnit.class));
 370         assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
 371     }
 372
 373 //    @Test
 374 //    public void testDeleteDerivateHierarchy_Sequence(){
 375 //        String assertMessage = "Incorrect number of specimens after deletion.";
 376 //
 377 //        FieldUnit fieldUnit = initDerivateHierarchy();
 378 //
 379 //        //delete sequence
 380 //        Sequence consensusSequence = ((DnaSample)fieldUnit.getDerivationEvents().iterator().next().getDerivatives().iterator().next()
 381 //        .getDerivationEvents().iterator().next().getDerivatives().iterator().next()).getSequences().iterator().next();
 382 //        occurrenceService.deleteDerivateHierarchy(consensusSequence);
 383 //        commit();
 384 //        assertEquals(assertMessage, 3, occurrenceService.count(SpecimenOrObservationBase.class));
 385 //        assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
 386 //        assertEquals(assertMessage, 2, occurrenceService.count(DerivedUnit.class));
 387 //        assertEquals(assertMessage, 1, occurrenceService.count(DnaSample.class));
 388 //    }
 389
 390     @Test
 391     @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class)
 392     public void testListAssociatedAndTypedTaxa(){
 393         FieldUnit associatedFieldUnit = (FieldUnit) occurrenceService.load(UUID.fromString("afbe6682-2bd6-4f9e-ae24-b7479e0e585f"));
 394         DerivedUnit typeSpecimen = (DerivedUnit) occurrenceService.load(UUID.fromString("3699806e-8d2b-4ae6-b96e-d065525b654a"));
 395         Taxon taxon = (Taxon) taxonService.load(UUID.fromString("d3668127-be97-47df-bb0b-f03bc1089bc5"));
 396         TaxonDescription taxonDescription = (TaxonDescription) descriptionService.load(UUID.fromString("6ef35ede-4906-4f9c-893a-e4186f84dfc4"));
 397         //check for FieldUnit (IndividualsAssociation)
 398         java.util.Collection<IndividualsAssociation> individualsAssociations = occurrenceService.listIndividualsAssociations(associatedFieldUnit, null, null, null,null);
 399         assertEquals("Number of individuals associations is incorrect", 1, individualsAssociations.size());
 400         IndividualsAssociation individualsAssociation = individualsAssociations.iterator().next();
 401         assertTrue("association has wrong type", individualsAssociation.getInDescription().isInstanceOf(TaxonDescription.class));
 402         //FIXME loading from XML of specimen.derivedFrom an taxonDescription.taxon fails
 403 //        TaxonDescription retrievedTaxonDescription = HibernateProxyHelper.deproxy(individualsAssociation.getInDescription(), TaxonDescription.class);
 404 //        assertEquals(taxonDescription, retrievedTaxonDescription);
 405 //        assertEquals("Associated taxon is incorrect", taxon, retrievedTaxonDescription.getTaxon());
 406
 407
 408         //check for DerivedUnit (Type Designation should exist)
 409         java.util.Collection<SpecimenTypeDesignation> typeDesignations = occurrenceService.listTypeDesignations(typeSpecimen, null, null, null,null);
 410         assertEquals("Number of type designations is incorrect", 1, typeDesignations.size());
 411         SpecimenTypeDesignation specimenTypeDesignation = typeDesignations.iterator().next();
 412         Set<TaxonNameBase> typifiedNames = specimenTypeDesignation.getTypifiedNames();
 413         assertEquals("number of typified names is incorrect", 1, typifiedNames.size());
 414         Set taxonBases = typifiedNames.iterator().next().getTaxonBases();
 415         assertEquals("number of taxa incorrect", 1, taxonBases.size());
 416         Object next = taxonBases.iterator().next();
 417         assertTrue(next instanceof CdmBase && ((CdmBase)next).isInstanceOf(Taxon.class));
 418         assertEquals("Typed taxon is incorrect", taxon, next);
 419     }
 420     /* (non-Javadoc)
