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/**
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* Copyright (C) 2007 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.model.occurrence;
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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.assertNotNull;
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import static org.junit.Assert.assertNotSame;
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import static org.junit.Assert.assertNull;
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import static org.junit.Assert.assertSame;
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import static org.junit.Assert.assertTrue;
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import java.util.Calendar;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import org.joda.time.DateTime;
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import org.junit.Assert;
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import org.junit.Before;
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import org.junit.Test;
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import org.springframework.beans.BeanUtils;
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import com.ibm.lsid.MalformedLSIDException;
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import eu.etaxonomy.cdm.model.agent.Person;
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import eu.etaxonomy.cdm.model.common.Annotation;
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import eu.etaxonomy.cdm.model.common.DefinedTerm;
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import eu.etaxonomy.cdm.model.common.Extension;
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import eu.etaxonomy.cdm.model.common.IdentifiableSource;
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import eu.etaxonomy.cdm.model.common.LSID;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.LanguageStringBase;
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import eu.etaxonomy.cdm.model.common.Marker;
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import eu.etaxonomy.cdm.model.common.MarkerType;
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import eu.etaxonomy.cdm.model.common.OriginalSourceBase;
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import eu.etaxonomy.cdm.model.description.SpecimenDescription;
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import eu.etaxonomy.cdm.model.media.Media;
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import eu.etaxonomy.cdm.model.media.Rights;
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import eu.etaxonomy.cdm.model.molecular.DnaSample;
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import eu.etaxonomy.cdm.model.name.BotanicalName;
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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.TaxonNameBase;
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/**
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* @author a.mueller
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* @created 28.10.2008
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*/
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public class SpecimenTest {
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private static final Logger logger = Logger.getLogger(SpecimenTest.class);
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private DerivedUnit specimen;
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@Before
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public void setUp() throws Exception {
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specimen = DerivedUnit.NewPreservedSpecimenInstance();
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}
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/**
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* Test method for {@link eu.etaxonomy.cdm.model.occurrence.Specimen#NewInstance()}.
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*/
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@Test
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public void testNewInstance() {
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DerivedUnit specimen = DerivedUnit.NewPreservedSpecimenInstance();
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assertNotNull(specimen);
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assertTrue(specimen instanceof DerivedUnit);
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assertTrue(specimen.getRecordBasis().equals(SpecimenOrObservationType.PreservedSpecimen));
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}
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/**
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* Test method for {@link eu.etaxonomy.cdm.model.occurrence.Specimen#getPreservation()} and
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* {@link eu.etaxonomy.cdm.model.occurrence.Specimen#setPreservation(eu.etaxonomy.cdm.model.occurrence.PreservationMethod)}.
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*/
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@Test
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public void testGetSetPreservation() {
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PreservationMethod preservation = PreservationMethod.NewInstance();
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specimen.setPreservation(preservation);
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assertSame(preservation, specimen.getPreservation());
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specimen.setPreservation(null);
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}
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@Test
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public void testBidirectionalSpecimenDescription(){
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Assert.assertNotNull("Specimen should exist", specimen);
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SpecimenDescription desc = SpecimenDescription.NewInstance(specimen);
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Assert.assertNotNull("Description should exist.", desc);
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Assert.assertSame("Descriptions specimen should be set correctly", desc.getDescribedSpecimenOrObservation(),specimen);
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Assert.assertTrue("Specimen should contain description", specimen.getDescriptions().contains(desc));
