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/**
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* Copyright (C) 2014 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.api.service;
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import static org.junit.Assert.assertEquals;
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import static org.junit.Assert.assertFalse;
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import static org.junit.Assert.assertNotEquals;
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import static org.junit.Assert.assertNotNull;
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import static org.junit.Assert.assertNull;
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import static org.junit.Assert.assertTrue;
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import java.io.FileNotFoundException;
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import java.util.Collection;
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import java.util.Collections;
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import java.util.List;
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import java.util.Set;
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import java.util.UUID;
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import java.util.stream.Collectors;
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import org.apache.log4j.Logger;
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import org.junit.Test;
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import org.unitils.dbunit.annotation.DataSet;
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import org.unitils.spring.annotation.SpringBeanByType;
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import eu.etaxonomy.cdm.api.service.config.FindOccurrencesConfigurator;
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import eu.etaxonomy.cdm.api.service.config.SpecimenDeleteConfigurator;
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import eu.etaxonomy.cdm.api.service.molecular.ISequenceService;
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
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import eu.etaxonomy.cdm.model.agent.Institution;
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import eu.etaxonomy.cdm.model.agent.Person;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.DefinedTerm;
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import eu.etaxonomy.cdm.model.common.Identifier;
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import eu.etaxonomy.cdm.model.common.TimePeriod;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
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import eu.etaxonomy.cdm.model.description.SpecimenDescription;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.molecular.DnaSample;
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import eu.etaxonomy.cdm.model.molecular.Sequence;
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import eu.etaxonomy.cdm.model.name.IBotanicalName;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
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import eu.etaxonomy.cdm.model.name.TypeDesignationBase;
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import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
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import eu.etaxonomy.cdm.model.occurrence.DerivationEventType;
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
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import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
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import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.SynonymType;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.persistence.dto.SpecimenNodeWrapper;
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import eu.etaxonomy.cdm.persistence.query.AssignmentStatus;
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import eu.etaxonomy.cdm.test.integration.CdmTransactionalIntegrationTest;
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import eu.etaxonomy.cdm.test.unitils.CleanSweepInsertLoadStrategy;
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/**
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* @author pplitzner
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* @since 31.03.2014
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*
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*/
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public class OccurrenceServiceTest extends CdmTransactionalIntegrationTest {
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(OccurrenceServiceTest.class);
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@SpringBeanByType
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private IOccurrenceService occurrenceService;
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@SpringBeanByType
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private ISequenceService sequenceService;
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@SpringBeanByType
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private ITaxonService taxonService;
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@SpringBeanByType
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private ITaxonNodeService taxonNodeService;
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@SpringBeanByType
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private IClassificationService classificationService;
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@SpringBeanByType
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private INameService nameService;
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@SpringBeanByType
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private ITermService termService;
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@SpringBeanByType
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private IDescriptionService descriptionService;
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private Reference getReference() {
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Reference result = ReferenceFactory.newGeneric();
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result.setTitle("some generic reference");
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return result;
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}
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private Taxon getTaxon() {
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Reference sec = getReference();
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TaxonName name = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());
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Taxon taxon = Taxon.NewInstance(name, sec);
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return taxon;
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}
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@Test
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@DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "OccurenceServiceTest.move.xml")
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public void testMoveDerivate() {
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DerivedUnit specimenA = (DerivedUnit) occurrenceService.load(UUID
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.fromString("35cfb0b3-588d-4eee-9db6-ac9caa44e39a"));
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DerivedUnit specimenB = (DerivedUnit) occurrenceService.load(UUID
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.fromString("09496534-efd0-44c8-b1ce-01a34a8a0229"));
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DerivedUnit dnaSample = (DnaSample) occurrenceService.load(UUID
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.fromString("5995f852-0e78-405c-b849-d923bd6781d9"));
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occurrenceService.saveOrUpdate(specimenA);
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occurrenceService.saveOrUpdate(specimenB);
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occurrenceService.saveOrUpdate(dnaSample);
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Person derivationActor = Person.NewTitledInstance("Derivation Actor");
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String derivationDescription = "Derivation Description";
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Institution derivationInstitution = Institution.NewInstance();
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TimePeriod derivationTimePeriod = TimePeriod.NewInstance(2015);
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DerivationEvent originalDerivedFromEvent = DerivationEvent.NewSimpleInstance(specimenA, dnaSample,
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DerivationEventType.DNA_EXTRACTION());
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originalDerivedFromEvent.setActor(derivationActor);
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originalDerivedFromEvent.setDescription(derivationDescription);
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originalDerivedFromEvent.setInstitution(derivationInstitution);
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originalDerivedFromEvent.setTimeperiod(derivationTimePeriod);
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occurrenceService.moveDerivate(specimenA, specimenB, dnaSample);
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assertTrue("DerivationEvent not removed from source!", specimenA.getDerivationEvents().isEmpty());
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assertEquals("DerivationEvent not moved to source!", 1, specimenB.getDerivationEvents().size());
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DerivationEvent derivationEvent = specimenB.getDerivationEvents().iterator().next();
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assertEquals("Moved DerivationEvent not of same type!", DerivationEventType.DNA_EXTRACTION(),
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derivationEvent.getType());
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assertEquals(derivationActor, derivationEvent.getActor());
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assertEquals(derivationDescription, derivationEvent.getDescription());
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assertEquals(derivationInstitution, derivationEvent.getInstitution());
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assertEquals(derivationTimePeriod, derivationEvent.getTimeperiod());
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assertEquals(DerivationEventType.DNA_EXTRACTION(), derivationEvent.getType());
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assertEquals("Wrong number of derivation originals!", 1, derivationEvent.getOriginals().size());
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SpecimenOrObservationBase<?> newOriginal = derivationEvent.getOriginals().iterator().next();
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assertEquals("Target of moved object not correct", specimenB, newOriginal);
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assertEquals("Wrong number of derivatives!", 1, derivationEvent.getDerivatives().size());
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DerivedUnit movedDerivate = derivationEvent.getDerivatives().iterator().next();
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assertEquals("Moved derivate has wrong type", SpecimenOrObservationType.DnaSample,
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movedDerivate.getRecordBasis());
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assertNotEquals("DerivationEvent 'derivedFrom' has not been changed after moving", originalDerivedFromEvent,
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movedDerivate.getDerivedFrom());
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}
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@Test
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@DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "../../database/BlankDataSet.xml")
