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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.name;
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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.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 org.apache.log4j.Logger;
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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 eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.RelationshipBase.Direction;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
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import eu.etaxonomy.cdm.model.description.TextData;
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import eu.etaxonomy.cdm.model.media.Media;
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
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import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;
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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.Taxon;
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import eu.etaxonomy.cdm.strategy.parser.TimePeriodParser;
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import eu.etaxonomy.cdm.test.unit.EntityTestBase;
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/**
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* @author a.mueller
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* @since 28.06.2008
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*/
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public class TaxonNameTest extends EntityTestBase {
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private static final Logger logger = Logger.getLogger(TaxonNameTest.class);
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private TaxonName nameBase1;
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private TaxonName nameBase2;
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private Reference ref1;
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@Before
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public void setUp() throws Exception {
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nameBase1 = TaxonNameFactory.NewNameInstance(NomenclaturalCode.NonViral, null);
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nameBase2 = TaxonNameFactory.NewNameInstance(NomenclaturalCode.NonViral, Rank.GENUS());
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ref1 = ReferenceFactory.newBook();
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ref1.setTitle("My book");
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ref1.setAbbrevTitle("M. bk.");
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ref1.setDatePublished(TimePeriodParser.parseStringVerbatim("1988"));
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}
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/*************************** TESTS ******************************************************/
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@Test
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public void testSetReferenceWithListener(){
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//prepare
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nameBase1.setGenusOrUninomial("Abies");
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nameBase1.setAuthorshipCache("Auth.");
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//before
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Assert.assertEquals("Abies Auth.", nameBase1.getFullTitleCache());
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//after
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//add ref
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nameBase1.setNomenclaturalReference(ref1);
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Assert.assertEquals("Using transient setNomenclaturalReference should reset the fullTitleCache",
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"Abies Auth., M. bk. 1988", nameBase1.getFullTitleCache());
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//add detail
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nameBase1.setNomenclaturalMicroReference("55");
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Assert.assertEquals("Using transient setNomenclaturalMicroReference should reset the fullTitleCache",
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"Abies Auth., M. bk.: 55. 1988", nameBase1.getFullTitleCache());
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//remove detail
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nameBase1.setNomenclaturalMicroReference(null);
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Assert.assertEquals("Using the source microcitation setter should reset the fullTitleCache",
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"Abies Auth., M. bk. 1988", nameBase1.getFullTitleCache());
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//remove ref
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nameBase1.setNomenclaturalReference(null);
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Assert.assertEquals("Using the source citation setter should reset the fullTitleCache",
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"Abies Auth.", nameBase1.getFullTitleCache());
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Assert.assertNull("Full emptying the source should remove it from the name (by method checkNullSource)",
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nameBase1.getNomenclaturalSource());
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//do the same again with setters on source
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//after
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//add ref
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nameBase1.getNomenclaturalSource(true).setCitation(ref1);
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Assert.assertEquals("Using transient setNomenclaturalReference should reset the fullTitleCache",
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"Abies Auth., M. bk. 1988", nameBase1.getFullTitleCache());
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//add detail
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nameBase1.getNomenclaturalSource().setCitationMicroReference("55");
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Assert.assertEquals("Using transient setNomenclaturalMicroReference should reset the fullTitleCache",
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"Abies Auth., M. bk.: 55. 1988", nameBase1.getFullTitleCache());
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//remove detail
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nameBase1.getNomenclaturalSource().setCitationMicroReference(null);
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Assert.assertEquals("Using the source microcitation setter should reset the fullTitleCache",
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"Abies Auth., M. bk. 1988", nameBase1.getFullTitleCache());
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//remove ref
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nameBase1.getNomenclaturalSource().setCitation(null);;
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Assert.assertEquals("Using the source citation setter should reset the fullTitleCache",
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"Abies Auth.", nameBase1.getFullTitleCache());
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Assert.assertNull("Full emptying the source should remove it from the name (by method checkNullSource)",
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nameBase1.getNomenclaturalSource());
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}
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@Test
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public void testTaxonName() {
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assertNotNull(nameBase1);
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}
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@Test
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public void testTaxonNameRank() {
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assertNotNull(nameBase2);
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assertEquals(Rank.GENUS(), nameBase2.getRank());
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Rank rank = null;
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TaxonName testName = TaxonNameFactory.NewNonViralInstance(rank, null);
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assertNull(testName.getRank());
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}
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@Test
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public void testTaxonNameHomotypicalGroup() {
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HomotypicalGroup hg = HomotypicalGroup.NewInstance();
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TaxonName testHG = TaxonNameFactory.NewNonViralInstance(null, hg);
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assertSame(hg, testHG.getHomotypicalGroup());
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HomotypicalGroup hgNull = null;
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TaxonName testHGNull = TaxonNameFactory.NewNonViralInstance(null, hgNull);
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assertNotNull(testHGNull.getHomotypicalGroup());
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}
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@Test
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public void testTaxonNameRankHomotypicalGroup() {
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Rank rank = Rank.SPECIES();
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HomotypicalGroup hg = HomotypicalGroup.NewInstance();
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TaxonName testHG = TaxonNameFactory.NewNonViralInstance(rank, hg);
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assertSame(rank, testHG.getRank());
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assertSame(hg, testHG.getHomotypicalGroup());
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Rank rankNull = null;
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HomotypicalGroup hgNull = null;
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TaxonName testHGNull = TaxonNameFactory.NewNonViralInstance(rankNull, hgNull);
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assertEquals(rankNull, testHGNull.getRank());
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assertNotNull(testHGNull.getHomotypicalGroup());
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}
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@Test
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public void testAddRelationshipToName() {
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logger.warn("not yet implemented");
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}
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@Test
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public void testAddRelationshipFromName() {
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logger.warn("not yet implemented");
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}
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@Test
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public void testAddNameRelationship() {
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logger.warn("not yet implemented");
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}
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@Test
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public void testRemoveNameRelationship() {
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logger.warn("not yet implemented");
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}
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@Test
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public void testAddRelationship() {
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logger.warn("not yet implemented");
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}
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/**
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* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonName#getStatus()}.