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SpecimenDescription desc2 = SpecimenDescription.NewInstance();
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Assert.assertNotNull("Description should exist.", desc2);
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specimen.addDescription(desc2);
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Assert.assertSame("Description2 specimen should be set correctly", desc2.getDescribedSpecimenOrObservation(),specimen);
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Assert.assertSame("Descriptions specimen should still be set correctly", desc.getDescribedSpecimenOrObservation(),specimen);
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Assert.assertTrue("Specimen should contain description2", specimen.getDescriptions().contains(desc2));
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Assert.assertTrue("Specimen should still contain description", specimen.getDescriptions().contains(desc));
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SpecimenDescription desc3 = SpecimenDescription.NewInstance();
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Assert.assertNotNull("Description should exist.", desc3);
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desc3.setDescribedSpecimenOrObservation(specimen);
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Assert.assertSame("Description3 specimen should be set correctly", desc3.getDescribedSpecimenOrObservation(),specimen);
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Assert.assertSame("Descriptions2 specimen should still be set correctly", desc2.getDescribedSpecimenOrObservation(),specimen);
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Assert.assertSame("Descriptions specimen should still be set correctly", desc.getDescribedSpecimenOrObservation(),specimen);
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Assert.assertTrue("Specimen should contain description3", specimen.getDescriptions().contains(desc3));
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Assert.assertTrue("Specimen should still contain description2", specimen.getDescriptions().contains(desc2));
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Assert.assertTrue("Specimen should still contain description", specimen.getDescriptions().contains(desc));
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//change specimen of a given description
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DerivedUnit specimen2 = DerivedUnit.NewPreservedSpecimenInstance();
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Assert.assertNotNull("Specimen should exist.", specimen2);
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desc3.setDescribedSpecimenOrObservation(specimen2);
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Assert.assertSame("Description3 new specimen should be set correctly", desc3.getDescribedSpecimenOrObservation(),specimen2);
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Assert.assertSame("Descriptions2 specimen should still be set correctly", desc2.getDescribedSpecimenOrObservation(),specimen);
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Assert.assertSame("Descriptions specimen should still be set correctly", desc.getDescribedSpecimenOrObservation(),specimen);
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Assert.assertTrue("Specimen2 should contain description3", specimen2.getDescriptions().contains(desc3));
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Assert.assertEquals("Specimen2 should contain exactly 1 description", 1, specimen2.getDescriptions().size());
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Assert.assertFalse("Specimen should no longer contain description3", specimen.getDescriptions().contains(desc3));
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Assert.assertTrue("Specimen should still contain description2", specimen.getDescriptions().contains(desc2));
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Assert.assertTrue("Specimen should still contain description", specimen.getDescriptions().contains(desc));
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//remove description which is not contained
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specimen.removeDescription(desc3);
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Assert.assertSame("Nothing should have changed", desc3.getDescribedSpecimenOrObservation(),specimen2);
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Assert.assertSame("Nothing should have changed", desc2.getDescribedSpecimenOrObservation(),specimen);
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Assert.assertSame("Nothing should have changed", desc.getDescribedSpecimenOrObservation(),specimen);
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Assert.assertTrue("Nothing should have changed", specimen2.getDescriptions().contains(desc3));
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Assert.assertEquals("Nothing should have changed", 1, specimen2.getDescriptions().size());
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Assert.assertFalse("Nothing should have changed", specimen.getDescriptions().contains(desc3));
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Assert.assertTrue("Nothing should have changed", specimen.getDescriptions().contains(desc2));
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Assert.assertTrue("Nothing should have changed", specimen.getDescriptions().contains(desc));
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//remove description
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specimen.removeDescription(desc2);
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Assert.assertNull("Descriptions2 specimen should not exist anymore", desc2.getDescribedSpecimenOrObservation());
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Assert.assertSame("Description3 specimen should still be set correctly", desc3.getDescribedSpecimenOrObservation(),specimen2);
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Assert.assertSame("Descriptions specimen should still be set correctly", desc.getDescribedSpecimenOrObservation(),specimen);
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Assert.assertTrue("Specimen2 should still contain description3", specimen2.getDescriptions().contains(desc3));
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Assert.assertEquals("Specimen2 should still contain exactly 1 description", 1, specimen2.getDescriptions().size());
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Assert.assertFalse("Specimen should not contain description2 anymore", specimen.getDescriptions().contains(desc2));