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public void testMoveDerivateNoParent() {
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DerivedUnit derivedUnit = DerivedUnit.NewInstance(SpecimenOrObservationType.PreservedSpecimen);
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FieldUnit fieldUnit = FieldUnit.NewInstance();
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occurrenceService.saveOrUpdate(fieldUnit);
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occurrenceService.saveOrUpdate(derivedUnit);
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assertEquals("DerivationEvent not moved to source!", 0, fieldUnit.getDerivationEvents().size());
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occurrenceService.moveDerivate(null, fieldUnit, derivedUnit);
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assertEquals("DerivationEvent not moved to source!", 1, fieldUnit.getDerivationEvents().size());
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DerivationEvent derivationEvent = fieldUnit.getDerivationEvents().iterator().next();
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assertNull(derivationEvent.getType());
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assertEquals("Wrong number of derivation originals!", 1, derivationEvent.getOriginals().size());
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SpecimenOrObservationBase<?> newOriginal = derivationEvent.getOriginals().iterator().next();
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assertEquals("Target of moved object not correct", fieldUnit, newOriginal);
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assertEquals("Wrong number of derivatives!", 1, derivationEvent.getDerivatives().size());
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}
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@Test
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@DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "OccurenceServiceTest.move.xml")
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public void testMoveSequence() {
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DnaSample dnaSampleA = (DnaSample) occurrenceService.load(UUID
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.fromString("5995f852-0e78-405c-b849-d923bd6781d9"));
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DnaSample dnaSampleB = (DnaSample) occurrenceService.load(UUID
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.fromString("85fccc2f-c796-46b3-b2fc-6c9a4d68cfda"));
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String consensusSequence = "ATTCG";
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Sequence sequence = sequenceService.load(UUID.fromString("6da4f378-9861-4338-861b-7b8073763e7a"));
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occurrenceService.saveOrUpdate(dnaSampleA);
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occurrenceService.saveOrUpdate(dnaSampleB);
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sequenceService.saveOrUpdate(sequence);
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dnaSampleA.addSequence(sequence);
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occurrenceService.moveSequence(dnaSampleA, dnaSampleB, sequence);
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assertEquals("Number of sequences is wrong", 0, dnaSampleA.getSequences().size());
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assertEquals("Number of sequences is wrong", 1, dnaSampleB.getSequences().size());
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Sequence next = dnaSampleB.getSequences().iterator().next();
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assertEquals("Sequences are not equals", sequence, next);
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assertEquals("Sequences are not equals", consensusSequence, next.getSequenceString());
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}
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@Test
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@DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "OccurrenceServiceTest.testDeleteIndividualAssociatedAndTypeSpecimen.xml")
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public void testDeleteIndividualAssociatedAndTypeSpecimen() {
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final UUID taxonDEscriptionUuid = UUID.fromString("a87a893e-2ea8-427d-a26b-dbd2515d6b8a");
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final UUID botanicalNameUuid = UUID.fromString("a604774e-d66a-4d47-b9d1-d0e38a8c787a");
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final UUID fieldUnitUuid = UUID.fromString("67e81ca8-ff91-4df6-bf48-e4600c7f15a2");
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final UUID derivedUnitUuid = UUID.fromString("d229713b-0123-4f15-bffc-76ae45c37564");
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// //how the XML was generated
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// FieldUnit fieldUnit = FieldUnit.NewInstance();
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// fieldUnit.setUuid(fieldUnitUuid);
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// //sub derivates (DerivedUnit, DnaSample)
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// DerivedUnit derivedUnit =
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// DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);
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// derivedUnit.setUuid(derivedUnitUuid);
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//
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// //derivation events
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// DerivationEvent.NewSimpleInstance(fieldUnit, derivedUnit,
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// DerivationEventType.ACCESSIONING());
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//
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// occurrenceService.save(fieldUnit);
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// occurrenceService.save(derivedUnit);
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//
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// //create name with type specimen
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// BotanicalName name =
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// BotanicalName.PARSED_NAME("Campanula patual sec L.");
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// name.setUuid(BOTANICAL_NAME_UUID);
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// SpecimenTypeDesignation typeDesignation =
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// SpecimenTypeDesignation.NewInstance();
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// typeDesignation.setTypeSpecimen(derivedUnit);
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// //add type designation to name
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// name.addTypeDesignation(typeDesignation, false);
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//
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// // create taxon with name and two taxon descriptions (one with
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// // IndividualsAssociations and a "described" voucher specimen, and an
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// // empty one)
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// Taxon taxon = Taxon.NewInstance(name, null);
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// taxon.setUuid(taxonUuid);
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// TaxonDescription taxonDescription = TaxonDescription.NewInstance();
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// taxonDescription.setUuid(TAXON_DESCRIPTION_UUID);
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// //add voucher
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// taxonDescription.addElement(IndividualsAssociation.NewInstance(fieldUnit));
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// taxon.addDescription(taxonDescription);
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// //add another taxon description to taxon which is not associated with
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// a specimen thus should not be taken into account
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// taxon.addDescription(TaxonDescription.NewInstance());
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// taxonService.saveOrUpdate(taxon);
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//
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//
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// commitAndStartNewTransaction(null);
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//
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// setComplete();
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// endTransaction();
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//
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//
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// try {
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// writeDbUnitDataSetFile(new String[] {
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// "SpecimenOrObservationBase",
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// "SpecimenOrObservationBase_DerivationEvent",
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// "DerivationEvent",
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// "Sequence",
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// "Sequence_SingleRead",
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// "SingleRead",
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// "AmplificationResult",
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// "DescriptionElementBase",
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// "DescriptionBase",
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// "TaxonBase",
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// "TypeDesignationBase",
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// "TaxonName",
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// "TaxonName_TypeDesignationBase",
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// "HomotypicalGroup"
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// }, "testDeleteIndividualAssociatedAndTypeSpecimen");
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// } catch (FileNotFoundException e) {
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// e.printStackTrace();
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// }
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FieldUnit associatedFieldUnit = (FieldUnit) occurrenceService.load(fieldUnitUuid);
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DerivedUnit typeSpecimen = (DerivedUnit) occurrenceService.load(derivedUnitUuid);
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IBotanicalName name = nameService.load(botanicalNameUuid);
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TaxonDescription taxonDescription = (TaxonDescription) descriptionService.load(taxonDEscriptionUuid);
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// check initial state (IndividualsAssociation)
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DescriptionElementBase descriptionElement = taxonDescription.getElements().iterator().next();
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assertTrue("wrong type of description element", descriptionElement.isInstanceOf(IndividualsAssociation.class));
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assertEquals("associated specimen is incorrect", associatedFieldUnit,
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((IndividualsAssociation) descriptionElement).getAssociatedSpecimenOrObservation());
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// check initial state (Type Designation)
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Set<TypeDesignationBase> typeDesignations = name.getTypeDesignations();
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TypeDesignationBase<?> typeDesignation = typeDesignations.iterator().next();
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assertTrue("wrong type of type designation", typeDesignation.isInstanceOf(SpecimenTypeDesignation.class));