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* and for {@link eu.etaxonomy.cdm.model.name.TaxonName#addStatus(eu.etaxonomy.cdm.model.name.NomenclaturalStatus)}.
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* and for {@link eu.etaxonomy.cdm.model.name.TaxonName#removeStatus(eu.etaxonomy.cdm.model.name.NomenclaturalStatus)}.
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*/
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@Test
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public void testGetAddStatus() {
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//Empty status set
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assertNotNull(nameBase1.getStatus());
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assertEquals(0, nameBase1.getStatus().size());
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//1 status set
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NomenclaturalStatus nomStatus = NomenclaturalStatus.NewInstance(NomenclaturalStatusType.ALTERNATIVE());
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nameBase1.addStatus(nomStatus);
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assertNotNull(nameBase1.getStatus());
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assertEquals(1, nameBase1.getStatus().size());
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assertEquals(nomStatus, nameBase1.getStatus().iterator().next());
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//2 status set
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NomenclaturalStatus nomStatus2 = NomenclaturalStatus.NewInstance(NomenclaturalStatusType.ALTERNATIVE());
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nameBase1.addStatus(nomStatus2);
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assertEquals(2, nameBase1.getStatus().size());
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assertTrue(nameBase1.getStatus().contains(nomStatus2));
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//remove
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nameBase1.removeStatus(nomStatus);
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assertEquals(1, nameBase1.getStatus().size());
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assertTrue(nameBase1.getStatus().contains(nomStatus2));
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//remove
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nameBase1.removeStatus(nomStatus2);
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assertEquals(0, nameBase1.getStatus().size());
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assertFalse(nameBase1.getStatus().contains(nomStatus2));
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}
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@Test
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public void testIsOriginalCombination() {
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logger.warn("not yet implemented");
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}
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@Test
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public void testGetBasionym() {
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TaxonName name1 = TaxonNameFactory.NewBotanicalInstance(null);
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TaxonName basionym1 = TaxonNameFactory.NewBotanicalInstance(null);
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TaxonName basionym2 = TaxonNameFactory.NewBotanicalInstance(null);
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assertEquals(null, name1.getBasionym());
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name1.addBasionym(basionym1);
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assertEquals(basionym1, name1.getBasionym());
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name1.addBasionym(basionym2);
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TaxonName oneOfThebasionyms = name1.getBasionym();
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assertTrue(oneOfThebasionyms == basionym1 || oneOfThebasionyms == basionym2 );
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name1.removeBasionyms();
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assertEquals(null, name1.getBasionym());
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}
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@Test
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public void testAddBasionymT() {
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assertNotSame(nameBase1.getHomotypicalGroup(), nameBase2.getHomotypicalGroup());
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assertFalse(nameBase1.getHomotypicalGroup().equals(nameBase2.getHomotypicalGroup()));
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nameBase1.addBasionym(nameBase2);
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assertTrue(nameBase1.getHomotypicalGroup().equals(nameBase2.getHomotypicalGroup()));
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assertSame(nameBase1.getHomotypicalGroup(), nameBase2.getHomotypicalGroup());
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logger.warn("not yet fully implemented");
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}
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@Test
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public void testAddBasionymTaxonNameString() {
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logger.warn("not yet implemented");
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}
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@Test
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public void testGetRank() {
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TaxonName name1 = TaxonNameFactory.NewBotanicalInstance(null);
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assertNull("Rank shall be null", name1.getRank());
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name1.setRank(Rank.SPECIES());
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assertNotNull("Rank shall not be null", name1.getRank());
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name1.setRank(null);
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assertNull("Rank shall be null", name1.getRank());
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}
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@Test
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public void testGetSetNomenclaturalReference() {
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INomenclaturalReference nr = nameBase1.getNomenclaturalReference();
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assertNull("Nomenclatural Reference shall be null", nr);
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nameBase1.setNomenclaturalReference(ReferenceFactory.newGeneric());
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nr = nameBase1.getNomenclaturalReference();
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assertNotNull("Nomenclatural Reference shall not be null", nr);
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}
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@Test
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public void testGetAppendedPhrase() {
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TaxonName name1 = TaxonNameFactory.NewBotanicalInstance(null);
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String appPhrase = "appPhrase";
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assertNull(name1.getAppendedPhrase());
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name1.setAppendedPhrase(appPhrase);
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assertSame(appPhrase, name1.getAppendedPhrase());
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name1.setAppendedPhrase(null);
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assertNull(name1.getAppendedPhrase());
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}
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@Test
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public void testGetSetNomenclaturalMicroReference() {
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TaxonName name1 = TaxonNameFactory.NewBotanicalInstance(null);
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String microRef = "micro";
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assertNull(name1.getNomenclaturalMicroReference());
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name1.setNomenclaturalMicroReference(microRef);
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assertSame(microRef, name1.getNomenclaturalMicroReference());
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name1.setNomenclaturalMicroReference(null);
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assertNull(name1.getNomenclaturalMicroReference());
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}
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@Test
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public void testGetSetHasProblem() {
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TaxonName name1 = TaxonNameFactory.NewBotanicalInstance(null);
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name1.setParsingProblem(0);
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assertFalse(name1.hasProblem());
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name1.setParsingProblem(1);
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assertTrue(name1.hasProblem());
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name1.setParsingProblem(0);
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assertFalse(name1.getParsingProblem()!=0);
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}
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@Test
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public void testAddNameTypeDesignation() {
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logger.warn("not yet implemented");
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}
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@Test
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public void testRemoveNameTypeDesignation() {
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logger.warn("not yet implemented");
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}
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@Test
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public void testGetSpecimenTypeDesignationsOfHomotypicalGroup() {
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logger.warn("not yet implemented");
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}
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@Test
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public void testAddSpecimenTypeDesignationSpecimenTypeDesignationStatusReferenceBaseStringStringBoolean() {
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logger.warn("not yet implemented");
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}
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@Test
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public void testAddSpecimenTypeDesignationSpecimenTypeDesignation() {
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logger.warn("not yet implemented");
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}
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@Test
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public void testRemoveSpecimenTypeDesignation() {
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logger.warn("not yet implemented");
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}
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@Test
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public void testRemoveTypeDesignation() {
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logger.warn("not yet implemented");
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}
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@Test
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public void testGetCitation() {
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logger.warn("not yet implemented");
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}
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@Test
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public void testGetCitationString() {
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String citation = nameBase1.getCitationString();
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logger.warn("not yet implemented");
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}
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@Test
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public void testGetReferenceYear() {
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logger.warn("not yet implemented");
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}
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/**
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* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonName#addTaxonBase(eu.etaxonomy.cdm.model.taxon.TaxonBase)}.