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Assert.assertFalse("Specimen should still no longer contain description3", specimen.getDescriptions().contains(desc3));
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Assert.assertTrue("Specimen should still contain description", specimen.getDescriptions().contains(desc));
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//remove description by setting null specimen
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desc3.setDescribedSpecimenOrObservation(null);
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Assert.assertNull("Description3 specimen should not exist anymore", desc3.getDescribedSpecimenOrObservation());
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Assert.assertNull("Descriptions2 specimen should still not exist anymore", desc2.getDescribedSpecimenOrObservation());
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Assert.assertSame("Descriptions specimen should still be set correctly", desc.getDescribedSpecimenOrObservation(),specimen);
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Assert.assertFalse("Specimen2 should not contain description3 anymore", specimen2.getDescriptions().contains(desc3));
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Assert.assertEquals("Specimen2 should contain no description now", 0, specimen2.getDescriptions().size());
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Assert.assertFalse("Specimen should still no longer contain description2", specimen.getDescriptions().contains(desc2));
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Assert.assertFalse("Specimen should still no longer contain description3", specimen.getDescriptions().contains(desc3));
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Assert.assertTrue("Specimen should still contain description", specimen.getDescriptions().contains(desc));
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}
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@Test
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public void testBidirectionalTypeDesignation(){
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SpecimenTypeDesignation desig1 = SpecimenTypeDesignation.NewInstance();
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SpecimenTypeDesignation desig2 = SpecimenTypeDesignation.NewInstance();
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DerivedUnit specimen2 = DerivedUnit.NewPreservedSpecimenInstance();
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specimen.addSpecimenTypeDesignation(desig1);
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Assert.assertEquals("Specimen1 should be the designations specimen", specimen, desig1.getTypeSpecimen());
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Assert.assertEquals("specimen1 should have exactly 1 designation", 1, specimen.getSpecimenTypeDesignations().size());
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Assert.assertEquals("specimen1's designation should be desig1", desig1, specimen.getSpecimenTypeDesignations().iterator().next());
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specimen.addSpecimenTypeDesignation(desig2);
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Assert.assertEquals("Specimen1 should be the desig2's specimen", specimen, desig2.getTypeSpecimen());
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Assert.assertEquals("specimen1 should have exactly 2 designation", 2, specimen.getSpecimenTypeDesignations().size());
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specimen2.addSpecimenTypeDesignation(desig2);
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Assert.assertEquals("Specimen2 should have replaced specimen1 as desig2's specimen", specimen2, desig2.getTypeSpecimen());
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Assert.assertEquals("Specimen2 should have exactly 1 designation", 1, specimen2.getSpecimenTypeDesignations().size());
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Assert.assertEquals("Specimen1's designation should be desig2", desig2, specimen2.getSpecimenTypeDesignations().iterator().next());
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Assert.assertEquals("specimen1 should have exactly 1 designation", 1, specimen.getSpecimenTypeDesignations().size());
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specimen2.removeSpecimenTypeDesignation(desig2);
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Assert.assertEquals("Desig2 should not have a specimen anymore", null, desig2.getTypeSpecimen());
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Assert.assertEquals("Specimen2 should have no designation", 0, specimen2.getSpecimenTypeDesignations().size());
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Assert.assertEquals("specimen1 should have exactly 1 designation", 1, specimen.getSpecimenTypeDesignations().size());
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specimen.addSpecimenTypeDesignation(desig2);
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Assert.assertEquals("Specimen1 should be the desig2's specimen", specimen, desig2.getTypeSpecimen());
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Assert.assertEquals("specimen1 should have exactly 2 designation", 2, specimen.getSpecimenTypeDesignations().size());
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desig1.setTypeSpecimen(null);
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Assert.assertEquals("Desig1 should not have a specimen anymore", null, desig1.getTypeSpecimen());
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Assert.assertEquals("Specimen1 should have 1 designation", 1, specimen.getSpecimenTypeDesignations().size());
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Assert.assertEquals("Specimen1's designation should be desig2", desig2, specimen.getSpecimenTypeDesignations().iterator().next());
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desig1.setTypeSpecimen(specimen);
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Assert.assertEquals("Desig1 should have specimen1 as specimen again", specimen, desig1.getTypeSpecimen());
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Assert.assertEquals("Specimen1 should have 2 designation", 2, specimen.getSpecimenTypeDesignations().size());
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}
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/**
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* Test method for {@link eu.etaxonomy.cdm.model.occurrence.Specimen#clone()}.