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assertEquals("type specimen is incorrect", typeSpecimen,
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((SpecimenTypeDesignation) typeDesignation).getTypeSpecimen());
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SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
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// delete type specimen from type designation
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config.setDeleteFromTypeDesignation(true);
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occurrenceService.delete(typeSpecimen, config);
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assertTrue(((SpecimenTypeDesignation) typeDesignation).getTypeSpecimen() == null);
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// delete associated field unit from IndividualsAssociation
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config.setDeleteFromIndividualsAssociation(true);
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occurrenceService.delete(associatedFieldUnit, config);
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322
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assertTrue(((IndividualsAssociation) descriptionElement).getAssociatedSpecimenOrObservation() == null);
|
|
323
|
|
|
324
|
}
|
|
325
|
|
|
326
|
@Test
|
|
327
|
@DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "OccurrenceService.loadData.xml")
|
|
328
|
public void testLoadData() {
|
|
329
|
String fieldUnitUuid = "5a31df5a-2e4d-40b1-8d4e-5754736ae7ef";
|
|
330
|
String derivedUnitUuid = "18f70977-5d9c-400a-96c4-0cb7a2cd287e";
|
|
331
|
|
|
332
|
FieldUnit fieldUnit = (FieldUnit) occurrenceService.load(UUID.fromString(fieldUnitUuid));
|
|
333
|
DerivedUnit derivedUnit = (DerivedUnit) occurrenceService.load(UUID.fromString(derivedUnitUuid));
|
|
334
|
|
|
335
|
assertFalse(fieldUnit.getDerivationEvents().iterator().next().getDerivatives().isEmpty());
|
|
336
|
assertTrue(derivedUnit.getDerivedFrom() != null);
|
|
337
|
}
|
|
338
|
|
|
339
|
@Test
|
|
340
|
@DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "OccurrenceServiceTest.testListAssociatedAndTypedTaxa.xml")
|
|
341
|
public void testListIndividualsAssociatensAndSpecimenTypeDesignations(){
|
|
342
|
UUID fieldUnitUuid = UUID.fromString("b359ff20-98de-46bf-aa43-3e10bb072cd4");
|
|
343
|
UUID typeSpecimenUuid = UUID.fromString("0f8608c7-ffe7-40e6-828c-cb3382580878");
|
|
344
|
UUID taxonDescriptionUuid = UUID.fromString("d77db2d4-45a1-4aa1-ab34-f33395f54965");
|
|
345
|
UUID taxonUuid = UUID.fromString("b0de794c-8cb7-4369-8f83-870ca37abbe0");
|
|
346
|
// //how the XML was generated
|
|
347
|
// FieldUnit associatedFieldUnit = FieldUnit.NewInstance();
|
|
348
|
// associatedFieldUnit.setUuid(fieldUnitUuid);
|
|
349
|
// //sub derivates (DerivedUnit, DnaSample)
|
|
350
|
// DerivedUnit typeSpecimen =
|
|
351
|
// DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);
|
|
352
|
// typeSpecimen.setUuid(typeSpecimenUuid);
|
|
353
|
//
|
|
354
|
// //derivation events
|
|
355
|
// DerivationEvent.NewSimpleInstance(associatedFieldUnit, typeSpecimen,
|
|
356
|
// DerivationEventType.ACCESSIONING());
|
|
357
|
//
|
|
358
|
// occurrenceService.save(associatedFieldUnit);
|
|
359
|
// occurrenceService.save(typeSpecimen);
|
|
360
|
//
|
|
361
|
// //create name with type specimen
|
|
362
|
// BotanicalName name =
|
|
363
|
// BotanicalName.PARSED_NAME("Campanula patual sec L.");
|
|
364
|
// SpecimenTypeDesignation typeDesignation =
|
|
365
|
// SpecimenTypeDesignation.NewInstance();
|
|
366
|
// typeDesignation.setTypeSpecimen(typeSpecimen);
|
|
367
|
//
|
|
368
|
// // create taxon with name and two taxon descriptions (one with
|
|
369
|
// // IndividualsAssociations and a "described" voucher specimen, and an
|
|
370
|
// // empty one)
|
|
371
|
// Taxon taxon = Taxon.NewInstance(name, null);
|
|
372
|
// taxon.setUuid(taxonUuid);
|
|
373
|
// TaxonDescription taxonDescription = TaxonDescription.NewInstance();
|
|
374
|
// taxonDescription.setUuid(taxonDescriptionUuid);
|
|
375
|
// //add voucher
|
|
376
|
// taxonDescription.addElement(IndividualsAssociation.NewInstance(associatedFieldUnit));
|
|
377
|
// taxon.addDescription(taxonDescription);
|
|
378
|
// //add type designation to name
|
|
379
|
// name.addTypeDesignation(typeDesignation, false);
|
|
380
|
// //add another taxon description to taxon which is not associated with
|
|
381
|
// a specimen thus should not be taken into account
|
|
382
|
// taxon.addDescription(TaxonDescription.NewInstance());
|
|
383
|
// taxonService.saveOrUpdate(taxon);
|
|
384
|
//
|
|
385
|
// commitAndStartNewTransaction(null);
|
|
386
|
//
|
|
387
|
// setComplete();
|
|
388
|
// endTransaction();
|
|
389
|
//
|
|
390
|
// try {
|
|
391
|
// writeDbUnitDataSetFile(new String[]{
|
|
392
|
// "SpecimenOrObservationBase",
|
|
393
|
// "SpecimenOrObservationBase_DerivationEvent",
|
|
394
|
// "DerivationEvent",
|
|
395
|
// "Sequence",
|
|
396
|
// "Sequence_SingleRead",
|
|
397
|
// "SingleRead",
|
|
398
|
// "AmplificationResult",
|
|
399
|
// "DescriptionElementBase",
|
|
400
|
// "DescriptionBase",
|
|
401
|
// "TaxonBase",
|
|
402
|
// "TypeDesignationBase",
|
|
403
|
// "TaxonName",
|
|
404
|
// "TaxonName_TypeDesignationBase",
|
|
405
|
// "HomotypicalGroup"}, "testListAssociatedAndTypedTaxa");
|
|
406
|
// } catch (FileNotFoundException e) {
|
|
407
|
// e.printStackTrace();
|
|
408
|
// }
|
|
409
|
//
|
|
410
|
// System.out.println("associatedFieldUnit.getUuid() " +
|
|
411
|
// associatedFieldUnit.getUuid());
|
|
412
|
// System.out.println("typeSpecimen.getUuid() "+typeSpecimen.getUuid());
|
|
413
|
// System.out.println("taxonDescription.getUuid() "+taxonDescription.getUuid());
|
|
414
|
// System.out.println("taxon.getUuid() "+taxon.getUuid());
|
|
415
|
|
|
416
|
FieldUnit associatedFieldUnit = (FieldUnit) occurrenceService.load(fieldUnitUuid);
|
|
417
|
DerivedUnit typeSpecimen = (DerivedUnit) occurrenceService.load(typeSpecimenUuid);
|
|
418
|
Taxon taxon = (Taxon) taxonService.load(taxonUuid);
|
|
419
|
TaxonDescription taxonDescription = (TaxonDescription) descriptionService.load(taxonDescriptionUuid);
|
|
420
|
// check for FieldUnit (IndividualsAssociation)
|
|
421
|
java.util.Collection<IndividualsAssociation> individualsAssociations = occurrenceService
|
|
422
|
.listIndividualsAssociations(associatedFieldUnit, null, null, null, null);
|
|
423
|
assertEquals("Number of individuals associations is incorrect", 1, individualsAssociations.size());
|
|
424
|
IndividualsAssociation individualsAssociation = individualsAssociations.iterator().next();
|
|
425
|
assertTrue("association has wrong type",
|
|
426
|
individualsAssociation.getInDescription().isInstanceOf(TaxonDescription.class));
|
|
427
|
TaxonDescription retrievedTaxonDescription = HibernateProxyHelper.deproxy(
|
|
428
|
individualsAssociation.getInDescription(), TaxonDescription.class);
|
|
429
|
assertEquals(taxonDescription, retrievedTaxonDescription);
|
|
430
|
assertEquals("Associated taxon is incorrect", taxon, retrievedTaxonDescription.getTaxon());
|
|
431
|
|
|
432
|
// check for DerivedUnit (Type Designation should exist)
|
|
433
|
java.util.Collection<SpecimenTypeDesignation> typeDesignations = occurrenceService.listTypeDesignations(
|
|
434
|
typeSpecimen, null, null, null, null);
|
|
435
|
assertEquals("Number of type designations is incorrect", 1, typeDesignations.size());
|
|
436
|
SpecimenTypeDesignation specimenTypeDesignation = typeDesignations.iterator().next();
|
|
437
|
Set<TaxonName> typifiedNames = specimenTypeDesignation.getTypifiedNames();
|
|
438
|
assertEquals("number of typified names is incorrect", 1, typifiedNames.size());
|
|
439
|
Set<?> taxonBases = typifiedNames.iterator().next().getTaxonBases();
|
|
440
|
assertEquals("number of taxa incorrect", 1, taxonBases.size());
|
|
441
|
Object next = taxonBases.iterator().next();
|
|
442
|
assertTrue(next instanceof CdmBase && ((CdmBase) next).isInstanceOf(Taxon.class));
|
|
443
|
assertEquals("Typed taxon is incorrect", taxon, next);
|
|
444
|
}
|
|
445
|
|
|
446
|
@Test
|
|
447
|
@DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "OccurrenceServiceTest.testIsDeletableWithSpecimenDescription.xml")
|
|
448
|
public void testIsDeletableWithSpecimenDescription() {
|
|
449
|
UUID derivedUnitUuid = UUID.fromString("68095c8e-025d-49f0-8bb2-ed36378b75c3");
|
|
450
|
UUID specimenDescriptionUuid = UUID.fromString("4094f947-ce84-47b1-bad5-e57e33239d3c");
|
|
451
|
// //how the XML was generated
|
|
452
|
// DerivedUnit derivedUnit =
|
|
453
|
// DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);
|
|
454
|
// derivedUnit.setUuid(derivedUnitUuid);
|
|
455
|
// SpecimenDescription specimenDescription =
|
|
456
|
// SpecimenDescription.NewInstance();
|
|
457
|
// specimenDescription.setUuid(specimenDescriptionUuid);
|
|
458
|
// derivedUnit.addDescription(specimenDescription);
|
|
459
|
// occurrenceService.save(derivedUnit);
|
|
460
|
//
|
|
461
|
// commitAndStartNewTransaction(null);
|
|
462
|
//
|
|
463
|
// setComplete();
|
|
464
|
// endTransaction();
|
|
465
|
//
|
|
466
|
// try {
|
|
467
|
// writeDbUnitDataSetFile(new String[] {
|
|
468
|
// "SpecimenOrObservationBase",
|
|
469
|
// "SpecimenOrObservationBase_DerivationEvent",
|
|
470
|
// "DerivationEvent",
|
|
471
|
// "Sequence",
|
|
472
|
// "Sequence_SingleRead",
|
|
473
|
// "SingleRead",
|
|
474
|
// "AmplificationResult",
|
|
475
|
// "DescriptionElementBase",
|
|
476
|
// "DescriptionBase",
|
|
477
|
// "TaxonBase",
|
|
478
|
// "TypeDesignationBase",
|
|
479
|
// "TaxonName",
|
|
480
|
// "TaxonName_TypeDesignationBase",
|
|
481
|
// "HomotypicalGroup"
|
|
482
|
// }, "testIsDeletableWithSpecimenDescription");
|
|
483
|
// } catch (FileNotFoundException e) {
|
|
484
|
// e.printStackTrace();
|
|
485
|
// }
|
|
486
|
|
|
487
|
DerivedUnit derivedUnit = (DerivedUnit) occurrenceService.load(derivedUnitUuid);
|
|
488
|
SpecimenDescription specimenDescription = (SpecimenDescription) descriptionService
|
|
489
|
.load(specimenDescriptionUuid);
|
|
490
|
|
|
491
|
SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
|
|
492
|
DeleteResult deleteResult = null;
|
|
493
|
// delete derivedUnit1
|
|
494
|
deleteResult = occurrenceService.isDeletable(derivedUnit.getUuid(), config);
|
|
495
|
//deletion of specimen description should always work because there are no
|
|
496
|
//specimen description without a specimen
|
|
497
|
assertTrue(deleteResult.toString(), deleteResult.isOk());
|
|
498
|
occurrenceService.delete(derivedUnit, config);
|
|
499
|
specimenDescription = (SpecimenDescription) descriptionService.find(specimenDescriptionUuid);
|
|
500
|
|
|
501
|
assertNull(specimenDescription);
|
|
502
|
}
|
|
503
|
|
|
504
|
@Test
|
|
505
|
@DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "OccurrenceServiceTest.testIsDeletableWithDescribedSpecimenInTaxonDescription.xml")
|
|
506
|
public void testIsDeletableWithDescribedSpecimenInTaxonDescription() {
|
|
507
|
UUID fieldUnitUuid = UUID.fromString("d656a004-38ee-404c-810a-87ffb0ab16c2");
|
|
508
|
// //how the XML was generated
|
|
509
|
// FieldUnit fieldUnit = FieldUnit.NewInstance();
|
|
510
|
// fieldUnit.setUuid(fieldUnitUuid);
|
|
511
|
// DerivedUnit derivedUnit =
|
|
512
|
// DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);
|
|
513
|
//
|
|
514
|
// //derivation events
|
|
515
|
// DerivationEvent.NewSimpleInstance(fieldUnit, derivedUnit,
|
|
516
|
// DerivationEventType.ACCESSIONING());
|
|
517
|
//
|
|
518
|
// occurrenceService.save(fieldUnit);
|
|
519
|
// occurrenceService.save(derivedUnit);
|
|
520
|
//
|
|
521
|
// // create taxon with name and two taxon descriptions
|
|
522
|
// //(one with a "described" voucher specimen, and an empty one)
|
|
523
|
// Taxon taxon =
|
|
524
|
// Taxon.NewInstance(BotanicalName.PARSED_NAME("Campanula patual sec L."),
|
|
525
|
// null);
|
|
526
|
// taxonDescription.setUuid(taxonDescriptionUuid);
|
|
527
|
// //add voucher
|
|
528
|
// taxonDescription.setDescribedSpecimenOrObservation(derivedUnit);
|
|
529
|
// taxon.addDescription(taxonDescription);
|
|
530
|