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*/
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@Test
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362
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public void testAddTaxonBase() {
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Taxon taxon = Taxon.NewInstance(null, null);
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364
|
nameBase2.addTaxonBase(taxon); //test if reflection method addTaxonBase() works
|
|
365
|
assertTrue("The taxon has not properly been added to the taxonName", nameBase2.getTaxonBases().contains(taxon));
|
|
366
|
assertEquals("The taxon name has not properly been added to the taxon", nameBase2, taxon.getName());
|
|
367
|
nameBase2.removeTaxonBase(taxon); //test if reflection method in removeTaxonBase() works
|
|
368
|
assertFalse("The taxon has not properly been removed from the taxon name", nameBase2.getTaxonBases().contains(taxon));
|
|
369
|
assertEquals("The taxon name has not properly been removed from the taxon", null, taxon.getName());
|
|
370
|
}
|
|
371
|
|
|
372
|
@Test
|
|
373
|
public void testAddAndRemoveDescriptionTaxonNameDescription() {
|
|
374
|
TaxonNameDescription description = TaxonNameDescription.NewInstance();
|
|
375
|
nameBase2.addDescription(description); //test if reflection method in addDescription() works
|
|
376
|
assertTrue("The description has not properly been added to the taxonName", nameBase2.getDescriptions().contains(description));
|
|
377
|
assertEquals("The taxon name has not properly been added to the description", nameBase2, description.getTaxonName());
|
|
378
|
nameBase2.removeDescription(description); //test if reflection method in removeDescription() works
|
|
379
|
assertFalse("The description has not properly been removed from the taxon name", nameBase2.getDescriptions().contains(description));
|
|
380
|
assertEquals("The taxon name has not properly been removed from the description", null, description.getTaxonName());
|
|
381
|
}
|
|
382
|
|
|
383
|
@Test
|
|
384
|
public void testGetSynonyms() {
|
|
385
|
logger.warn("not yet implemented");
|
|
386
|
}
|
|
387
|
|
|
388
|
@Test
|
|
389
|
public void testMergeHomotypicGroups() {
|
|
390
|
TaxonName name1 = TaxonNameFactory.NewBotanicalInstance(null);
|
|
391
|
TaxonName name2 = TaxonNameFactory.NewBotanicalInstance(null);
|
|
392
|
TaxonName name3 = TaxonNameFactory.NewBotanicalInstance(null);
|
|
393
|
|
|
394
|
assertFalse(name1.getHomotypicalGroup().equals(name2.getHomotypicalGroup()));
|
|
395
|
int numberOfTypifiedNames = name1.getHomotypicalGroup().getTypifiedNames().size();
|
|
396
|
assertEquals(1, numberOfTypifiedNames);
|
|
397
|
|
|
398
|
name1.mergeHomotypicGroups(name2);
|
|
399
|
assertEquals(name1.getHomotypicalGroup(), name2.getHomotypicalGroup());
|
|
400
|
assertSame(name1.getHomotypicalGroup(), name2.getHomotypicalGroup());
|
|
401
|
numberOfTypifiedNames = name1.getHomotypicalGroup().getTypifiedNames().size();
|
|
402
|
assertEquals(2, numberOfTypifiedNames);
|
|
403
|
numberOfTypifiedNames = name2.getHomotypicalGroup().getTypifiedNames().size();
|
|
404
|
assertEquals(2, numberOfTypifiedNames);
|
|
405
|
assertTrue(name1.getHomotypicalGroup().getTypifiedNames().contains(name2));
|
|
406
|
assertTrue(name2.getHomotypicalGroup().getTypifiedNames().contains(name1));
|
|
407
|
|
|
408
|
name3.mergeHomotypicGroups(name2);
|
|
409
|
assertEquals(name1.getHomotypicalGroup(), name3.getHomotypicalGroup());
|
|
410
|
assertSame(name1.getHomotypicalGroup(), name3.getHomotypicalGroup());
|
|
411
|
numberOfTypifiedNames = name1.getHomotypicalGroup().getTypifiedNames().size();
|
|
412
|
assertEquals(3, numberOfTypifiedNames);
|
|
413
|
numberOfTypifiedNames = name2.getHomotypicalGroup().getTypifiedNames().size();
|
|
414
|
assertEquals(3, numberOfTypifiedNames);
|
|
415
|
numberOfTypifiedNames = name3.getHomotypicalGroup().getTypifiedNames().size();
|
|
416
|
assertEquals(3, numberOfTypifiedNames);
|
|
417
|
assertTrue(name1.getHomotypicalGroup().getTypifiedNames().contains(name2));
|
|
418
|
assertTrue(name2.getHomotypicalGroup().getTypifiedNames().contains(name1));
|
|
419
|
assertTrue(name1.getHomotypicalGroup().getTypifiedNames().contains(name3));
|
|
420
|
assertTrue(name3.getHomotypicalGroup().getTypifiedNames().contains(name1));
|
|
421
|
assertTrue(name2.getHomotypicalGroup().getTypifiedNames().contains(name3));
|
|
422
|
assertTrue(name3.getHomotypicalGroup().getTypifiedNames().contains(name2));
|
|
423
|
}
|
|
424
|
|
|
425
|
@Test
|
|
426
|
public void testIsBasionymFor() {
|
|
427
|
TaxonName name1 = TaxonNameFactory.NewBotanicalInstance(null);
|
|
428
|
TaxonName name2 = TaxonNameFactory.NewBotanicalInstance(null);
|
|
429
|
|
|
430
|
assertFalse(name2.isBasionymFor(name1));
|
|
431
|
assertFalse(name1.isBasionymFor(name2));
|
|
432
|