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*/
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@Test
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public void testClone() {
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logger.debug("Start testClone");
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//Null test is not full implemented, but an error is thrown if null throws
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//null pointer exception somewhere
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DerivedUnit specimenNullClone = (DerivedUnit)specimen.clone();
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String accessionNumber = "accNumber";
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String catalogNumber = "catNumber";
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Collection collection = Collection.NewInstance();
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collection.setCode("code");
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DateTime created = new DateTime();
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Person createdBy = Person.NewTitledInstance("creator");
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DerivationEvent derivedFrom = DerivationEvent.NewInstance(null);
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int id = 22;
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int individualCount = 25;
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DefinedTerm lifeStage = DefinedTerm.NewStageInstance(null, null, null);
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LSID lsid = null;
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try {
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lsid = new LSID("urn:lsid:example.com:foo:1");
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} catch (MalformedLSIDException e) {
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// TODO Auto-generated catch block
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e.printStackTrace();
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}
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DerivedUnit nextVersion = DerivedUnit.NewPreservedSpecimenInstance();
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DerivedUnit previousVersion = DerivedUnit.NewPreservedSpecimenInstance();
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PreservationMethod preservation = PreservationMethod.NewInstance();
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boolean protectedTitleCache = true;
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DefinedTerm sex = DefinedTerm.SEX_FEMALE();
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TaxonNameBase<?, ?> storedUnder = BotanicalName.NewInstance(Rank.GENUS());
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String titleCache = "title";
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Calendar updated = Calendar.getInstance();
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Person updatedBy = Person.NewTitledInstance("updatedPerson");
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UUID uuid = UUID.randomUUID();
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Annotation annotation = Annotation.NewDefaultLanguageInstance("annotation");
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String definition = "definition";
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//TODO
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DerivationEvent derivationEvent = DerivationEvent.NewInstance(null);
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SpecimenDescription description = SpecimenDescription.NewInstance();
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DeterminationEvent determination = DeterminationEvent.NewInstance();
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Extension extension = Extension.NewInstance();
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extension.setValue("extension");
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Marker marker = Marker.NewInstance(MarkerType.COMPLETE(), false);
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Rights right = Rights.NewInstance("right", Language.DEFAULT());
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Media media = Media.NewInstance();
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IdentifiableSource source = IdentifiableSource.NewDataImportInstance("12", "idNamespace");
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specimen.setAccessionNumber(accessionNumber);
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specimen.setCatalogNumber(catalogNumber);
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specimen.setCollection(collection);
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specimen.setCreated(created);
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// specimen.setCreatedBy(createdBy);
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specimen.setDerivedFrom(derivedFrom);
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specimen.setId(id);
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specimen.setIndividualCount(individualCount);
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specimen.setLifeStage(lifeStage);
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specimen.setLsid(lsid);
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specimen.setPreservation(preservation);
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specimen.setProtectedTitleCache(protectedTitleCache);
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specimen.setSex(sex);
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specimen.setStoredUnder(storedUnder);
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specimen.setTitleCache(titleCache, protectedTitleCache);
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// specimen.setUpdated(updated);
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// specimen.setUpdatedBy(updatedBy);
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specimen.setUuid(uuid);
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specimen.addAnnotation(annotation);