// //add another taxon description to taxon which is not associated with
|
|
531
|
// a specimen thus should not be taken into account
|
|
532
|
// taxon.addDescription(TaxonDescription.NewInstance());
|
|
533
|
// taxonService.saveOrUpdate(taxon);
|
|
534
|
//
|
|
535
|
//
|
|
536
|
// commitAndStartNewTransaction(null);
|
|
537
|
//
|
|
538
|
// setComplete();
|
|
539
|
// endTransaction();
|
|
540
|
//
|
|
541
|
//
|
|
542
|
// try {
|
|
543
|
// writeDbUnitDataSetFile(new String[] {
|
|
544
|
// "SpecimenOrObservationBase",
|
|
545
|
// "SpecimenOrObservationBase_DerivationEvent",
|
|
546
|
// "DerivationEvent",
|
|
547
|
// "Sequence",
|
|
548
|
// "Sequence_SingleRead",
|
|
549
|
// "SingleRead",
|
|
550
|
// "AmplificationResult",
|
|
551
|
// "DescriptionElementBase",
|
|
552
|
// "DescriptionBase",
|
|
553
|
// "TaxonBase",
|
|
554
|
// "TypeDesignationBase",
|
|
555
|
// "TaxonName",
|
|
556
|
// "TaxonName_TypeDesignationBase",
|
|
557
|
// "HomotypicalGroup"
|
|
558
|
// }, "testIsDeletableWithDescribedSpecimenInTaxonDescription");
|
|
559
|
// } catch (FileNotFoundException e) {
|
|
560
|
// e.printStackTrace();
|
|
561
|
// }
|
|
562
|
|
|
563
|
FieldUnit associatedFieldUnit = (FieldUnit) occurrenceService.load(fieldUnitUuid);
|
|
564
|
|
|
565
|
SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
|
|
566
|
DeleteResult deleteResult = null;
|
|
567
|
// check deletion of field unit -> should fail because of voucher
|
|
568
|
// specimen (describedSpecimen) in TaxonDescription
|
|
569
|
deleteResult = occurrenceService.isDeletable(associatedFieldUnit.getUuid(), config);
|
|
570
|
assertFalse(deleteResult.toString(), deleteResult.isOk());
|
|
571
|
|
|
572
|
// allow deletion from TaxonDescription and deletion of child derivates
|
|
573
|
config.setDeleteFromDescription(true);
|
|
574
|
config.setDeleteChildren(true);
|
|
575
|
deleteResult = occurrenceService.isDeletable(associatedFieldUnit.getUuid(), config);
|
|
576
|
assertTrue(deleteResult.toString(), deleteResult.isOk());
|
|
577
|
}
|
|
578
|
|
|
579
|
@Test
|
|
580
|
@DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "OccurrenceServiceTest.testIsDeletableWithIndividualsAssociationTaxonDescription.xml")
|
|
581
|
public void testIsDeletableWithIndividualsAssociationTaxonDescription() {
|
|
582
|
UUID fieldUnitUuid = UUID.fromString("7978b978-5100-4c7a-82ef-3a23e0f3c723");
|
|
583
|
UUID taxonDescriptionUuid = UUID.fromString("d4b0d561-6e7e-4fd8-bf3c-925530f949eb");
|
|
584
|
// //how the XML was generated
|
|
585
|
// FieldUnit fieldUnit = FieldUnit.NewInstance();
|
|
586
|
// fieldUnit.setUuid(fieldUnitUuid);
|
|
587
|
//
|
|
588
|
// occurrenceService.save(fieldUnit);
|
|
589
|
//
|
|
590
|
// // create taxon with name and two taxon descriptions (one with
|
|
591
|
// // IndividualsAssociations and a "described" voucher specimen, and an
|
|
592
|
// // empty one)
|
|
593
|
// Taxon taxon =
|
|
594
|
// Taxon.NewInstance(BotanicalName.PARSED_NAME("Campanula patual sec L."),
|
|
595
|
// null);
|
|
596
|
// TaxonDescription taxonDescription = TaxonDescription.NewInstance();
|
|
597
|
// taxonDescription.setUuid(taxonDescriptionUuid);
|
|
598
|
// //add voucher
|
|
599
|
// taxonDescription.addElement(IndividualsAssociation.NewInstance(fieldUnit));
|
|
600
|
// taxon.addDescription(taxonDescription);
|
|
601
|
// //add another taxon description to taxon which is not associated with
|
|
602
|
// a specimen thus should not be taken into account
|
|
603
|
// taxon.addDescription(TaxonDescription.NewInstance());
|
|
604
|
// taxonService.saveOrUpdate(taxon);
|
|
605
|
//
|
|
606
|
//
|
|
607
|
// commitAndStartNewTransaction(null);
|
|
608
|
//
|
|
609
|
// setComplete();
|
|
610
|
// endTransaction();
|
|
611
|
//
|
|
612
|
//
|
|
613
|
// try {
|
|
614
|
// writeDbUnitDataSetFile(new String[] {
|
|
615
|
// "SpecimenOrObservationBase",
|
|
616
|
// "SpecimenOrObservationBase_DerivationEvent",
|
|
617
|
// "DerivationEvent",
|
|
618
|
// "Sequence",
|
|
619
|
// "Sequence_SingleRead",
|
|
620
|
// "SingleRead",
|
|
621
|
// "AmplificationResult",
|
|
622
|
// "DescriptionElementBase",
|
|
623
|
// "DescriptionBase",
|
|
624
|
// "TaxonBase",
|
|
625
|
// "TypeDesignationBase",
|
|
626
|
// "TaxonName",
|
|
627
|
// "TaxonName_TypeDesignationBase",
|
|
628
|
// "HomotypicalGroup"
|
|
629
|
// }, "testIsDeletableWithIndividualsAssociationTaxonDescription");
|
|
630
|
// } catch (FileNotFoundException e) {
|
|
631
|
// e.printStackTrace();
|
|
632
|
// }
|
|
633
|
|
|
634
|
FieldUnit associatedFieldUnit = (FieldUnit) occurrenceService.load(fieldUnitUuid);
|
|
635
|
TaxonDescription taxonDescription = (TaxonDescription) descriptionService.load(taxonDescriptionUuid);
|
|
636
|
IndividualsAssociation individualsAssociation = (IndividualsAssociation) taxonDescription.getElements()
|
|
637
|
.iterator().next();
|
|
638
|
|
|
639
|
SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
|
|
640
|
DeleteResult deleteResult = null;
|
|
641
|
// check deletion of field unit -> should fail because of
|
|
642
|
// IndividualAssociation
|
|
643
|
deleteResult = occurrenceService.isDeletable(associatedFieldUnit.getUuid(), config);
|
|
644
|
assertFalse(deleteResult.toString(), deleteResult.isOk());
|
|
645
|
assertTrue(deleteResult.toString(), deleteResult.getRelatedObjects().contains(individualsAssociation));
|
|
646
|
|
|
647
|
// allow deletion of individuals association
|
|
648
|
config.setDeleteFromIndividualsAssociation(true);
|
|
649
|
deleteResult = occurrenceService.isDeletable(associatedFieldUnit.getUuid(), config);
|
|
650
|
assertTrue(deleteResult.toString(), deleteResult.isOk());
|
|
651
|
|
|
652
|
}
|
|
653
|
|
|
654
|
@Test
|
|
655
|
@DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "OccurrenceServiceTest.testIsDeletableWithTypeDesignation.xml")
|
|
656
|
public void testIsDeletableWithTypeDesignation() {
|
|
657
|
UUID derivedUnitUuid = UUID.fromString("f7fd1dc1-3c93-42a7-8279-cde5bfe37ea0");
|
|
658
|
UUID botanicalNameUuid = UUID.fromString("7396430c-c932-4dd3-a45a-40c2808b132e");
|
|
659
|
// DerivedUnit derivedUnit =
|
|
660
|
// DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);
|
|
661
|
// derivedUnit.setUuid(derivedUnitUuid);
|
|
662
|
//
|
|
663
|
// occurrenceService.save(derivedUnit);
|
|
664
|
//
|
|
665
|
// //create name with type specimen
|
|
666
|
// BotanicalName name =
|
|
667
|
// BotanicalName.PARSED_NAME("Campanula patual sec L.");
|
|
668
|
// name.setUuid(botanicalNameUuid);
|
|
669
|
// SpecimenTypeDesignation typeDesignation =
|
|
670
|
// SpecimenTypeDesignation.NewInstance();
|
|
671
|
// typeDesignation.setTypeSpecimen(derivedUnit);
|
|
672
|
// //add type designation to name
|
|
673
|
// name.addTypeDesignation(typeDesignation, false);
|
|
674
|
//
|
|
675
|
// nameService.saveOrUpdate(name);
|
|
676
|
//
|
|
677
|
// commitAndStartNewTransaction(null);
|
|
678
|
//
|
|
679
|
// setComplete();
|
|
680
|
// endTransaction();
|
|
681
|
//
|
|
682
|
//
|
|
683
|
// try {
|
|
684
|
// writeDbUnitDataSetFile(new String[] {
|
|
685
|
// "SpecimenOrObservationBase",
|
|
686
|
// "SpecimenOrObservationBase_DerivationEvent",
|
|
687
|
// "DerivationEvent",
|
|
688
|
// "Sequence",
|
|
689
|
// "Sequence_SingleRead",
|
|
690
|
// "SingleRead",
|
|
691
|
// "AmplificationResult",
|
|
692
|
// "DescriptionElementBase",
|
|
693
|
// "DescriptionBase",
|
|
694
|
// "TaxonBase",
|
|
695
|
// "TypeDesignationBase",
|
|
696
|
// "TaxonName",
|
|
697
|
// "TaxonName_TypeDesignationBase",
|
|
698
|
// "HomotypicalGroup"
|
|
699
|
// }, "testIsDeletableWithTypeDesignation");
|
|
700
|
// } catch (FileNotFoundException e) {
|
|
701
|
// e.printStackTrace();
|
|
702
|
// }
|
|
703
|
|
|
704
|
DerivedUnit typeSpecimen = (DerivedUnit) occurrenceService.load(derivedUnitUuid);
|
|
705
|
|
|
706
|
// create name with type specimen
|
|
707
|
IBotanicalName name = nameService.load(botanicalNameUuid);
|
|
708
|
SpecimenTypeDesignation typeDesignation = (SpecimenTypeDesignation) name.getTypeDesignations().iterator()
|
|
709
|
.next();
|
|
710
|
|
|
711
|
// add type designation to name
|
|
712
|
name.addTypeDesignation(typeDesignation, false);
|
|
713
|
|
|
714
|
SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
|
|
715
|
DeleteResult deleteResult = null;
|
|
716
|
|
|
717
|
// check deletion of specimen
|
|
718
|
deleteResult = occurrenceService.isDeletable(typeSpecimen.getUuid(), config);
|
|
719
|
assertFalse(deleteResult.toString(), deleteResult.isOk());
|
|
720
|
assertTrue(deleteResult.toString(), deleteResult.getRelatedObjects().contains(typeDesignation));
|
|
721
|
|
|
722
|
// allow deletion of type designation
|
|
723
|
config.setDeleteFromTypeDesignation(true);
|
|
724
|
|
|
725
|
deleteResult = occurrenceService.isDeletable(typeSpecimen.getUuid(), config);
|
|
726
|
assertTrue(deleteResult.toString(), deleteResult.isOk());
|
|
727
|
}
|
|
728
|
|
|
729
|
@Test
|
|
730
|
@DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "OccurrenceServiceTest.testIsDeletableWithChildren.xml")
|
|
731
|
public void testIsDeletableWithChildren() {
|
|
732
|
UUID fieldUnitUuid = UUID.fromString("92ada058-4c14-4131-8ecd-b82dc1dd2882");
|
|
733
|
UUID derivedUnitUuid = UUID.fromString("896dffdc-6809-4914-8950-5501fee1c0fd");
|
|
734
|
UUID dnaSampleUuid = UUID.fromString("7efd1d66-ac7f-4202-acdf-a72cbb9c3a21");
|
|
735
|
// if this test fails be sure to check if there are left-over elements
|
|
736
|
// in the DB
|
|
737
|
// e.g. clear by adding "<AMPLIFICATIONRESULT/>" to the data set XML
|
|
738
|
|
|
739
|
// //how the XML was generated
|
|
740
|
// FieldUnit fieldUnit = FieldUnit.NewInstance();
|
|
741
|
// fieldUnit.setUuid(fieldUnitUuid);
|
|
742
|
// //sub derivates (DerivedUnit, DnaSample)
|
|
743
|
// DerivedUnit derivedUnit =
|
|
744
|
// DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);
|
|
745
|
// derivedUnit.setUuid(derivedUnitUuid);
|
|
746
|
// DnaSample dnaSample = DnaSample.NewInstance();
|
|
747
|
// dnaSample.setUuid(dnaSampleUuid);
|
|
748
|
//
|
|
749
|
// //derivation events
|
|
750
|
// DerivationEvent.NewSimpleInstance(fieldUnit, derivedUnit,
|
|
751
|
// DerivationEventType.ACCESSIONING());
|
|
752
|
// DerivationEvent.NewSimpleInstance(derivedUnit, dnaSample,
|
|
753
|
// DerivationEventType.DNA_EXTRACTION());
|
|
754
|
//
|
|
755
|
// occurrenceService.save(fieldUnit);
|
|
756
|
// occurrenceService.save(derivedUnit);
|
|
757
|
// occurrenceService.save(dnaSample);
|
|
758
|
//
|
|
759
|
// commitAndStartNewTransaction(null);
|
|
760
|
//
|
|
761
|
// setComplete();
|
|
762
|
// endTransaction();
|
|
763
|
//
|
|
764
|
// try {
|
|
765
|
// writeDbUnitDataSetFile(new String[] {
|
|
766
|
// "SpecimenOrObservationBase",
|
|
767
|
// "SpecimenOrObservationBase_DerivationEvent",
|
|
768
|
// "DerivationEvent",
|
|
769
|
// "Sequence",
|
|
770
|
// "SingleRead",
|
|
771
|
// "SingleReadAlignment",
|
|
772
|
// "Amplification",
|
|
773
|
// "AmplificationResult",
|
|
774
|
// "DescriptionElementBase",
|
|
775
|
// "DescriptionBase",
|
|
776
|
// "TaxonBase",
|
|
777
|
// "TypeDesignationBase",
|
|
778
|
// "TaxonName",
|
|
779
|
// "TaxonName_TypeDesignationBase",
|
|
780
|
// "HomotypicalGroup"
|
|
781
|
// }, "testIsDeletableWithChildren");
|
|
782
|
// } catch (FileNotFoundException e) {
|
|
783
|
// e.printStackTrace();
|
|
784
|
// }
|
|
785
|
FieldUnit fieldUnit = (FieldUnit) occurrenceService.load(fieldUnitUuid);
|
|
786
|
// sub derivates (DerivedUnit, DnaSample)
|
|
787
|
DerivedUnit derivedUnit = (DerivedUnit) occurrenceService.load(derivedUnitUuid);
|
|
788
|
DnaSample dnaSample = (DnaSample) occurrenceService.load(dnaSampleUuid);
|
|
789
|
|
|
790
|
// derivation events
|
|
791
|
DerivationEvent fieldUnitToDerivedUnitEvent = fieldUnit.getDerivationEvents().iterator().next();
|
|
792
|
DerivationEvent derivedUnitToDnaSampleEvent = derivedUnit.getDerivationEvents().iterator().next();
|
|
793
|
|
|
794
|
SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
|
|
795
|
|
|
796
|
DeleteResult deleteResult = null;
|
|
797
|
// check deletion of DnaSample
|
|
798
|
deleteResult = occurrenceService.isDeletable(dnaSample.getUuid(), config);
|
|
799
|
assertTrue(deleteResult.toString(), deleteResult.isOk());
|
|
800
|
|
|
801
|