name1.addBasionym(name2);
|
|
433
|
assertTrue(name2.isBasionymFor(name1));
|
|
434
|
assertFalse(name1.isBasionymFor(name2));
|
|
435
|
}
|
|
436
|
|
|
437
|
@Test
|
|
438
|
public void testIsHomotypic() {
|
|
439
|
TaxonName name1 = TaxonNameFactory.NewBotanicalInstance(null);
|
|
440
|
TaxonName name2 = TaxonNameFactory.NewBotanicalInstance(null);
|
|
441
|
TaxonName name3 = TaxonNameFactory.NewBotanicalInstance(null);
|
|
442
|
TaxonName name4 = TaxonNameFactory.NewBotanicalInstance(null);
|
|
443
|
name1.mergeHomotypicGroups(name2);
|
|
444
|
name2.mergeHomotypicGroups(name4);
|
|
445
|
|
|
446
|
assertTrue(name1.isHomotypic(name4));
|
|
447
|
assertTrue(name4.isHomotypic(name1));
|
|
448
|
assertFalse(name1.isHomotypic(name3));
|
|
449
|
assertFalse(name3.isHomotypic(name1));
|
|
450
|
assertTrue(name2.isHomotypic(name1));
|
|
451
|
}
|
|
452
|
|
|
453
|
@Test
|
|
454
|
public void testMakeGroupsBasionym(){
|
|
455
|
TaxonName name1 = TaxonNameFactory.NewBotanicalInstance(null);
|
|
456
|
TaxonName name2 = TaxonNameFactory.NewBotanicalInstance(null);
|
|
457
|
TaxonName name3 = TaxonNameFactory.NewBotanicalInstance(null);
|
|
458
|
TaxonName name4 = TaxonNameFactory.NewBotanicalInstance(null);
|
|
459
|
|
|
460
|
name1.mergeHomotypicGroups(name2);
|
|
461
|
name1.mergeHomotypicGroups(name3);
|
|
462
|
name2.mergeHomotypicGroups(name4);
|
|
463
|
|
|
464
|
name1.makeGroupsBasionym();
|
|
465
|
|
|
466
|
assertEquals(1, name2.getBasionyms().size());
|
|
467
|
assertEquals(1, name3.getBasionyms().size());
|
|
468
|
assertEquals(1, name4.getBasionyms().size());
|
|
469
|
assertEquals(name1, name4.getBasionym());
|
|
470
|
}
|
|
471
|
|
|
472
|
@Test
|
|
473
|
public void testIsGroupsBasionym(){
|
|
474
|
TaxonName name1 = TaxonNameFactory.NewBotanicalInstance(null);
|
|
475
|
TaxonName name2 = TaxonNameFactory.NewBotanicalInstance(null);
|
|
476
|
TaxonName name3 = TaxonNameFactory.NewBotanicalInstance(null);
|
|
477
|
TaxonName name4 = TaxonNameFactory.NewBotanicalInstance(null);
|
|
478
|
|
|
479
|
assertFalse(name1.isGroupsBasionym());
|
|
480
|
|
|
481
|
name1.mergeHomotypicGroups(name2);
|
|
482
|
name2.mergeHomotypicGroups(name4);
|
|
483
|
|
|
484
|
name1.makeGroupsBasionym();
|
|
485
|
|
|
486
|
assertTrue(name1.isGroupsBasionym());
|
|
487
|
assertFalse(name2.isGroupsBasionym());
|
|
488
|
name1.mergeHomotypicGroups(name3);
|
|
489
|
assertFalse(name1.isGroupsBasionym());
|
|
490
|
}
|
|
491
|
|
|
492
|
@Test
|
|
493
|
public void testRemoveBasionyms(){
|
|
494
|
TaxonName name1 = TaxonNameFactory.NewBotanicalInstance(null);
|
|
495
|
TaxonName basionym1 = TaxonNameFactory.NewBotanicalInstance(null);
|
|
496
|
TaxonName basionym2 = TaxonNameFactory.NewBotanicalInstance(null);
|
|
497
|
|
|
498
|
name1.addBasionym(basionym1);
|
|
499
|
assertEquals(1, name1.getBasionyms().size());
|
|
500
|
name1.addBasionym(basionym2);
|
|
501
|
assertEquals(2, name1.getBasionyms().size());
|
|
502
|
name1.removeBasionyms();
|
|
503
|
assertEquals(0, name1.getBasionyms().size());
|
|
504
|
}
|
|
505
|
|
|
506
|
@Test
|
|
507
|
public void testRemoveRelationWithTaxonName(){
|
|
508
|
TaxonName name1 = TaxonNameFactory.NewBotanicalInstance(null);
|
|
509
|
TaxonName basionym1 = TaxonNameFactory.NewBotanicalInstance(null);
|
|
510
|
TaxonName basionym2 = TaxonNameFactory.NewBotanicalInstance(null);
|
|
511
|
|
|
512
|
name1.addBasionym(basionym1);
|
|
513
|
assertEquals(1, name1.getBasionyms().size());
|
|
514
|
name1.addBasionym(basionym2);
|
|
515
|
assertEquals(2, name1.getBasionyms().size());
|
|
516
|
name1.removeRelationWithTaxonName(basionym1, Direction.relatedTo, NameRelationshipType.BASIONYM());
|
|
517
|
assertEquals(1, name1.getBasionyms().size());
|
|
518
|
}
|
|
519
|
|
|
520
|
@Test
|
|
521
|
public void testIsSupraGeneric() {
|
|
522
|
nameBase1.setRank(Rank.FAMILY());
|
|
523
|
assertTrue(nameBase1.isSupraGeneric());
|
|
524
|
nameBase1.setRank(Rank.GENUS());
|
|
525
|
assertFalse(nameBase1.isSupraGeneric());
|
|
526
|
nameBase1.setRank(Rank.FORM());
|
|
527
|
assertFalse(nameBase1.isSupraGeneric());
|
|
528
|
nameBase1.setRank(null);
|
|
529
|
assertFalse(nameBase1.isSupraGeneric());
|
|
530
|
}
|
|
531
|
|
|
532
|
@Test
|
|
533
|
public void testRemoveTaxonBases(){
|
|
534
|
|
|
535
|
Taxon newTaxon = Taxon.NewInstance(nameBase1, null);
|
|
536
|
assertEquals(1, nameBase1.getTaxonBases().size());
|
|
537
|
|
|
538
|
nameBase1.removeTaxonBase(newTaxon);
|
|
539
|
assertEquals(0, nameBase1.getTaxonBases().size());
|
|
540
|
}
|
|
541
|
|
|
542
|
@Test
|
|
543
|
public void testIsGenus() {
|
|
544
|
nameBase1.setRank(Rank.FAMILY());
|
|
545
|
assertFalse(nameBase1.isGenus());
|
|
546
|
nameBase1.setRank(Rank.GENUS());
|
|
547
|
assertTrue(nameBase1.isGenus());
|
|
548
|
nameBase1.setRank(Rank.FORM());
|
|
549
|
assertFalse(nameBase1.isGenus());
|
|
550
|
nameBase1.setRank(null);