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specimen.putDefinition(Language.DEFAULT(), definition);
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specimen.addDerivationEvent(derivationEvent);
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specimen.addDescription(description);
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specimen.addDetermination(determination);
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specimen.addExtension(extension);
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specimen.addMarker(marker);
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// specimen.addMedia(media); #3597
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specimen.addRights(right);
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specimen.addSource(source);
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290
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try {
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Thread.sleep(200);
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} catch (InterruptedException e) {
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//ignore
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}
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DerivedUnit specimenClone = (DerivedUnit)specimen.clone();
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assertFalse(id == specimenClone.getId());
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assertFalse(created.equals(specimenClone.getCreated()));
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assertFalse(createdBy.equals(specimenClone.getCreatedBy()));
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assertFalse(updated.equals(specimenClone.getUpdated()));
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assertFalse(updatedBy.equals(specimenClone.getUpdatedBy()));
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assertNull(specimenClone.getUpdatedBy());
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assertNull(specimenClone.getCreatedBy());
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assertFalse(uuid.equals(specimenClone.getUuid()));
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assertEquals(accessionNumber, specimenClone.getAccessionNumber());
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assertEquals(catalogNumber, specimenClone.getCatalogNumber());
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assertEquals(collection, specimenClone.getCollection());
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assertEquals(derivedFrom, specimenClone.getDerivedFrom());
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assertEquals(lifeStage, specimenClone.getLifeStage());
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assertEquals(lsid, specimenClone.getLsid());
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assertEquals(preservation, specimenClone.getPreservation());
|
|
315
|
assertEquals(protectedTitleCache, specimenClone.isProtectedTitleCache());
|
|
316
|
assertEquals(storedUnder, specimenClone.getStoredUnder());
|
|
317
|
assertEquals(sex, specimenClone.getSex());
|
|
318
|
assertEquals(titleCache, specimenClone.getTitleCache());
|
|
319
|
|
|
320
|
Annotation clonedAnnotation = specimenClone.getAnnotations().iterator().next();
|
|
321
|
assertFalse(annotation.equals(clonedAnnotation));
|
|
322
|
assertEquals(annotation.getText(), ((LanguageStringBase)specimenClone.getAnnotations().iterator().next()).getText() );
|
|
323
|
assertNotSame(annotation, specimenClone.getAnnotations().iterator().next() );
|
|
324
|
|
|
325
|
assertEquals(definition, specimenClone.getDefinition().get(Language.DEFAULT()).getText());
|
|
326
|
//TODO
|
|
327
|
// assertNotSame(definition, specimenClone.getDefinition().getText(Language.DEFAULT()));
|
|
328
|
|
|
329
|
assertEquals(derivationEvent, specimenClone.getDerivationEvents().iterator().next());
|
|
330
|
assertSame(derivationEvent, specimenClone.getDerivationEvents().iterator().next());
|
|
331
|
|
|
332
|
assertEquals(description, specimenClone.getDescriptions().iterator().next());
|
|
333
|
// TODO ?
|
|
334
|
assertSame(description, specimenClone.getDescriptions().iterator().next());
|
|
335
|
|
|
336
|
assertEquals(determination, specimenClone.getDeterminations().iterator().next());
|
|
337
|
// TODO ?
|
|
338
|
assertSame(determination, specimenClone.getDeterminations().iterator().next());
|
|
339
|
|
|
340
|
assertFalse(extension.equals(specimenClone.getExtensions().iterator().next()));
|
|
341
|
assertEquals(extension.getValue(), specimenClone.getExtensions().iterator().next().getValue());
|
|
342
|
assertNotSame(extension, specimenClone.getExtensions().iterator().next());
|
|
343
|
assertEquals(1, specimen.getExtensions().size());
|
|
344
|
|
|
345
|
assertFalse(marker.equals(specimenClone.getMarkers().iterator().next()));
|
|
346
|
assertEquals(marker.getFlag(), specimenClone.getMarkers().iterator().next().getFlag());
|
|
347
|
assertNotSame(marker, specimenClone.getMarkers().iterator().next());
|
|
348
|
assertEquals(1, specimenClone.getMarkers().size());
|
|
349
|
|
|
350
|
// assertEquals(media, specimenClone.getMedia().iterator().next()); #3597
|
|
351
|
assertEquals(right, specimenClone.getRights().iterator().next());
|
|
352
|
|
|
353
|
assertFalse(source.equals(specimenClone.getSources().iterator().next()));
|
|
354
|
assertEquals(source.getId(), ((OriginalSourceBase)specimenClone.getSources().iterator().next()).getId());
|
|
355
|
assertNotSame(source, specimenClone.getSources().iterator().next());
|
|
356
|
assertEquals(1, specimenClone.getSources().size());
|
|
357
|
}
|
|
358
|
|
|
359
|
|
|
360
|
@Test
|
|
361
|
public void beanTests(){
|
|
362
|
// #5307 Test that BeanUtils does not fail
|
|
363
|
BeanUtils.getPropertyDescriptors(DerivedUnit.class);
|
|
364
|
BeanUtils.getPropertyDescriptors(SpecimenOrObservationBase.class);
|
|
365
|
BeanUtils.getPropertyDescriptors(FieldUnit.class);
|
|
366
|
BeanUtils.getPropertyDescriptors(MediaSpecimen.class);
|
|
367
|
BeanUtils.getPropertyDescriptors(DnaSample.class);
|
|
368
|
}
|
|
369
|
}
|