// check deletion of Specimen
|
|
802
|
deleteResult = occurrenceService.isDeletable(derivedUnit.getUuid(), config);
|
|
803
|
assertFalse(deleteResult.toString(), deleteResult.isOk());
|
|
804
|
assertTrue(deleteResult.toString(), deleteResult.getRelatedObjects().contains(derivedUnitToDnaSampleEvent));
|
|
805
|
|
|
806
|
// check deletion of fieldUnit
|
|
807
|
deleteResult = occurrenceService.isDeletable(fieldUnit.getUuid(), config);
|
|
808
|
assertFalse(deleteResult.toString(), deleteResult.isOk());
|
|
809
|
assertTrue(deleteResult.toString(), deleteResult.getRelatedObjects().contains(fieldUnitToDerivedUnitEvent));
|
|
810
|
|
|
811
|
// check deletion of Specimen
|
|
812
|
config.setDeleteChildren(true);
|
|
813
|
deleteResult = occurrenceService.isDeletable(derivedUnit.getUuid(), config);
|
|
814
|
assertTrue(deleteResult.toString(), deleteResult.isOk());
|
|
815
|
assertTrue(deleteResult.toString(), deleteResult.getRelatedObjects().contains(derivedUnitToDnaSampleEvent));
|
|
816
|
|
|
817
|
// check deletion of fieldUnit
|
|
818
|
config.setDeleteFromDescription(true);
|
|
819
|
deleteResult = occurrenceService.isDeletable(fieldUnit.getUuid(), config);
|
|
820
|
assertTrue(deleteResult.toString(), deleteResult.isOk());
|
|
821
|
|
|
822
|
}
|
|
823
|
|
|
824
|
@Test
|
|
825
|
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="OccurrenceServiceTest.testListAssociatedTaxaAndListByAssociatedTaxon.xml")
|
|
826
|
public void testListAssociatedTaxaAndListByAssociatedTaxon(){
|
|
827
|
UUID associatedSpecimenUuid = UUID.fromString("6478a387-bc77-4f1b-bfab-671ad786a27e");
|
|
828
|
UUID unassociatedSpecimenUuid = UUID.fromString("820e1af6-9bff-4244-97d3-81fd9a49c91c");
|
|
829
|
UUID typeSpecimenUuid = UUID.fromString("b6f31b9f-f9e2-4bc7-883e-35bd6a9978b4");
|
|
830
|
UUID taxonUuid = UUID.fromString("5613698d-840b-4034-b9b1-1302938e183b");
|
|
831
|
// DerivedUnit typeSpecimen = DerivedUnit.NewInstance(SpecimenOrObservationType.TissueSample);
|
|
832
|
// DerivedUnit associatedSpecimen = DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);
|
|
833
|
// DerivedUnit unassociatedSpecimen = DerivedUnit.NewInstance(SpecimenOrObservationType.PreservedSpecimen);
|
|
834
|
// typeSpecimen.setUuid(typeSpecimenUuid);
|
|
835
|
// associatedSpecimen.setUuid(associatedSpecimenUuid);
|
|
836
|
// unassociatedSpecimen.setUuid(unassociatedSpecimenUuid);
|
|
837
|
//
|
|
838
|
// occurrenceService.save(typeSpecimen);
|
|
839
|
// occurrenceService.save(associatedSpecimen);
|
|
840
|
// occurrenceService.save(unassociatedSpecimen);
|
|
841
|
//
|
|
842
|
// BotanicalName name = BotanicalName.PARSED_NAME("Campanula patula");
|
|
843
|
// SpecimenTypeDesignation typeDesignation = SpecimenTypeDesignation.NewInstance();
|
|
844
|
// typeDesignation.setTypeSpecimen(typeSpecimen);
|
|
845
|
// name.addTypeDesignation(typeDesignation, false);
|
|
846
|
//
|
|
847
|
// Taxon taxon = Taxon.NewInstance(name, null);
|
|
848
|
// taxon.setUuid(taxonUuid);
|
|
849
|
// TaxonDescription taxonDescription = TaxonDescription.NewInstance();
|
|
850
|
//// taxonDescription.setUuid(taxonDescriptionUuid);
|
|
851
|
//
|
|
852
|
// taxonDescription.addElement(IndividualsAssociation.NewInstance(associatedSpecimen));
|
|
853
|
// taxon.addDescription(taxonDescription);
|
|
854
|
//
|
|
855
|
// taxonService.saveOrUpdate(taxon);
|
|
856
|
//
|
|
857
|
// commitAndStartNewTransaction(null);
|
|
858
|
//
|
|
859
|
// setComplete();
|
|
860
|
// endTransaction();
|
|
861
|
//
|
|
862
|
// try {
|
|
863
|
// writeDbUnitDataSetFile(new String[]{
|
|
864
|
// "SpecimenOrObservationBase",
|
|
865
|
// "SpecimenOrObservationBase_DerivationEvent",
|
|
866
|
// "DerivationEvent",
|
|
867
|
// "Sequence",
|
|
868
|
// "Sequence_SingleRead",
|
|
869
|
// "SingleRead",
|
|
870
|
// "AmplificationResult",
|
|
871
|
// "DescriptionElementBase",
|
|
872
|
// "DescriptionBase",
|
|
873
|
// "TaxonBase",
|
|
874
|
// "TypeDesignationBase",
|
|
875
|
// "TaxonName",
|
|
876
|
// "TaxonName_TypeDesignationBase",
|
|
877
|
// "TeamOrPersonBase",
|
|
878
|
// "HomotypicalGroup"}, "testListAssociatedTaxaAndListByAssociatedTaxon");
|
|
879
|
// } catch (FileNotFoundException e) {
|
|
880
|
// e.printStackTrace();
|
|
881
|
// }
|
|
882
|
//check initial state
|
|
883
|
SpecimenOrObservationBase typeSpecimen = occurrenceService.load(typeSpecimenUuid);
|
|
884
|
SpecimenOrObservationBase associatedSpecimen = occurrenceService.load(associatedSpecimenUuid);
|
|
885
|
SpecimenOrObservationBase unassociatedSpecimen = occurrenceService.load(unassociatedSpecimenUuid);
|
|
886
|
Taxon taxon = (Taxon) taxonService.load(taxonUuid);
|
|
887
|
|
|
888
|
assertNotNull(typeSpecimen);
|
|
889
|
assertNotNull(associatedSpecimen);
|
|
890
|
assertNotNull(unassociatedSpecimen);
|
|
891
|
assertNotNull(taxon);
|
|
892
|
|
|
893
|
//check association (IndividualsAssociations + TypeDesignations) specimen -> taxon (name)
|
|
894
|
|
|
895
|
//unassociated specimen
|
|
896
|
java.util.Collection<TaxonBase<?>> associatedTaxa = occurrenceService.listAssociatedTaxa(unassociatedSpecimen, null, null, null, null);
|
|
897
|
assertNotNull(associatedTaxa);
|
|
898
|
assertTrue(associatedTaxa.isEmpty());
|
|
899
|
|
|
900
|
//type specimen
|
|
901
|
associatedTaxa = occurrenceService.listAssociatedTaxa(typeSpecimen, null, null, null, null);
|
|
902
|
assertNotNull(associatedTaxa);
|
|
903
|
assertEquals(1, associatedTaxa.size());
|
|
904
|
assertEquals(taxon, associatedTaxa.iterator().next());
|
|
905
|
|
|
906
|
//associated specimen
|
|
907
|
associatedTaxa = occurrenceService.listAssociatedTaxa(associatedSpecimen, null, null, null, null);
|
|
908
|
assertNotNull(associatedTaxa);
|
|
909
|
assertEquals(1, associatedTaxa.size());
|
|
910
|
assertEquals(taxon, associatedTaxa.iterator().next());
|
|
911
|
|
|
912
|
|
|
913
|
//check association (IndividualsAssociations + TypeDesignations) taxon (name) -> specimen
|
|
914
|
List<DerivedUnit> byAssociatedTaxon = occurrenceService.listByAssociatedTaxon(DerivedUnit.class, null, taxon, null, null, null, null, null);
|
|
915
|
assertNotNull(byAssociatedTaxon);
|
|
916
|
assertEquals(2, byAssociatedTaxon.size());
|
|
917
|
assertTrue(byAssociatedTaxon.contains(associatedSpecimen));
|
|
918
|
assertTrue(byAssociatedTaxon.contains(typeSpecimen));
|
|
919
|
assertTrue(!byAssociatedTaxon.contains(unassociatedSpecimen));
|
|
920
|
|
|
921
|
}
|
|
922
|
|
|
923
|
@Test
|
|
924
|
@DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "OccurrenceServiceTest.testFindOcurrences.xml")
|
|
925
|
public void testFindOccurrences() {
|
|
926
|
UUID derivedUnit1Uuid = UUID.fromString("843bc8c9-c0fe-4735-bf40-82f1996dcefb");
|
|
927
|
UUID derivedUnit2Uuid = UUID.fromString("40cd9cb1-7c74-4e7d-a1f8-8a1e0314e940");
|
|
928
|
UUID dnaSampleUuid = UUID.fromString("364969a6-2457-4e2e-ae1e-29a6fcaa741a");
|
|
929
|
UUID tissueUuid = UUID.fromString("b608613c-1b5a-4882-8b14-d643b6fc5998");
|
|
930
|
|
|
931
|
UUID taxonUuid = UUID.fromString("dfca7629-8a60-4d51-998d-371897f725e9");
|
|
932
|
|
|
933
|
// DerivedUnit derivedUnit =
|
|
934
|
// DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);
|
|
935
|
// derivedUnit.setTitleCache("testUnit1");
|
|
936
|
// derivedUnit.setAccessionNumber("ACC1");
|
|
937
|
// DerivedUnit derivedUnit2 =
|
|
938
|
// DerivedUnit.NewInstance(SpecimenOrObservationType.PreservedSpecimen);
|
|
939
|
// derivedUnit2.setTitleCache("testUnit2");
|
|
940
|
// derivedUnit2.setBarcode("ACC2");
|
|
941
|
// DerivedUnit dnaSample =
|
|
942
|
// DerivedUnit.NewInstance(SpecimenOrObservationType.DnaSample);
|
|
943
|
// dnaSample.setTitleCache("dna");
|
|
944
|
// dnaSample.setCatalogNumber("ACC1");
|
|
945
|
// DerivedUnit tissue =
|
|
946
|
// DerivedUnit.NewInstance(SpecimenOrObservationType.TissueSample);
|
|
947
|
// tissue.setTitleCache("tissue");
|
|
948
|
//
|
|
949
|
// DerivationEvent.NewSimpleInstance(derivedUnit, dnaSample,
|
|
950
|
// DerivationEventType.DNA_EXTRACTION());
|
|
951
|
//
|
|
952
|
// derivedUnit.setUuid(derivedUnit1Uuid);
|
|
953
|
// derivedUnit2.setUuid(derivedUnit2Uuid);
|
|
954
|
// dnaSample.setUuid(dnaSampleUuid);
|
|
955
|
// tissue.setUuid(tissueUuid);
|
|
956
|
//
|
|
957
|
// occurrenceService.save(derivedUnit);
|
|
958
|
// occurrenceService.save(derivedUnit2);
|
|
959
|
// occurrenceService.save(dnaSample);
|
|
960
|
// occurrenceService.save(tissue);
|
|
961
|
//
|
|
962
|
// Taxon taxon =
|
|
963
|
// Taxon.NewInstance(BotanicalName.PARSED_NAME("Campanula patual"),
|
|
964
|
// null);
|
|
965
|
// taxon.setUuid(taxonUuid);
|
|
966
|
// TaxonDescription taxonDescription = TaxonDescription.NewInstance();
|
|
967
|
// taxonDescription.setUuid(UUID.fromString("272d4d28-662c-468e-94d8-16993fab91ba"));
|
|
968
|
// //add voucher
|
|
969
|
// taxonDescription.addElement(IndividualsAssociation.NewInstance(derivedUnit));
|
|
970
|
// taxonDescription.addElement(IndividualsAssociation.NewInstance(tissue));
|
|
971
|
// taxon.addDescription(taxonDescription);
|
|
972
|
// taxonService.saveOrUpdate(taxon);
|
|
973
|
//
|
|
974
|
// commitAndStartNewTransaction(null);
|
|
975
|
//
|
|
976
|
// setComplete();
|
|
977
|
// endTransaction();
|
|
978
|
//
|
|
979
|
//
|
|
980
|
// try {
|
|
981
|
// writeDbUnitDataSetFile(new String[] {
|
|
982
|
// "SpecimenOrObservationBase",
|
|
983
|
// "SpecimenOrObservationBase_DerivationEvent",
|
|
984
|
// "DerivationEvent",
|
|
985
|
// "DescriptionElementBase",
|
|
986
|
// "DescriptionBase",
|
|
987
|
// "TaxonBase",
|
|
988
|
// "TypeDesignationBase",
|
|
989
|
// "TaxonName",
|
|
990
|
// "TaxonName_TypeDesignationBase",
|
|
991
|
// "HomotypicalGroup",
|
|
992
|
// "TeamOrPersonBase"
|
|
993
|
// }, "testFindOcurrences");
|
|
994
|
// } catch (FileNotFoundException e) {
|
|
995
|
// e.printStackTrace();
|
|
996
|
// }
|
|
997
|
|
|
998
|
SpecimenOrObservationBase derivedUnit1 = occurrenceService.load(derivedUnit1Uuid);
|
|
999
|
SpecimenOrObservationBase derivedUnit2 = occurrenceService.load(derivedUnit2Uuid);
|
|
1000
|
SpecimenOrObservationBase tissue = occurrenceService.load(tissueUuid);
|
|
1001
|
SpecimenOrObservationBase dnaSample = occurrenceService.load(dnaSampleUuid);
|
|
1002
|
Taxon taxon = (Taxon) taxonService.load(taxonUuid);
|
|
1003
|
|
|
1004
|
assertNotNull(derivedUnit1);
|
|
1005
|
assertNotNull(derivedUnit2);
|
|
1006
|
assertNotNull(tissue);
|
|
1007
|
assertNotNull(dnaSample);
|
|
1008
|
assertNotNull(taxon);
|
|
1009
|
|
|
1010
|
// wildcard search => all derivates
|
|
1011
|
FindOccurrencesConfigurator config = new FindOccurrencesConfigurator();
|
|
1012
|
config.setTitleSearchString("*");
|
|
1013
|
assertEquals(4, occurrenceService.countOccurrences(config));
|
|
1014
|
List<SpecimenOrObservationBase> allDerivates = occurrenceService.findByTitle(config).getRecords();
|
|
1015
|
assertEquals(4, allDerivates.size());
|
|
1016
|
assertTrue(allDerivates.contains(derivedUnit1));
|
|
1017
|
assertTrue(allDerivates.contains(derivedUnit2));
|
|
1018
|
assertTrue(allDerivates.contains(tissue));
|
|
1019
|
assertTrue(allDerivates.contains(dnaSample));
|
|
1020
|
|
|
1021
|
// queryString search => 2 derivates
|
|
1022
|
config = new FindOccurrencesConfigurator();
|
|
1023
|
config.setTitleSearchString("test*");
|
|
1024
|
// config.setClazz(SpecimenOrObservationBase.class);
|
|
1025
|
assertEquals(2, occurrenceService.countOccurrences(config));
|
|
1026
|
List<SpecimenOrObservationBase> queryStringDerivates = occurrenceService.findByTitle(config).getRecords();
|
|
1027
|
assertEquals(2, queryStringDerivates.size());
|
|
1028
|
assertTrue(queryStringDerivates.contains(derivedUnit1));
|
|
1029
|
assertTrue(queryStringDerivates.contains(derivedUnit2));
|
|
1030
|
|
|
1031
|
// class search => 4 results
|
|
1032
|
config = new FindOccurrencesConfigurator();
|
|
1033
|
config.setClazz(SpecimenOrObservationBase.class);
|
|
1034
|
assertEquals(4, occurrenceService.countOccurrences(config));
|
|
1035
|
List<SpecimenOrObservationBase> specimenOrObservationBases = occurrenceService.findByTitle(config).getRecords();
|
|
1036
|
assertEquals(4, specimenOrObservationBases.size());
|
|
1037
|
|
|
1038
|
// class search => 0 results
|
|
1039
|
config = new FindOccurrencesConfigurator();
|
|
1040
|