|
|
551
|
assertFalse(nameBase1.isGenus());
|
|
552
|
}
|
|
553
|
|
|
554
|
@Test
|
|
555
|
public void testIsInfraGeneric() {
|
|
556
|
nameBase1.setRank(Rank.FAMILY());
|
|
557
|
assertFalse(nameBase1.isInfraGeneric());
|
|
558
|
nameBase1.setRank(Rank.GENUS());
|
|
559
|
assertFalse(nameBase1.isInfraGeneric());
|
|
560
|
nameBase1.setRank(Rank.SUBGENUS());
|
|
561
|
assertTrue(nameBase1.isInfraGeneric());
|
|
562
|
nameBase1.setRank(Rank.SPECIES());
|
|
563
|
assertFalse(nameBase1.isInfraGeneric());
|
|
564
|
nameBase1.setRank(Rank.FORM());
|
|
565
|
assertFalse(nameBase1.isInfraGeneric());
|
|
566
|
nameBase1.setRank(Rank.INFRAGENERICTAXON());
|
|
567
|
assertTrue(nameBase1.isInfraGeneric());
|
|
568
|
nameBase1.setRank(null);
|
|
569
|
assertFalse(nameBase1.isInfraGeneric());
|
|
570
|
}
|
|
571
|
|
|
572
|
@Test
|
|
573
|
public void testIsSpecies() {
|
|
574
|
nameBase1.setRank(Rank.FAMILY());
|
|
575
|
assertFalse(nameBase1.isSpecies());
|
|
576
|
nameBase1.setRank(Rank.GENUS());
|
|
577
|
assertFalse(nameBase1.isSpecies());
|
|
578
|
nameBase1.setRank(Rank.SUBGENUS());
|
|
579
|
assertFalse(nameBase1.isSpecies());
|
|
580
|
nameBase1.setRank(Rank.SPECIES());
|
|
581
|
assertTrue(nameBase1.isSpecies());
|
|
582
|
nameBase1.setRank(Rank.FORM());
|
|
583
|
assertFalse(nameBase1.isSpecies());
|
|
584
|
nameBase1.setRank(null);
|
|
585
|
assertFalse(nameBase1.isSpecies());
|
|
586
|
}
|
|
587
|
|
|
588
|
@Test
|
|
589
|
public void testIsInfraSpecific() {
|
|
590
|
nameBase1.setRank(Rank.FAMILY());
|
|
591
|
assertFalse(nameBase1.isInfraSpecific());
|
|
592
|
nameBase1.setRank(Rank.GENUS());
|
|
593
|
assertFalse(nameBase1.isInfraSpecific());
|
|
594
|
nameBase1.setRank(Rank.SUBGENUS());
|
|
595
|
assertFalse(nameBase1.isInfraSpecific());
|
|
596
|
nameBase1.setRank(Rank.SPECIES());
|
|
597
|
assertFalse(nameBase1.isInfraSpecific());
|
|
598
|
nameBase1.setRank(Rank.FORM());
|
|
599
|
assertTrue(nameBase1.isInfraSpecific());
|
|
600
|
nameBase1.setRank(Rank.INFRASPECIFICTAXON());
|
|
601
|
assertTrue(nameBase1.isInfraSpecific());
|
|
602
|
nameBase1.setRank(null);
|
|
603
|
assertFalse(nameBase1.isInfraSpecific());
|
|
604
|
}
|
|
605
|
|
|
606
|
//descriptions, fullTitleCache, homotypicalGroup,
|
|
607
|
|
|
608
|
//no changes to: appendedPharse, nomenclaturalReference,
|
|
609
|
//nomenclaturalMicroReference, parsingProblem, problemEnds, problemStarts
|
|
610
|
//protectedFullTitleCache
|
|
611
|
|
|
612
|
@Test
|
|
613
|
public void testClone(){
|
|
614
|
|
|
615
|
//Create data
|
|
616
|
TaxonName taxonName1 = TaxonNameFactory.NewNonViralInstance(Rank.SPECIES());
|
|
617
|
TaxonName genusName = TaxonNameFactory.NewNonViralInstance(Rank.GENUS());
|
|
618
|
Taxon.NewInstance(taxonName1, null);
|
|
619
|
|
|
620
|
//basionym & homonym
|
|
621
|
TaxonName basionym = TaxonNameFactory.NewNonViralInstance(Rank.SPECIES());
|
|
622
|
TaxonName earlierHomonym = TaxonNameFactory.NewNonViralInstance(Rank.SPECIES());
|
|
623
|
NameRelationship basionymRelation = taxonName1.addBasionym(basionym);
|
|
624
|
NameRelationship homonymRelation = taxonName1.addRelationshipToName(earlierHomonym, NameRelationshipType.LATER_HOMONYM(), "later homonym rule", null);
|
|
625
|
//status
|
|
626
|
Reference statusReference = ReferenceFactory.newArticle();
|
|
627
|
NomenclaturalStatus nomStatus = NomenclaturalStatus.NewInstance(NomenclaturalStatusType.CONSERVED(), statusReference, "55");
|
|
628
|
taxonName1.addStatus(nomStatus);
|
|
629
|
//typeDesignation
|
|
630
|
DerivedUnit typeSpecimen = DerivedUnit.NewPreservedSpecimenInstance();
|
|
631
|
Reference specimenTypeCitation = ReferenceFactory.newArticle();
|
|
632
|
Reference nameTypeCitation = ReferenceFactory.newArticle();
|
|
633
|
SpecimenTypeDesignation specimenTypeDesignationOriginal = taxonName1.addSpecimenTypeDesignation(typeSpecimen, SpecimenTypeDesignationStatus.HOLOTYPE(), specimenTypeCitation, null, null, false, false);
|
|
634
|
NameTypeDesignation nameTypeDesignationOriginal = genusName.addNameTypeDesignation(taxonName1, nameTypeCitation, null, null, NameTypeDesignationStatus.LECTOTYPE(), true, false, false, false);
|
|
635
|
|
|
636
|
//description
|
|
637
|
TaxonNameDescription description = TaxonNameDescription.NewInstance(taxonName1);
|
|
638
|
TextData textData = TextData.NewInstance(Feature.IMAGE());
|
|
639
|
textData.putText(Language.DEFAULT(), "My media text data");
|
|
640
|
Media media = Media.NewInstance();
|
|
641
|
textData.addMedia(media);
|
|
642
|
description.addElement(textData);
|
|
643
|
|
|
644
|
//CLONE
|
|
645
|
TaxonName clone = taxonName1.clone();
|
|
646
|
TaxonName genusClone = genusName.clone();
|
|
647
|
assertSame("Rank should be same", taxonName1.getRank(), clone.getRank());
|
|
648
|
assertTrue("TaxonBases should not be cloned", clone.getTaxonBases().isEmpty());
|
|
649
|