 421      * @see eu.etaxonomy.cdm.test.integration.CdmIntegrationTest#createTestData()
 422      */
 423     @Override
 424     protected void createTestDataSet() throws FileNotFoundException {
 425         //how the XML was generated
 426       FieldUnit associatedFieldUnit = FieldUnit.NewInstance();
 427       //sub derivates (DerivedUnit, DnaSample)
 428       DerivedUnit typeSpecimen = DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);
 429       DerivedUnit voucherSpecimen = DerivedUnit.NewInstance(SpecimenOrObservationType.HumanObservation);
 430       DnaSample dnaSample = DnaSample.NewInstance();
 431       //description for voucher specimen (with InidividualsAssociation to type specimen just to make it complex ;) )
 432       SpecimenDescription voucherSpecimenDescription = SpecimenDescription.NewInstance(voucherSpecimen);
 433       voucherSpecimenDescription.addElement(IndividualsAssociation.NewInstance(typeSpecimen));
 434
 435       //derivation events
 436       DerivationEvent.NewSimpleInstance(associatedFieldUnit, typeSpecimen, DerivationEventType.ACCESSIONING());
 437       DerivationEvent.NewSimpleInstance(associatedFieldUnit, voucherSpecimen, DerivationEventType.ACCESSIONING());
 438       DerivationEvent.NewSimpleInstance(typeSpecimen, dnaSample, DerivationEventType.DNA_EXTRACTION());
 439
 440       //DNA (Sequence, SingleRead, Amplification)
 441       Sequence consensusSequence = Sequence.NewInstance(dnaSample, "ATTCG", 5);
 442       SingleRead singleRead = SingleRead.NewInstance();
 443       consensusSequence.addSingleRead(singleRead);
 444       dnaSample.addSequence(consensusSequence);
 445       Amplification amplification = Amplification.NewInstance(dnaSample);
 446       amplification.addSingleRead(singleRead);
 447       occurrenceService.save(associatedFieldUnit);
 448       occurrenceService.save(typeSpecimen);
 449       occurrenceService.save(dnaSample);
 450
 451       //create name with type specimen
 452       BotanicalName name = BotanicalName.PARSED_NAME("Campanula patual sec L.");
 453       SpecimenTypeDesignation typeDesignation = SpecimenTypeDesignation.NewInstance();
 454       typeDesignation.setTypeSpecimen(typeSpecimen);
 455
 456       // create taxon with name and two taxon descriptions (one with
 457       // IndividualsAssociations and a "described" voucher specimen, and an
 458       // empty one)
 459       Taxon taxon = Taxon.NewInstance(name, null);
 460       TaxonDescription taxonDescription = TaxonDescription.NewInstance();
 461       //add voucher
 462       taxonDescription.setDescribedSpecimenOrObservation(voucherSpecimen);
 463       taxonDescription.addElement(IndividualsAssociation.NewInstance(associatedFieldUnit));
 464       taxon.addDescription(taxonDescription);
 465       //add type designation to name
 466       name.addTypeDesignation(typeDesignation, false);
 467       //add another taxon description to taxon which is not associated with a specimen thus should not be taken into account
 468       taxon.addDescription(TaxonDescription.NewInstance());
 469       taxonService.saveOrUpdate(taxon);
 470
 471
 472       commitAndStartNewTransaction(new String[]{"SpecimenOrObservationBase",
 473               "SpecimenOrObservationBase_DerivationEvent",
 474               "DerivationEvent",
 475               "Sequence",
 476               "Sequence_SingleRead",
 477               "SingleRead",
 478               "Amplification",
 479               "Amplification_SingleRead",
 480               "DescriptionElementBase",
 481               "DescriptionBase",
 482               "TaxonBase",
 483               "TypeDesignationBase",
 484               "TaxonNameBase",
 485               "TaxonNameBase_TypeDesignationBase",
 486               "HomotypicalGroup"});
 487     }
 488
 489 }