config.setClazz(FieldUnit.class);
|
|
1041
|
assertEquals(0, occurrenceService.countOccurrences(config));
|
|
1042
|
List<SpecimenOrObservationBase> fieldUnits = occurrenceService.findByTitle(config).getRecords();
|
|
1043
|
assertEquals(0, fieldUnits.size());
|
|
1044
|
|
|
1045
|
// class search => 4 results
|
|
1046
|
config = new FindOccurrencesConfigurator();
|
|
1047
|
config.setClazz(DerivedUnit.class);
|
|
1048
|
assertEquals(4, occurrenceService.countOccurrences(config));
|
|
1049
|
List<SpecimenOrObservationBase> derivedUnits = occurrenceService.findByTitle(config).getRecords();
|
|
1050
|
assertEquals(4, derivedUnits.size());
|
|
1051
|
assertTrue(derivedUnits.contains(derivedUnit1));
|
|
1052
|
assertTrue(derivedUnits.contains(derivedUnit2));
|
|
1053
|
assertTrue(derivedUnits.contains(tissue));
|
|
1054
|
assertTrue(derivedUnits.contains(dnaSample));
|
|
1055
|
|
|
1056
|
// significant identifier search
|
|
1057
|
config = new FindOccurrencesConfigurator();
|
|
1058
|
config.setClazz(DerivedUnit.class);
|
|
1059
|
config.setSignificantIdentifier("ACC1");
|
|
1060
|
assertEquals(2, occurrenceService.countOccurrences(config));
|
|
1061
|
List<SpecimenOrObservationBase> accessionedUnits = occurrenceService.findByTitle(config).getRecords();
|
|
1062
|
assertEquals(2, accessionedUnits.size());
|
|
1063
|
assertTrue(accessionedUnits.contains(derivedUnit1));
|
|
1064
|
assertFalse(accessionedUnits.contains(derivedUnit2));
|
|
1065
|
assertFalse(accessionedUnits.contains(tissue));
|
|
1066
|
assertTrue(accessionedUnits.contains(dnaSample));
|
|
1067
|
|
|
1068
|
config = new FindOccurrencesConfigurator();
|
|
1069
|
config.setClazz(DerivedUnit.class);
|
|
1070
|
config.setSignificantIdentifier("ACC2");
|
|
1071
|
assertEquals(1, occurrenceService.countOccurrences(config));
|
|
1072
|
List<SpecimenOrObservationBase> barcodedUnits = occurrenceService.findByTitle(config).getRecords();
|
|
1073
|
assertEquals(1, barcodedUnits.size());
|
|
1074
|
assertFalse(barcodedUnits.contains(derivedUnit1));
|
|
1075
|
assertTrue(barcodedUnits.contains(derivedUnit2));
|
|
1076
|
assertFalse(barcodedUnits.contains(tissue));
|
|
1077
|
assertFalse(barcodedUnits.contains(dnaSample));
|
|
1078
|
|
|
1079
|
// recordBasis search => 1 Fossil
|
|
1080
|
config = new FindOccurrencesConfigurator();
|
|
1081
|
config.setSpecimenType(SpecimenOrObservationType.Fossil);
|
|
1082
|
assertEquals(1, occurrenceService.countOccurrences(config));
|
|
1083
|
List<SpecimenOrObservationBase> fossils = occurrenceService.findByTitle(config).getRecords();
|
|
1084
|
assertEquals(1, fossils.size());
|
|
1085
|
assertTrue(fossils.contains(derivedUnit1));
|
|
1086
|
|
|
1087
|
// taxon determination search => 2 associated specimens
|
|
1088
|
config = new FindOccurrencesConfigurator();
|
|
1089
|
config.setClazz(DerivedUnit.class);
|
|
1090
|
config.setAssociatedTaxonUuid(taxon.getUuid());
|
|
1091
|
assertEquals(2, occurrenceService.countOccurrences(config));
|
|
1092
|
List<SpecimenOrObservationBase> associatedSpecimens = occurrenceService.findByTitle(config).getRecords();
|
|
1093
|
assertEquals(2, associatedSpecimens.size());
|
|
1094
|
assertTrue(associatedSpecimens.contains(derivedUnit1));
|
|
1095
|
assertTrue(associatedSpecimens.contains(tissue));
|
|
1096
|
|
|
1097
|
// taxon determination search (indirectly associated) => 3 associated
|
|
1098
|
// specimens
|
|
1099
|
config = new FindOccurrencesConfigurator();
|
|
1100
|
config.setClazz(DerivedUnit.class);
|
|
1101
|
config.setAssociatedTaxonUuid(taxon.getUuid());
|
|
1102
|
config.setRetrieveIndirectlyAssociatedSpecimens(true);
|
|
1103
|
assertEquals(3, occurrenceService.countOccurrences(config));
|
|
1104
|
List<SpecimenOrObservationBase> indirectlyAssociatedSpecimens = occurrenceService.findByTitle(config)
|
|
1105
|
.getRecords();
|
|
1106
|
assertEquals(3, indirectlyAssociatedSpecimens.size());
|
|
1107
|
assertTrue(indirectlyAssociatedSpecimens.contains(derivedUnit1));
|
|
1108
|
assertTrue(indirectlyAssociatedSpecimens.contains(dnaSample));
|
|
1109
|
assertTrue(indirectlyAssociatedSpecimens.contains(tissue));
|
|
1110
|
|
|
1111
|
// taxon association search
|
|
1112
|
config = new FindOccurrencesConfigurator();
|
|
1113
|
config.setClazz(SpecimenOrObservationBase.class);
|
|
1114
|
config.setAssociatedTaxonUuid(taxon.getUuid());
|
|
1115
|
assertEquals(2, occurrenceService.countOccurrences(config));
|
|
1116
|
List<SpecimenOrObservationBase> specimensOrObservations = occurrenceService.findByTitle(config).getRecords();
|
|
1117
|
assertEquals(2, specimensOrObservations.size());
|
|
1118
|
assertTrue(specimensOrObservations.contains(tissue));
|
|
1119
|
assertTrue(specimensOrObservations.contains(derivedUnit1));
|
|
1120
|
|
|
1121
|
//test assignment status
|
|
1122
|
//all specimen
|
|
1123
|
config = new FindOccurrencesConfigurator();
|
|
1124
|
config.setAssignmentStatus(AssignmentStatus.ALL_SPECIMENS);
|
|
1125
|
assertEquals(4, occurrenceService.countOccurrences(config));
|
|
1126
|
List<SpecimenOrObservationBase> allSpecimens = occurrenceService.findByTitle(config).getRecords();
|
|
1127
|
assertEquals(4, allSpecimens.size());
|
|
1128
|
assertTrue(allSpecimens.contains(derivedUnit1));
|
|
1129
|
assertTrue(allSpecimens.contains(derivedUnit2));
|
|
1130
|
assertTrue(allSpecimens.contains(tissue));
|
|
1131
|
assertTrue(allSpecimens.contains(dnaSample));
|
|
1132
|
|
|
1133
|
//assigned specimen
|
|
1134
|
config = new FindOccurrencesConfigurator();
|
|
1135
|
config.setAssignmentStatus(AssignmentStatus.ASSIGNED_SPECIMENS);
|
|
1136
|
assertEquals(2, occurrenceService.countOccurrences(config));
|
|
1137
|
List<SpecimenOrObservationBase> assignedSpecimens = occurrenceService.findByTitle(config).getRecords();
|
|
1138
|
assertEquals(2, assignedSpecimens.size());
|
|
1139
|
assertTrue(assignedSpecimens.contains(derivedUnit1));
|
|
1140
|
assertTrue(assignedSpecimens.contains(tissue));
|
|
1141
|
|
|
1142
|
//unassigned specimen
|
|
1143
|
config = new FindOccurrencesConfigurator();
|
|
1144
|
config.setAssignmentStatus(AssignmentStatus.UNASSIGNED_SPECIMENS);
|
|
1145
|
assertEquals(2, occurrenceService.countOccurrences(config));
|
|
1146
|
List<SpecimenOrObservationBase> unAssignedSpecimens = occurrenceService.findByTitle(config).getRecords();
|
|
1147
|
assertEquals(2, unAssignedSpecimens.size());
|
|
1148
|
assertTrue(unAssignedSpecimens.contains(derivedUnit2));
|
|
1149
|
assertTrue(unAssignedSpecimens.contains(dnaSample));
|
|
1150
|
|
|
1151
|
//ignore assignment status because taxon uuid is set
|
|
1152
|
config = new FindOccurrencesConfigurator();
|
|
1153
|
config.setAssociatedTaxonUuid(taxon.getUuid());
|
|
1154
|
config.setAssignmentStatus(AssignmentStatus.UNASSIGNED_SPECIMENS);
|
|
1155
|
assertEquals(2, occurrenceService.countOccurrences(config));
|
|
1156
|
List<SpecimenOrObservationBase> ignoreAssignmentStatusSpecimens = occurrenceService.findByTitle(config).getRecords();
|
|
1157
|
assertEquals(2, ignoreAssignmentStatusSpecimens.size());
|
|
1158
|
assertTrue(ignoreAssignmentStatusSpecimens.contains(derivedUnit1));
|
|
1159
|
assertTrue(ignoreAssignmentStatusSpecimens.contains(tissue));
|
|
1160
|
|
|
1161
|
|
|
1162
|
}
|
|
1163
|
|
|
1164
|
@Test
|
|
1165
|
@DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "OccurrenceServiceTest-testAllKindsOfSpecimenAssociations.xml")
|
|
1166
|
public void testListUuidAndTitleCacheByAssociatedTaxon() {
|
|
1167
|
UUID taxonNodeUuid = UUID.fromString("6b8b6ff9-66e4-4496-8e5a-7d03bdf9a076");
|
|
1168
|
/**
|
|
1169
|
* Structure is as follows:
|
|
1170
|
*
|
|
1171
|
* Taxon ----IndividualsAssociation---> DnaSample
|
|
1172
|
* Taxon ----TypeDesignation---> Fossil
|
|
1173
|
* Taxon ----Determination ---> PreservedSpecimenA
|
|
1174
|
*
|
|
1175
|
* Taxon ---> Taxon Name ----Determination ---> PreservedSpecimenB
|
|
1176
|
*
|
|
1177
|
* Taxon ---> Synonym ---> SynonymName ----Determination---> PreservedSpecimenC
|
|
1178
|
*
|
|
1179
|
* Orphan Name (not associated with any taxon) ----Determination ---> PreservedSpecimenD
|
|
1180
|
*/
|
|
1181
|
|
|
1182
|
//UUIDS
|
|
1183
|
UUID derivedUnitDeterminationTaxonUuid = UUID.fromString("941b8b22-1925-4b91-8ff8-97114499bb22");
|
|
1184
|
UUID derivedUnitDeterminationNameUuid = UUID.fromString("0cdc7a57-6f55-45c8-b3e5-523748c381e7");
|
|
1185
|
UUID derivedUnitDeterminationSynonymNameUuid = UUID.fromString("d940a940-8caf-4a52-b1d8-ba4aad7ddae2");
|
|
1186
|
UUID derivedUnitDeterminationOrphanNameUuid = UUID.fromString("587b7297-7d59-4f59-8ef3-c7a559cadeca");
|
|
1187
|
UUID tissueUuidNoAssociationUuid = UUID.fromString("93e94260-5107-4b2c-9ce4-da9e1a4e7cb9");
|
|
1188
|
UUID dnaSampleUuidIndividualsAssociationUuid = UUID.fromString("1fb53903-c9b9-4078-8297-5b86aec7fe21");
|
|
1189
|
UUID fossilTypeDesignationUuid = UUID.fromString("42ec8dcf-a923-4256-bbd5-b0d10f4de5e2");
|
|
1190
|
UUID taxonUuid = UUID.fromString("07cc47a5-1a63-46a1-8366-0d59d2b90d5b");
|
|
1191
|
|
|
1192
|
/*
|
|
1193
|
* search for taxon node
|
|
1194
|
* should retrieve all specimens associated via
|
|
1195
|
* - type designations (fossil)
|
|
1196
|
* - individuals associations (dnaSample)
|
|
1197
|
* - determinations on
|
|
1198
|
* - taxon (specimenA)
|
|
1199
|
* - taxon name (specimenA, specimenB)
|
|
1200
|
*/
|
|
1201
|
FindOccurrencesConfigurator config = new FindOccurrencesConfigurator();
|
|
1202
|
config.setAssociatedTaxonUuid(taxonUuid);
|
|
1203
|
Collection<SpecimenNodeWrapper> specimens = occurrenceService
|
|
1204
|
.listUuidAndTitleCacheByAssociatedTaxon(Collections.singletonList(taxonNodeUuid), null, null);
|
|
1205
|
List<UUID> uuidList = specimens.stream().map(specimen ->
|
|
1206
|
specimen.getUuidAndTitleCache().getUuid()).collect(Collectors.toList());
|
|
1207
|
assertTrue(uuidList.contains(derivedUnitDeterminationNameUuid));
|
|
1208
|
assertTrue(uuidList.contains(derivedUnitDeterminationTaxonUuid));
|
|
1209
|
assertFalse(uuidList.contains(derivedUnitDeterminationSynonymNameUuid));
|
|
1210
|
assertTrue(uuidList.contains(dnaSampleUuidIndividualsAssociationUuid));
|
|
1211
|
assertTrue(uuidList.contains(fossilTypeDesignationUuid));
|
|
1212
|
assertFalse(uuidList.contains(tissueUuidNoAssociationUuid));
|
|
1213
|
assertFalse(uuidList.contains(derivedUnitDeterminationOrphanNameUuid));
|
|
1214
|
assertEquals("Wrong number of associated specimens", 4, specimens.size());
|
|
1215
|
}
|
|
1216
|
|
|
1217
|
/**
|
|
1218
|
* This will test the retrieval of specimens that are in any way associated
|
|
1219
|
* with a taxon resp. taxon name via type designation, determination event
|
|
1220
|
* or individuals associations. It will also consider synonym relationships.
|
|
1221
|
*/
|
|
1222
|
@Test
|
|
1223
|
@DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "OccurrenceServiceTest-testAllKindsOfSpecimenAssociations.xml")
|
|
1224
|
public void testAllKindsOfSpecimenAssociations() {
|
|
1225
|
|
|
1226
|
/**
|
|
1227
|
* Structure is as follows:
|
|
1228
|
*
|
|
1229
|
* Taxon ----IndividualsAssociation---> DnaSample
|
|
1230
|
* Taxon ----TypeDesignation---> Fossil
|
|
1231
|
* Taxon ----Determination ---> PreservedSpecimenA
|
|
1232
|
*
|
|
1233
|
* Taxon ---> Taxon Name ----Determination ---> PreservedSpecimenB
|
|
1234
|
*
|
|
1235
|
* Taxon ---> Synonym ---> SynonymName ----Determination---> PreservedSpecimenC
|
|
1236
|
*
|
|
1237
|
* Orphan Name (not associated with any taxon) ----Determination ---> PreservedSpecimenD
|
|
1238
|
*/
|
|
1239
|
|
|
1240
|
//UUIDS
|
|
1241
|
UUID derivedUnitDeterminationTaxonUuid = UUID.fromString("941b8b22-1925-4b91-8ff8-97114499bb22");
|
|
1242
|
UUID derivedUnitDeterminationNameUuid = UUID.fromString("0cdc7a57-6f55-45c8-b3e5-523748c381e7");
|
|
1243
|
|
|
1244
|
UUID derivedUnitDeterminationSynonymUuid = UUID.fromString("8eb94a7d-c802-49a7-bc10-c26de20a52c2");
|
|
1245
|
UUID derivedUnitDeterminationSynonymNameUuid = UUID.fromString("d940a940-8caf-4a52-b1d8-ba4aad7ddae2");
|
|
1246
|
|
|
1247
|
UUID derivedUnitDeterminationOrphanNameUuid = UUID.fromString("587b7297-7d59-4f59-8ef3-c7a559cadeca");
|
|
1248
|
|
|
1249
|
UUID tissueUuidNoAssociationUuid = UUID.fromString("93e94260-5107-4b2c-9ce4-da9e1a4e7cb9");
|
|
1250
|
UUID dnaSampleUuidIndividualsAssociationUuid = UUID.fromString("1fb53903-c9b9-4078-8297-5b86aec7fe21");