assertEquals("TaxonBases of original name should not be empty", 1, taxonName1.getTaxonBases().size());
|
|
650
|
//homotypical groups are not cloned, see documentation
|
|
651
|
assertNotSame("The clone must have a new homotypical group", taxonName1.getHomotypicalGroup(), clone.getHomotypicalGroup());
|
|
652
|
assertNotSame("The genusClone must a new homotypical group", genusName.getHomotypicalGroup(), genusClone.getHomotypicalGroup());
|
|
653
|
assertEquals("Only the name should be part of the new homotypical group", 1, clone.getHomotypicalGroup().getTypifiedNames().size());
|
|
654
|
|
|
655
|
//description
|
|
656
|
assertEquals("There should be exactly 1 name description", 1, clone.getDescriptions().size());
|
|
657
|
TaxonNameDescription descriptionClone = clone.getDescriptions().iterator().next();
|
|
658
|
assertEquals("There should be exactly 1 description element", 1, descriptionClone.getElements().size());
|
|
659
|
TextData textDataClone = (TextData)descriptionClone.getElements().iterator().next();
|
|
660
|
String text = textDataClone.getText(Language.DEFAULT());
|
|
661
|
assertEquals("Textdata should be equal", "My media text data", text);
|
|
662
|
assertEquals("There should be exactly 1 media attached", 1, textDataClone.getMedia().size());
|
|
663
|
Media mediaClone = textDataClone.getMedia().get(0);
|
|
664
|
assertSame("Media must be the same", media, mediaClone);
|
|
665
|
|
|
666
|
//type designation
|
|
667
|
assertEquals("There should be exactly 1 specimen type designation", 1, clone.getTypeDesignations().size());
|
|
668
|
assertNotSame("type designation sets should not be the same", taxonName1.getTypeDesignations(), clone.getTypeDesignations());
|
|
669
|
SpecimenTypeDesignation specimenTypeDesignationClone = (SpecimenTypeDesignation)clone.getTypeDesignations().iterator().next();
|
|
670
|
assertNotSame("The specimen type designation should not be the same", specimenTypeDesignationOriginal, specimenTypeDesignationClone);
|
|
671
|
assertSame("The derived unit of the specimen type designation needs to be the same", specimenTypeDesignationOriginal.getTypeSpecimen(), specimenTypeDesignationClone.getTypeSpecimen());
|
|
672
|
assertSame("The status of the specimen type designation needs to be the same", specimenTypeDesignationOriginal.getTypeStatus(), specimenTypeDesignationClone.getTypeStatus());
|
|
673
|
assertEquals("The specimen type designation must have exactly 1 typified name which is 'clone'", 1, specimenTypeDesignationClone.getTypifiedNames().size());
|
|
674
|
assertTrue("The specimen type designation must have 'clone' as typified name", specimenTypeDesignationClone.getTypifiedNames().contains(clone));
|
|
675
|
// assertSame("The specimen type designation must have the same homotypical group as the typified name", specimenTypeDesignationClone.getHomotypicalGroup(), clone.getHomotypicalGroup());
|
|
676
|
|
|
677
|
assertEquals("There should be exactly 1 name type designation", 1, genusClone.getTypeDesignations().size());
|
|
678
|
assertNotSame("type designation sets should not be the same", genusName.getTypeDesignations(), genusClone.getTypeDesignations());
|
|
679
|
NameTypeDesignation nameTypeDesignationClone = (NameTypeDesignation)genusClone.getTypeDesignations().iterator().next();
|
|
680
|
assertNotSame("The name type designation should not be the same", nameTypeDesignationOriginal, nameTypeDesignationClone);
|
|
681
|
assertSame("The nyme type of the name type designation needs to be the same", taxonName1, nameTypeDesignationClone.getTypeName());
|
|
682
|
assertSame("The status of the name type designation needs to be the same", nameTypeDesignationOriginal.getTypeStatus(), nameTypeDesignationClone.getTypeStatus());
|
|
683
|
assertEquals("The name type designation must have exactly 1 typified name which is 'genusClone'", 1, nameTypeDesignationClone.getTypifiedNames().size());
|
|
684
|
assertTrue("The name type designation must have 'genusClone' as typified name", nameTypeDesignationClone.getTypifiedNames().contains(genusClone));
|
|
685
|
// assertSame("The name type designation must have the same homotypical group as the typified name", nameTypeDesignationClone.getHomotypicalGroup(), genusClone.getHomotypicalGroup());
|
|
686
|
|
|
687
|
//status
|
|
688
|
assertEquals("There should be exactly 1 status", 1, clone.getStatus().size());
|
|
689
|
assertNotSame("Status sets should not be the same", taxonName1.getStatus(), clone.getStatus());
|
|
690
|
NomenclaturalStatus cloneStatus = clone.getStatus().iterator().next();
|
|
691
|
assertSame("The type of the nomStatus needs to be the same", nomStatus.getType(), cloneStatus.getType());
|
|
692
|
assertSame("The citation of the nomStatus needs to be the same", nomStatus.getCitation(), cloneStatus.getCitation());
|
|
693
|
assertSame("The rule considered of the nomStatus needs to be the same", nomStatus.getRuleConsidered(), cloneStatus.getRuleConsidered());
|
|
694
|
assertNotSame("The nomStatus should be cloned as it is orphan removal", nomStatus, cloneStatus);
|
|
695
|
|
|
696
|
// //hybrid parents of clone
|
|
697
|
// assertEquals("There should be exactly 2 hybrid relationships in which the clone takes the child role", 2, clone.getChildRelationships().size());
|
|
698
|
// Set<NonViralName> parentSet = new HashSet<>();
|
|
699
|
// Set<NonViralName> childSet = new HashSet<>();
|
|
700
|
// for (Object object : clone.getChildRelationships()){
|
|
701
|
// HybridRelationship childRelation = (HybridRelationship)object;
|
|
702
|
// NonViralName relatedFrom = childRelation.getRelatedFrom();
|
|
703
|
// parentSet.add(relatedFrom);
|
|
704
|
// NonViralName relatedTo = childRelation.getRelatedTo();
|
|
705
|
// childSet.add(relatedTo);
|
|
706
|
// }
|
|
707
|
// assertTrue("Parent set should contain parent1", parentSet.contains(parent));
|
|
708
|
// assertTrue("Parent set should contain parent2", parentSet.contains(parent2));
|
|
709
|
// assertTrue("Child set should contain clone", childSet.contains(clone));
|
|
710
|
|
|
711
|
//basionym of clone
|
|
712
|
assertEquals("There should be exactly 1 relationship in which the clone takes the -to- role", 1, clone.getRelationsToThisName().size());
|
|
713
|
NameRelationship basionymRelationClone = clone.getRelationsToThisName().iterator().next();
|
|
714
|
assertNotEquals(basionymRelation, basionymRelationClone);
|
|
715
|
//related name should not be cloned, if needed e.g. for basionyms this should be handled by the calling method (see documentation)
|
|
716
|
assertSame("Basionym should be from-object in relationship", basionym, basionymRelationClone.getRelatedFrom());
|
|
717
|
assertSame("Clone should be to-object in relationship", clone, basionymRelationClone.getRelatedTo());
|
|
718
|
assertSame("Relationship type should be cloned correctly", NameRelationshipType.BASIONYM(), basionymRelationClone.getType());
|
|
719
|
|
|
720
|
//homonym of clone
|
|
721
|
assertEquals("There should be exactly 1 relationship in which the clone takes the from role", 1, clone.getRelationsFromThisName().size());
|
|
722
|
NameRelationship homonymRelationClone = clone.getRelationsFromThisName().iterator().next();
|
|
723
|
assertNotEquals(homonymRelation, homonymRelationClone);
|
|
724
|
assertSame("Clone should be from-object in relationship", clone, homonymRelationClone.getRelatedFrom());
|
|
725
|
assertSame("Homonym should be to-object in relationship", earlierHomonym, homonymRelationClone.getRelatedTo());
|
|
726
|
assertSame("Relationship type should be cloned correctly", NameRelationshipType.LATER_HOMONYM(), homonymRelationClone.getType());
|
|
727
|
assertEquals("Rule should be cloned correctly", "later homonym rule", homonymRelationClone.getRuleConsidered());
|
|
728
|
}
|
|
729
|
|
|
730
|
|
|
731
|
/*
|
|
732
|
* Moved from IdentifiableEntityTest to here due to #922
|
|
733
|
*/
|
|
734
|
@Test
|
|
735
|
public void testCompareTo() {
|
|
736
|
TaxonName abies = TaxonNameFactory.NewNonViralInstance(Rank.GENUS(), null);
|
|
737
|
abies.setNameCache("Abies");
|
|
738
|
abies.setTitleCache("Abies", true);
|
|
739
|
|
|
740
|
TaxonName abiesMill = TaxonNameFactory.NewNonViralInstance(Rank.GENUS(), null);
|
|
741
|
abiesMill.setNameCache("Abies");
|
|
742
|
abiesMill.setTitleCache("Abies Mill.", true);
|
|
743
|
|
|
744
|
TaxonName abiesAlba = TaxonNameFactory.NewNonViralInstance(Rank.SPECIES(), null);
|
|
745
|
abiesAlba.setNameCache("Abies alba");
|
|
746
|
abiesAlba.setTitleCache("Abies alba", true);
|
|
747
|
|
|
748
|
TaxonName abiesAlbaMichx = TaxonNameFactory.NewNonViralInstance(Rank.SPECIES(), null);
|
|
749
|
abiesAlbaMichx.setNameCache("Abies alba");
|
|
750
|
abiesAlbaMichx.setTitleCache("Abies alba Michx.", true);
|
|
751
|
|
|
752
|
TaxonName abiesAutonym = TaxonNameFactory.NewNonViralInstance(Rank.SECTION_BOTANY());
|
|
753
|
abiesAutonym.setGenusOrUninomial("Abies");
|
|
754
|
abiesAutonym.setInfraGenericEpithet("Abies");
|
|
755
|
|
|
756
|
abiesAutonym.setTitleCache("Abies Mill. sect. Abies", true);
|
|
757
|
abiesAutonym.getNameCache();
|
|
758
|
|
|
759
|
TaxonName abiesBalsamea = TaxonNameFactory.NewNonViralInstance(Rank.SECTION_BOTANY());
|
|
760
|
abiesBalsamea.setGenusOrUninomial("Abies");
|
|
761
|
abiesBalsamea.setInfraGenericEpithet("Balsamea");
|
|
762
|
abiesBalsamea.getNameCache();
|
|
763
|
abiesBalsamea.setTitleCache("Abies sect. Balsamea L.", true);
|
|
764
|
|
|
765
|
TaxonName abiesAlbaxPinusBeta = TaxonNameFactory.NewNonViralInstance(Rank.SPECIES());
|
|
766
|
abiesAlbaxPinusBeta.setHybridFormula(true);
|
|
767
|
abiesAlbaxPinusBeta.addHybridParent(abiesAlba, HybridRelationshipType.FIRST_PARENT(), null);
|
|
768
|
|
|
769
|
int result = 0;
|
|
770
|
|
|
771
|
// "Abies" < "Abies Mill."