|
|
1251
|
UUID fossilTypeDesignationUuid = UUID.fromString("42ec8dcf-a923-4256-bbd5-b0d10f4de5e2");
|
|
1252
|
|
|
1253
|
UUID taxonUuid = UUID.fromString("07cc47a5-1a63-46a1-8366-0d59d2b90d5b");
|
|
1254
|
UUID synoymUuid = UUID.fromString("c16bcd9b-7d18-4fb5-af60-f9ef14c1d3a9");
|
|
1255
|
|
|
1256
|
UUID taxonNameUuid = UUID.fromString("e59b95c0-9ad6-48be-af62-a982ba72b917");
|
|
1257
|
UUID synonymNameUuid = UUID.fromString("39f04b2a-b8bd-46e8-9102-ab665c64ec8e");
|
|
1258
|
UUID orphanNameUuid = UUID.fromString("d8e56365-3ad9-4b0e-88bf-acaaab223a9b");
|
|
1259
|
|
|
1260
|
//load cdm entities
|
|
1261
|
DerivedUnit derivedUnitDeterminationTaxon = (DerivedUnit) occurrenceService.load(derivedUnitDeterminationTaxonUuid);
|
|
1262
|
DerivedUnit derivedUnitDeterminationName = (DerivedUnit) occurrenceService.load(derivedUnitDeterminationNameUuid);
|
|
1263
|
DerivedUnit derivedUnitDeterminationSynonym = (DerivedUnit) occurrenceService.load(derivedUnitDeterminationSynonymUuid);
|
|
1264
|
DerivedUnit derivedUnitDeterminationSynonymName = (DerivedUnit) occurrenceService.load(derivedUnitDeterminationSynonymNameUuid);
|
|
1265
|
DerivedUnit derivedUnitDeterminationOrphanName = (DerivedUnit) occurrenceService.load(derivedUnitDeterminationOrphanNameUuid);
|
|
1266
|
DerivedUnit tissueUuidNoAssociation = (DerivedUnit) occurrenceService.load(tissueUuidNoAssociationUuid);
|
|
1267
|
DnaSample dnaSampleUuidIndividualsAssociation = (DnaSample) occurrenceService.load(dnaSampleUuidIndividualsAssociationUuid);
|
|
1268
|
DerivedUnit fossilTypeDesignation = (DerivedUnit) occurrenceService.load(fossilTypeDesignationUuid);
|
|
1269
|
Taxon taxon = (Taxon) taxonService.load(taxonUuid);
|
|
1270
|
Synonym synonym = (Synonym) taxonService.load(synoymUuid);
|
|
1271
|
TaxonName taxonName = nameService.load(taxonNameUuid);
|
|
1272
|
TaxonName synonymName = nameService.load(synonymNameUuid);
|
|
1273
|
TaxonName orphanName = nameService.load(orphanNameUuid);
|
|
1274
|
|
|
1275
|
//check initial state
|
|
1276
|
assertNotNull(derivedUnitDeterminationTaxon);
|
|
1277
|
assertNotNull(derivedUnitDeterminationName);
|
|
1278
|
assertNotNull(derivedUnitDeterminationSynonym);
|
|
1279
|
assertNotNull(derivedUnitDeterminationSynonymName);
|
|
1280
|
assertNotNull(derivedUnitDeterminationOrphanName);
|
|
1281
|
assertNotNull(tissueUuidNoAssociation);
|
|
1282
|
assertNotNull(dnaSampleUuidIndividualsAssociation);
|
|
1283
|
assertNotNull(fossilTypeDesignation);
|
|
1284
|
assertNotNull(taxon);
|
|
1285
|
assertNotNull(synonym);
|
|
1286
|
assertNotNull(taxonName);
|
|
1287
|
assertNotNull(synonymName);
|
|
1288
|
assertNotNull(orphanName);
|
|
1289
|
|
|
1290
|
/*
|
|
1291
|
* search for taxon
|
|
1292
|
* should retrieve all specimens associated via
|
|
1293
|
* - type designations (fossil)
|
|
1294
|
* - individuals associations (dnaSample)
|
|
1295
|
* - determinations on
|
|
1296
|
* - taxon (specimenA)
|
|
1297
|
* - taxon name (specimenA, specimenB)
|
|
1298
|
* - synonym names (specimenC)
|
|
1299
|
*/
|
|
1300
|
FindOccurrencesConfigurator config = new FindOccurrencesConfigurator();
|
|
1301
|
config.setAssociatedTaxonUuid(taxonUuid);
|
|
1302
|
List<SpecimenOrObservationBase> specimens = occurrenceService.findByTitle(config).getRecords();
|
|
1303
|
assertTrue(specimens.contains(derivedUnitDeterminationName));
|
|
1304
|
assertTrue(specimens.contains(derivedUnitDeterminationTaxon));
|
|
1305
|
assertTrue(specimens.contains(derivedUnitDeterminationSynonymName));
|
|
1306
|
assertTrue(specimens.contains(dnaSampleUuidIndividualsAssociation));
|
|
1307
|
assertTrue(specimens.contains(fossilTypeDesignation));
|
|
1308
|
assertTrue(!specimens.contains(tissueUuidNoAssociation));
|
|
1309
|
assertTrue(!specimens.contains(derivedUnitDeterminationOrphanName));
|
|
1310
|
assertEquals("Wrong number of associated specimens", 5, specimens.size());
|
|
1311
|
|
|
1312
|
/*
|
|
1313
|
* search for taxon name
|
|
1314
|
* should retrieve all specimens associated via
|
|
1315
|
* - determinations on
|
|
1316
|
* - taxon name (specimenA, specimenB)
|
|
1317
|
*/
|
|
1318
|
config = new FindOccurrencesConfigurator();
|
|
1319
|
config.setAssociatedTaxonNameUuid(taxonNameUuid);
|
|
1320
|
specimens = occurrenceService.findByTitle(config).getRecords();
|
|
1321
|
assertTrue(specimens.contains(derivedUnitDeterminationName));
|
|
1322
|
assertTrue(specimens.contains(derivedUnitDeterminationTaxon));
|
|
1323
|
assertTrue(!specimens.contains(derivedUnitDeterminationSynonymName));
|
|
1324
|
assertTrue(!specimens.contains(dnaSampleUuidIndividualsAssociation));
|
|
1325
|
assertTrue(!specimens.contains(fossilTypeDesignation));
|
|
1326
|
assertTrue(!specimens.contains(tissueUuidNoAssociation));
|
|
1327
|
assertTrue(!specimens.contains(derivedUnitDeterminationOrphanName));
|
|
1328
|
assertEquals("Wrong number of associated specimens", 2, specimens.size());
|
|
1329
|
|
|
1330
|
/*
|
|
1331
|
* search for synonym name
|
|
1332
|
* should retrieve all specimens associated via
|
|
1333
|
* - determinations on
|
|
1334
|
* - synonym names (specimenC)
|
|
1335
|
*/
|
|
1336
|
config = new FindOccurrencesConfigurator();
|
|
1337
|
config.setAssociatedTaxonNameUuid(synonymNameUuid);
|
|
1338
|
specimens = occurrenceService.findByTitle(config).getRecords();
|
|
1339
|
assertTrue(!specimens.contains(derivedUnitDeterminationName));
|
|
1340
|
assertTrue(!specimens.contains(derivedUnitDeterminationTaxon));
|
|
1341
|
assertTrue(specimens.contains(derivedUnitDeterminationSynonymName));
|
|
1342
|
assertTrue(!specimens.contains(dnaSampleUuidIndividualsAssociation));
|
|
1343
|
assertTrue(!specimens.contains(fossilTypeDesignation));
|
|
1344
|
assertTrue(!specimens.contains(tissueUuidNoAssociation));
|
|
1345
|
assertTrue(!specimens.contains(derivedUnitDeterminationOrphanName));
|
|
1346
|
assertEquals("Wrong number of associated specimens", 1, specimens.size());
|
|
1347
|
|
|
1348
|
/*
|
|
1349
|
* search for orphan name
|
|
1350
|
* should retrieve all specimens associated via
|
|
1351
|
* - determinations on
|
|
1352
|
* - taxon name (specimenD)
|
|
1353
|
*/
|
|
1354
|
config = new FindOccurrencesConfigurator();
|
|
1355
|
config.setAssociatedTaxonNameUuid(orphanNameUuid);
|
|
1356
|
specimens = occurrenceService.findByTitle(config).getRecords();
|
|
1357
|
assertTrue(!specimens.contains(derivedUnitDeterminationName));
|
|
1358
|
assertTrue(!specimens.contains(derivedUnitDeterminationTaxon));
|
|
1359
|
assertTrue(!specimens.contains(derivedUnitDeterminationSynonymName));
|
|
1360
|
assertTrue(!specimens.contains(dnaSampleUuidIndividualsAssociation));
|
|
1361
|
assertTrue(!specimens.contains(fossilTypeDesignation));
|
|
1362
|
assertTrue(!specimens.contains(tissueUuidNoAssociation));
|
|
1363
|
assertTrue(specimens.contains(derivedUnitDeterminationOrphanName));
|
|
1364
|
assertEquals("Wrong number of associated specimens", 1, specimens.size());
|
|
1365
|
|
|
1366
|
// //DERIVATIVES
|
|
1367
|
// //determination: taxon
|
|
1368
|
// DerivedUnit derivedUnitDeterminationTaxon = DerivedUnit.NewInstance(SpecimenOrObservationType.PreservedSpecimen);
|
|
1369
|
// derivedUnitDeterminationTaxon.setTitleCache("Derived Unit determined as taxon");
|
|
1370
|
// //determination: taxon name
|
|
1371
|
// DerivedUnit derivedUnitDeterminationName = DerivedUnit.NewInstance(SpecimenOrObservationType.PreservedSpecimen);
|
|
1372
|
// derivedUnitDeterminationName.setTitleCache("Derived Unit determined as name");
|
|
1373
|
// //determination: synonym
|
|
1374
|
// DerivedUnit derivedUnitDeterminationSynonym = DerivedUnit.NewInstance(SpecimenOrObservationType.PreservedSpecimen);
|
|
1375
|
// derivedUnitDeterminationSynonym.setTitleCache("Derived Unit determined as synonym");
|
|
1376
|
// //determination: synonym name
|
|
1377
|
// DerivedUnit derivedUnitDeterminationSynonymName = DerivedUnit.NewInstance(SpecimenOrObservationType.PreservedSpecimen);
|
|
1378
|
// derivedUnitDeterminationSynonymName.setTitleCache("Derived Unit determined as synonym name");
|
|
1379
|
// //determination: orphan name
|
|
1380
|
// DerivedUnit derivedUnitDeterminationOrphanName = DerivedUnit.NewInstance(SpecimenOrObservationType.PreservedSpecimen);
|
|
1381
|
// derivedUnitDeterminationOrphanName.setTitleCache("Derived Unit determined as orphan name");
|
|
1382
|
// //no association
|
|
1383
|
// DerivedUnit tissueUuidNoAssociation = DerivedUnit.NewInstance(SpecimenOrObservationType.TissueSample);
|
|
1384
|
// tissueUuidNoAssociation.setTitleCache("tissue sample no association");
|
|
1385
|
// //individuals association with taxon
|
|
1386
|
// DerivedUnit dnaSampleUuidIndividualsAssociation = DerivedUnit.NewInstance(SpecimenOrObservationType.DnaSample);
|
|
1387
|
// dnaSampleUuidIndividualsAssociation.setTitleCache("dna associated via IndividualsAssociation");
|
|
1388
|
// //type specimen of taxon
|
|
1389
|
// DerivedUnit fossilTypeDesignation = DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);
|
|
1390
|
// fossilTypeDesignation.setTitleCache("Fossil with type designation");
|
|
1391
|
//
|
|
1392
|
// derivedUnitDeterminationTaxon.setUuid(derivedUnitDeterminationTaxonUuid);
|
|
1393
|
// derivedUnitDeterminationName.setUuid(derivedUnitDeterminationNameUuid);
|
|
1394
|
// derivedUnitDeterminationSynonym.setUuid(derivedUnitDeterminationSynonymUuid);
|
|
1395
|
// derivedUnitDeterminationSynonymName.setUuid(derivedUnitDeterminationSynonymNameUuid);
|
|
1396
|
// derivedUnitDeterminationOrphanName.setUuid(derivedUnitDeterminationOrphanNameUuid);
|
|
1397
|
// tissueUuidNoAssociation.setUuid(tissueUuidNoAssociationUuid);
|
|
1398
|
// dnaSampleUuidIndividualsAssociation.setUuid(dnaSampleUuidIndividualsAssociationUuid);
|
|
1399
|
// fossilTypeDesignation.setUuid(fossilTypeDesignationUuid);
|
|
1400
|
//
|
|
1401
|
// occurrenceService.save(derivedUnitDeterminationTaxon);
|
|
1402
|
// occurrenceService.save(derivedUnitDeterminationName);
|
|
1403
|
// occurrenceService.save(derivedUnitDeterminationSynonym);
|
|
1404
|
// occurrenceService.save(derivedUnitDeterminationSynonymName);
|
|
1405
|
// occurrenceService.save(derivedUnitDeterminationOrphanName);
|
|
1406
|
// occurrenceService.save(tissueUuidNoAssociation);
|
|
1407
|
// occurrenceService.save(dnaSampleUuidIndividualsAssociation);
|
|
1408
|
// occurrenceService.save(fossilTypeDesignation);
|
|
1409
|
//
|
|
1410
|
// //NAMES
|
|
1411
|
// TaxonName taxonName = TaxonNameFactory.PARSED_BOTANICAL("Campanula patual");
|
|
1412
|
// TaxonName synonymName = TaxonNameFactory.PARSED_BOTANICAL("Syno nyma");
|
|
1413
|
// TaxonName orphanName = TaxonNameFactory.PARSED_BOTANICAL("Orphanus lonelia");
|
|
1414
|
// taxonName.setUuid(taxonNameUuid);
|
|
1415
|
// synonymName.setUuid(synonymNameUuid);
|
|
1416
|
// orphanName.setUuid(orphanNameUuid);
|
|
1417
|
//
|
|
1418
|
// //TAXON
|
|
1419
|
// Taxon taxon = Taxon.NewInstance(taxonName, null);
|
|
1420
|
// taxon.setUuid(taxonUuid);
|
|
1421
|
//
|
|
1422
|
// Classification classification = Classification.NewInstance("Test Classification");
|
|
1423
|
// TaxonNode taxonNode = classification.addChildTaxon(taxon, null, null);
|
|
1424
|
// taxonNode.setUuid(taxonNodeUuid);
|
|
1425
|
//
|
|
1426
|
// //SYNONYM
|
|
1427
|
// Synonym synonym = Synonym.NewInstance(synonymName, null);
|
|
1428
|
// synonym.setUuid(synoymUuid);
|
|
1429
|
// taxon.addSynonym(synonym, SynonymType.HOMOTYPIC_SYNONYM_OF());
|
|
1430
|
//
|
|
1431
|
// //IndividualsAssociation
|
|
1432
|
// TaxonDescription taxonDescription = TaxonDescription.NewInstance();
|
|
1433
|
// IndividualsAssociation association = IndividualsAssociation.NewInstance(dnaSampleUuidIndividualsAssociation);
|
|
1434
|
// association.setFeature(Feature.SPECIMEN());
|
|
1435
|
// taxonDescription.addElement(association);
|
|
1436
|
// taxon.addDescription(taxonDescription);
|
|
1437
|
//
|
|
1438
|
// //DETERMINATION EVENTS
|
|
1439
|
// DeterminationEvent.NewInstance(taxon, derivedUnitDeterminationTaxon);
|
|
1440
|
// DeterminationEvent.NewInstance(taxonName, derivedUnitDeterminationName);
|
|
1441
|
// // DeterminationEvent.NewInstance(synonym, derivedUnitDeterminationSynonym);//TODO determinationa on synonym not possible?