|
|
772
|
result = abies.compareToName(abiesMill);
|
|
773
|
assertTrue(result < 0);
|
|
774
|
|
|
775
|
// "Abies Mill." > "Abies"
|
|
776
|
result = abiesMill.compareToName(abies);
|
|
777
|
assertTrue(result > 0);
|
|
778
|
|
|
779
|
// "Abies" < "Abies alba"
|
|
780
|
result = abies.compareToName(abiesAlba);
|
|
781
|
assertTrue(result < 0);
|
|
782
|
|
|
783
|
// "Abies alba" > "Abies"
|
|
784
|
result = abiesAlba.compareToName(abies);
|
|
785
|
assertTrue(result > 0);
|
|
786
|
|
|
787
|
// "Abies Mill." < "Abies alba Michx."
|
|
788
|
result = abiesMill.compareToName(abiesAlbaMichx);
|
|
789
|
assertTrue(result < 0);
|
|
790
|
|
|
791
|
// "Abies alba Michx." > "Abies Mill."
|
|
792
|
result = abiesAlbaMichx.compareToName(abiesMill);
|
|
793
|
assertTrue(result > 0);
|
|
794
|
|
|
795
|
//Autonym should be sorted without the author string
|
|
796
|
|
|
797
|
result = abiesAutonym.compareToName(abiesBalsamea);
|
|
798
|
assertTrue(result < 0);
|
|
799
|
// Test consistency of compareTo() with equals():
|
|
800
|
// Is consistent if and only if for every e1 and e2 of class C
|
|
801
|
// e1.compareTo(e2) == 0 has the same boolean value as e1.equals(e2)
|
|
802
|
|
|
803
|
boolean compareResult = false;
|
|
804
|
boolean equalsResult = false;
|
|
805
|
|
|
806
|
compareResult = (abies.compareToName(abies) == 0);
|
|
807
|
equalsResult = abies.equals(abies);
|
|
808
|
assertEquals(compareResult, equalsResult);
|
|
809
|
|
|
810
|
compareResult = (abies.compareToName(abiesAlba) == 0);
|
|
811
|
equalsResult = abies.equals(abiesAlba);
|
|
812
|
assertEquals(compareResult, equalsResult);
|
|
813
|
|
|
814
|
compareResult = (abiesMill.compareToName(abies) == 0);
|
|
815
|
equalsResult = abiesMill.equals(abies);
|
|
816
|
assertEquals(compareResult, equalsResult);
|
|
817
|
|
|
818
|
//Abies alba x Pinus beta < Abies alba xinus
|
|
819
|
TaxonName abiesAlbaXinus = TaxonNameFactory.NewBotanicalInstance(Rank.SUBSPECIES());
|
|
820
|
abiesAlbaXinus.setGenusOrUninomial("Abies");
|
|
821
|
abiesAlbaXinus.setSpecificEpithet("alba");
|
|
822
|
abiesAlbaXinus.setInfraSpecificEpithet("xinus");
|
|
823
|
result = abiesAlbaxPinusBeta.compareToName(abiesAlbaXinus);
|
|
824
|
assertTrue(result < 0);
|
|
825
|
}
|
|
826
|
|
|
827
|
@Test
|
|
828
|
public void testNomenclaturalStanding() {
|
|
829
|
//The status and relationship combinations in this test are not semantically consistent
|
|
830
|
//but only used for testing
|
|
831
|
Assert.assertTrue(nameBase1.isNoStatus());
|
|
832
|
nameBase1.addRelationshipFromName(nameBase2, NameRelationshipType.CONSERVED_AGAINST());
|
|
833
|
Assert.assertTrue(nameBase1.isDesignationOnly());
|
|
834
|
nameBase1.addStatus(NomenclaturalStatus.NewInstance(NomenclaturalStatusType.AMBIGUOUS()));
|
|
835
|
Assert.assertTrue("nothing changed", nameBase1.isDesignationOnly());
|
|
836
|
Assert.assertTrue(nameBase1.isInvalid());
|
|
837
|
nameBase1.addStatus(NomenclaturalStatus.NewInstance(NomenclaturalStatusType.ILLEGITIMATE()));
|
|
838
|
Assert.assertFalse(nameBase1.isIllegitimate());
|
|
839
|
Assert.assertTrue(nameBase1.isDesignationOnly());
|
|
840
|
nameBase1.addStatus(NomenclaturalStatus.NewInstance(NomenclaturalStatusType.INVALID()));
|
|
841
|
Assert.assertFalse(nameBase1.isDesignationOnly());
|
|
842
|
Assert.assertTrue(nameBase1.isInvalid());
|
|
843
|
nameBase1.addRelationshipToName(nameBase2, NameRelationshipType.CONSERVED_AGAINST());
|
|
844
|
Assert.assertTrue(nameBase1.isValid());
|
|
845
|
}
|
|
846
|
}
|