|
|
1442
|
// DeterminationEvent.NewInstance(synonymName, derivedUnitDeterminationSynonymName);
|
|
1443
|
// DeterminationEvent.NewInstance(orphanName, derivedUnitDeterminationOrphanName);
|
|
1444
|
//
|
|
1445
|
// //type designation
|
|
1446
|
// SpecimenTypeDesignation specimenTypeDesignation = SpecimenTypeDesignation.NewInstance();
|
|
1447
|
// specimenTypeDesignation.setTypeSpecimen(fossilTypeDesignation);
|
|
1448
|
// taxonName.addTypeDesignation(specimenTypeDesignation, false);
|
|
1449
|
//
|
|
1450
|
// classificationService.save(classification);
|
|
1451
|
// taxonService.saveOrUpdate(taxon);
|
|
1452
|
// taxonNodeService.save(taxonNode);
|
|
1453
|
//
|
|
1454
|
// commitAndStartNewTransaction(null);
|
|
1455
|
//
|
|
1456
|
// setComplete();
|
|
1457
|
// endTransaction();
|
|
1458
|
//
|
|
1459
|
//
|
|
1460
|
// try {
|
|
1461
|
// writeDbUnitDataSetFile(new String[] {
|
|
1462
|
// "SpecimenOrObservationBase",
|
|
1463
|
// "SpecimenOrObservationBase_DerivationEvent",
|
|
1464
|
// "DerivationEvent",
|
|
1465
|
// "DescriptionElementBase",
|
|
1466
|
// "DescriptionBase",
|
|
1467
|
// "TaxonBase",
|
|
1468
|
// "TaxonNode",
|
|
1469
|
// "Classification",
|
|
1470
|
// "TypeDesignationBase",
|
|
1471
|
// "TaxonName",
|
|
1472
|
// "TaxonName_TypeDesignationBase",
|
|
1473
|
// "HomotypicalGroup",
|
|
1474
|
// "TeamOrPersonBase",
|
|
1475
|
// "LanguageString",
|
|
1476
|
// "DeterminationEvent"
|
|
1477
|
// }, "testAllKindsOfSpecimenAssociations");
|
|
1478
|
// } catch (FileNotFoundException e) {
|
|
1479
|
// e.printStackTrace();
|
|
1480
|
// }
|
|
1481
|
|
|
1482
|
|
|
1483
|
}
|
|
1484
|
|
|
1485
|
@Test
|
|
1486
|
@DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "OccurrenceServiceTest.testDnaSampleDesignation.xml")
|
|
1487
|
public void testDnaSampleDesignation(){
|
|
1488
|
DefinedTerm sampleDesignationTermType = (DefinedTerm) termService.load(UUID.fromString("fadeba12-1be3-4bc7-9ff5-361b088d86fc"));
|
|
1489
|
|
|
1490
|
UUID dnaSampleUuid = UUID.fromString("4bee91b9-23d8-438b-8569-6d6aaa5b6587");
|
|
1491
|
DnaSample dnaSample = HibernateProxyHelper.deproxy(occurrenceService.load(dnaSampleUuid), DnaSample.class);
|
|
1492
|
assertEquals(1, dnaSample.getIdentifiers().size());
|
|
1493
|
Identifier<?> identifier = dnaSample.getIdentifiers().iterator().next();
|
|
1494
|
assertEquals("NK 2088", identifier.getIdentifier());
|
|
1495
|
assertEquals(sampleDesignationTermType, identifier.getType());
|
|
1496
|
|
|
1497
|
//change identifier, save and reload
|
|
1498
|
identifier.setIdentifier("WB10");
|
|
1499
|
occurrenceService.saveOrUpdate(dnaSample);
|
|
1500
|
SpecimenOrObservationBase<?> dnaSampleReloaded = occurrenceService.load(dnaSampleUuid);
|
|
1501
|
assertEquals(1, dnaSample.getIdentifiers().size());
|
|
1502
|
Identifier<?> identifierReloaded = dnaSample.getIdentifiers().iterator().next();
|
|
1503
|
assertEquals("WB10", identifierReloaded.getIdentifier());
|
|
1504
|
assertEquals(sampleDesignationTermType, identifierReloaded.getType());
|
|
1505
|
|
|
1506
|
|
|
1507
|
// DefinedTerm sampleDesignationTermType = (DefinedTerm) termService.load(UUID.fromString("fadeba12-1be3-4bc7-9ff5-361b088d86fc"));
|
|
1508
|
// //UUIDS
|
|
1509
|
// UUID dnaSampleUuid = UUID.fromString("4bee91b9-23d8-438b-8569-6d6aaa5b6587");
|
|
1510
|
// DerivedUnit dnaSample = DnaSample.NewInstance();
|
|
1511
|
// dnaSample.setUuid(dnaSampleUuid);
|
|
1512
|
// Identifier.NewInstance(dnaSample, "NK 2088", sampleDesignationTermType);
|
|
1513
|
//
|
|
1514
|
// occurrenceService.save(dnaSample);
|
|
1515
|
//
|
|
1516
|
// commitAndStartNewTransaction(null);
|
|
1517
|
//
|
|
1518
|
// setComplete();
|
|
1519
|
// endTransaction();
|
|
1520
|
//
|
|
1521
|
//
|
|
1522
|
// try {
|
|
1523
|
// writeDbUnitDataSetFile(new String[] {
|
|
1524
|
// "SpecimenOrObservationBase",
|
|
1525
|
// "IDENTIFIER",
|
|
1526
|
// "SpecimenOrObservationBase_Identifier"
|
|
1527
|
// }, "testDnaSampleDesignation");
|
|
1528
|
// } catch (FileNotFoundException e) {
|
|
1529
|
// e.printStackTrace();
|
|
1530
|
// }
|
|
1531
|
}
|
|
1532
|
@Override
|
|
1533
|
// @Test
|
|
1534
|
public void createTestDataSet() throws FileNotFoundException {
|
|
1535
|
//UUIDS
|
|
1536
|
UUID derivedUnitDeterminationTaxonUuid = UUID.fromString("941b8b22-1925-4b91-8ff8-97114499bb22");
|
|
1537
|
UUID derivedUnitDeterminationNameUuid = UUID.fromString("0cdc7a57-6f55-45c8-b3e5-523748c381e7");
|
|
1538
|
|
|
1539
|
UUID derivedUnitDeterminationSynonymUuid = UUID.fromString("8eb94a7d-c802-49a7-bc10-c26de20a52c2");
|
|
1540
|
UUID derivedUnitDeterminationSynonymNameUuid = UUID.fromString("d940a940-8caf-4a52-b1d8-ba4aad7ddae2");
|
|
1541
|
|
|
1542
|
UUID derivedUnitDeterminationOrphanNameUuid = UUID.fromString("587b7297-7d59-4f59-8ef3-c7a559cadeca");
|
|
1543
|
|
|
1544
|
UUID tissueUuidNoAssociationUuid = UUID.fromString("93e94260-5107-4b2c-9ce4-da9e1a4e7cb9");
|
|
1545
|
UUID dnaSampleUuidIndividualsAssociationUuid = UUID.fromString("1fb53903-c9b9-4078-8297-5b86aec7fe21");
|
|
1546
|
UUID fossilTypeDesignationUuid = UUID.fromString("42ec8dcf-a923-4256-bbd5-b0d10f4de5e2");
|
|
1547
|
|
|
1548
|
UUID taxonNodeUuid = UUID.fromString("6b8b6ff9-66e4-4496-8e5a-7d03bdf9a076");
|
|
1549
|
UUID taxonUuid = UUID.fromString("07cc47a5-1a63-46a1-8366-0d59d2b90d5b");
|
|
1550
|
UUID synoymUuid = UUID.fromString("c16bcd9b-7d18-4fb5-af60-f9ef14c1d3a9");
|
|
1551
|
|
|
1552
|
UUID taxonNameUuid = UUID.fromString("e59b95c0-9ad6-48be-af62-a982ba72b917");
|
|
1553
|
UUID synonymNameUuid = UUID.fromString("39f04b2a-b8bd-46e8-9102-ab665c64ec8e");
|
|
1554
|
UUID orphanNameUuid = UUID.fromString("d8e56365-3ad9-4b0e-88bf-acaaab223a9b");
|
|
1555
|
|
|
1556
|
//DERIVATIVES
|
|
1557
|
//determination: taxon
|
|
1558
|
DerivedUnit derivedUnitDeterminationTaxon = DerivedUnit.NewInstance(SpecimenOrObservationType.PreservedSpecimen);
|
|
1559
|
derivedUnitDeterminationTaxon.setTitleCache("Derived Unit determined as taxon");
|
|
1560
|
//determination: taxon name
|
|
1561
|
DerivedUnit derivedUnitDeterminationName = DerivedUnit.NewInstance(SpecimenOrObservationType.PreservedSpecimen);
|
|
1562
|
derivedUnitDeterminationName.setTitleCache("Derived Unit determined as name");
|
|
1563
|
//determination: synonym
|
|
1564
|
DerivedUnit derivedUnitDeterminationSynonym = DerivedUnit.NewInstance(SpecimenOrObservationType.PreservedSpecimen);
|
|
1565
|
derivedUnitDeterminationSynonym.setTitleCache("Derived Unit determined as synonym");
|
|
1566
|
//determination: synonym name
|
|
1567
|
DerivedUnit derivedUnitDeterminationSynonymName = DerivedUnit.NewInstance(SpecimenOrObservationType.PreservedSpecimen);
|
|
1568
|
derivedUnitDeterminationSynonymName.setTitleCache("Derived Unit determined as synonym name");
|
|
1569
|
//determination: orphan name
|
|
1570
|
DerivedUnit derivedUnitDeterminationOrphanName = DerivedUnit.NewInstance(SpecimenOrObservationType.PreservedSpecimen);
|
|
1571
|
derivedUnitDeterminationOrphanName.setTitleCache("Derived Unit determined as orphan name");
|
|
1572
|
//no association
|
|
1573
|
DerivedUnit tissueUuidNoAssociation = DerivedUnit.NewInstance(SpecimenOrObservationType.TissueSample);
|
|
1574
|
tissueUuidNoAssociation.setTitleCache("tissue sample no association");
|
|
1575
|
//individuals association with taxon
|
|
1576
|
DerivedUnit dnaSampleUuidIndividualsAssociation = DerivedUnit.NewInstance(SpecimenOrObservationType.DnaSample);
|
|
1577
|
dnaSampleUuidIndividualsAssociation.setTitleCache("dna associated via IndividualsAssociation");
|
|
1578
|
//type specimen of taxon
|
|
1579
|
DerivedUnit fossilTypeDesignation = DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);
|
|
1580
|
fossilTypeDesignation.setTitleCache("Fossil with type designation");
|
|
1581
|
|
|
1582
|
derivedUnitDeterminationTaxon.setUuid(derivedUnitDeterminationTaxonUuid);
|
|
1583
|
derivedUnitDeterminationName.setUuid(derivedUnitDeterminationNameUuid);
|
|
1584
|
derivedUnitDeterminationSynonym.setUuid(derivedUnitDeterminationSynonymUuid);
|
|
1585
|
derivedUnitDeterminationSynonymName.setUuid(derivedUnitDeterminationSynonymNameUuid);
|
|
1586
|
derivedUnitDeterminationOrphanName.setUuid(derivedUnitDeterminationOrphanNameUuid);
|
|
1587
|
tissueUuidNoAssociation.setUuid(tissueUuidNoAssociationUuid);
|
|
1588
|
dnaSampleUuidIndividualsAssociation.setUuid(dnaSampleUuidIndividualsAssociationUuid);
|
|
1589
|
fossilTypeDesignation.setUuid(fossilTypeDesignationUuid);
|
|
1590
|
|
|
1591
|
occurrenceService.save(derivedUnitDeterminationTaxon);
|
|
1592
|
occurrenceService.save(derivedUnitDeterminationName);
|
|
1593
|
occurrenceService.save(derivedUnitDeterminationSynonym);
|
|
1594
|
occurrenceService.save(derivedUnitDeterminationSynonymName);
|
|
1595
|
occurrenceService.save(derivedUnitDeterminationOrphanName);
|
|
1596
|
occurrenceService.save(tissueUuidNoAssociation);
|
|
1597
|
occurrenceService.save(dnaSampleUuidIndividualsAssociation);
|
|
1598
|
occurrenceService.save(fossilTypeDesignation);
|
|
1599
|
|
|
1600
|
//NAMES
|
|
1601
|
TaxonName taxonName = TaxonNameFactory.PARSED_BOTANICAL("Campanula patual");
|
|
1602
|
TaxonName synonymName = TaxonNameFactory.PARSED_BOTANICAL("Syno nyma");
|
|
1603
|
TaxonName orphanName = TaxonNameFactory.PARSED_BOTANICAL("Orphanus lonelia");
|
|
1604
|
taxonName.setUuid(taxonNameUuid);
|
|
1605
|
synonymName.setUuid(synonymNameUuid);
|
|
1606
|
orphanName.setUuid(orphanNameUuid);
|
|
1607
|
|
|
1608
|
//TAXON
|
|
1609
|
Taxon taxon = Taxon.NewInstance(taxonName, null);
|
|
1610
|
taxon.setUuid(taxonUuid);
|
|
1611
|
|
|
1612
|
Classification classification = Classification.NewInstance("Test Classification");
|
|
1613
|
TaxonNode taxonNode = classification.addChildTaxon(taxon, null, null);
|
|
1614
|
taxonNode.setUuid(taxonNodeUuid);
|
|
1615
|
|
|
1616
|
//SYNONYM
|
|
1617
|
Synonym synonym = Synonym.NewInstance(synonymName, null);
|
|
1618
|
synonym.setUuid(synoymUuid);
|
|
1619
|
taxon.addSynonym(synonym, SynonymType.HOMOTYPIC_SYNONYM_OF());
|
|
1620
|
|
|
1621
|
//IndividualsAssociation
|
|
1622
|
TaxonDescription taxonDescription = TaxonDescription.NewInstance();
|
|
1623
|
IndividualsAssociation association = IndividualsAssociation.NewInstance(dnaSampleUuidIndividualsAssociation);
|
|
1624
|
association.setFeature(Feature.SPECIMEN());
|
|
1625
|
taxonDescription.addElement(association);
|
|
1626
|
taxon.addDescription(taxonDescription);
|
|
1627
|
|
|
1628
|
//DETERMINATION EVENTS
|
|
1629
|
DeterminationEvent.NewInstance(taxon, derivedUnitDeterminationTaxon);
|
|
1630
|
DeterminationEvent.NewInstance(taxonName, derivedUnitDeterminationName);
|
|
1631
|
// DeterminationEvent.NewInstance(synonym, derivedUnitDeterminationSynonym);//TODO determinationa on synonym not possible?
|
|
1632
|
DeterminationEvent.NewInstance(synonymName, derivedUnitDeterminationSynonymName);
|
|
1633
|
DeterminationEvent.NewInstance(orphanName, derivedUnitDeterminationOrphanName);
|
|
1634
|
|
|
1635
|
//type designation
|
|
1636
|
SpecimenTypeDesignation specimenTypeDesignation = SpecimenTypeDesignation.NewInstance();
|
|
1637
|
specimenTypeDesignation.setTypeSpecimen(fossilTypeDesignation);
|
|
1638
|
taxonName.addTypeDesignation(specimenTypeDesignation, false);
|
|
1639
|
|
|
1640
|
classificationService.saveOrUpdate(classification);
|
|
1641
|
taxonService.saveOrUpdate(taxon);
|
|
1642
|
taxonNodeService.saveOrUpdate(taxonNode);
|
|
1643
|
|
|
1644
|
commitAndStartNewTransaction(null);
|
|
1645
|
|
|
1646
|
setComplete();
|
|
1647
|
endTransaction();
|
|
1648
|
|
|
1649
|
|
|
1650
|
try {
|
|
1651
|
writeDbUnitDataSetFile(new String[] {
|
|
1652
|
"SpecimenOrObservationBase",
|
|
1653
|
"SpecimenOrObservationBase_DerivationEvent",
|
|
1654
|
"DerivationEvent",
|
|
1655
|
"DescriptionElementBase",
|
|
1656
|
"DescriptionBase",
|
|
1657
|
"TaxonBase",
|
|
1658
|
"TaxonNode",
|
|
1659
|
"Classification",
|
|
1660
|
"TypeDesignationBase",
|
|
1661
|
"TaxonName",
|
|
1662
|
"TaxonName_TypeDesignationBase",
|
|
1663
|
"HomotypicalGroup",
|
|
1664
|
"TeamOrPersonBase",
|
|
1665
|
"LanguageString",
|
|
1666
|
"DeterminationEvent"
|
|
1667
|
}, "testAllKindsOfSpecimenAssociations");
|
|
1668
|
} catch (FileNotFoundException e) {
|
|
1669
|
e.printStackTrace();
|
|
1670
|
}
|
|
1671
|
|
|
1672
|
}
|
|
1673
|
}
|