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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.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.Map;
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import org.apache.log4j.Logger;
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import org.junit.Before;
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import org.junit.BeforeClass;
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import org.junit.Test;
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import eu.etaxonomy.cdm.model.common.DefaultTermInitializer;
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import eu.etaxonomy.cdm.model.common.Language;
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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.cache.name.INameCacheStrategy;
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/**
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* @author a.mueller
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* @created 28.06.2008
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* @version 1.0
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*/
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public class TaxonNameBaseTest {
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private static final Logger logger = Logger.getLogger(TaxonNameBaseTest.class);
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private TaxonNameBaseTestClass nameBase1;
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private TaxonNameBaseTestClass nameBase2;
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@BeforeClass
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public static void setUpBeforeClass() {
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DefaultTermInitializer vocabularyStore = new DefaultTermInitializer();
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vocabularyStore.initialize();
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}
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/**
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* @throws java.lang.Exception
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*/
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@Before
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public void setUp() throws Exception {
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nameBase1 = new TaxonNameBaseTestClass(null,null);
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nameBase2 = new TaxonNameBaseTestClass(Rank.GENUS());
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}
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private class TaxonNameBaseTestClass extends TaxonNameBase<TaxonNameBaseTestClass, INameCacheStrategy<TaxonNameBaseTestClass>>{
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public TaxonNameBaseTestClass(){super();};
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public TaxonNameBaseTestClass(Rank rank){super(rank);};
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public TaxonNameBaseTestClass(HomotypicalGroup hg){super(hg);};
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public TaxonNameBaseTestClass(Rank rank, HomotypicalGroup hg){super(rank, hg);};
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@Override
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public boolean isCodeCompliant(){return false;};
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@Override
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public void setCacheStrategy(INameCacheStrategy strategy){};
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@Override
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public INameCacheStrategy getCacheStrategy(){return null;};
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@Override
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public NomenclaturalCode getNomenclaturalCode(){return null;};
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@Override
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public String generateFullTitle(){return null;}
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@Override
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public String generateTitle() {
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return null;
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}
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@Override
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protected Map<String, java.lang.reflect.Field> getAllFields() {
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return null;
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}
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}
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/** ************************* TESTS ******************************************************/
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@Test
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public void testGenerateFullTitle() {
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//abstract
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}
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/**
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* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#TaxonNameBase()}.
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*/
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@Test
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public void testTaxonNameBase() {
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assertNotNull(nameBase1);
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}
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/**
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* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#TaxonNameBase(eu.etaxonomy.cdm.model.name.Rank)}.
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*/
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@Test
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public void testTaxonNameBaseRank() {
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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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TaxonNameBase testName = new TaxonNameBaseTestClass(rank);
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assertNull(testName.getRank());
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}
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/**
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* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#TaxonNameBase(eu.etaxonomy.cdm.model.name.HomotypicalGroup)}.
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*/
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@Test
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public void testTaxonNameBaseHomotypicalGroup() {
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HomotypicalGroup hg = HomotypicalGroup.NewInstance();
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TaxonNameBase testHG = new TaxonNameBaseTestClass(hg);
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assertSame(hg, testHG.getHomotypicalGroup());
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HomotypicalGroup hgNull = null;
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TaxonNameBase testHGNull = new TaxonNameBaseTestClass(hgNull);
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assertNotNull(testHGNull.getHomotypicalGroup());
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}
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/**
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* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#TaxonNameBase(eu.etaxonomy.cdm.model.name.Rank, eu.etaxonomy.cdm.model.name.HomotypicalGroup)}.
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*/
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@Test
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public void testTaxonNameBaseRankHomotypicalGroup() {
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Rank rank = Rank.SPECIES();
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HomotypicalGroup hg = HomotypicalGroup.NewInstance();
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TaxonNameBase testHG = new TaxonNameBaseTestClass(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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TaxonNameBase testHGNull = new TaxonNameBaseTestClass(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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/**
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* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#isCodeCompliant()}.
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*/
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@Test
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public void testIsCodeCompliant() {
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//is abstract
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}
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/**
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* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#getNameRelations()}.
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*/
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@Test
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public void testGetNameRelations() {
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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.TaxonNameBase#addRelationshipToName(eu.etaxonomy.cdm.model.name.TaxonNameBase, eu.etaxonomy.cdm.model.name.NameRelationshipType, java.lang.String)}.
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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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/**
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* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#addRelationshipFromName(eu.etaxonomy.cdm.model.name.TaxonNameBase, eu.etaxonomy.cdm.model.name.NameRelationshipType, java.lang.String)}.
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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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/**
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* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#addNameRelationship(eu.etaxonomy.cdm.model.name.NameRelationship)}.
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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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/**
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* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#removeNameRelationship(eu.etaxonomy.cdm.model.name.NameRelationship)}.
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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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/**
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* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#addRelationship(eu.etaxonomy.cdm.model.common.RelationshipBase)}.
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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.TaxonNameBase#getRelationsFromThisName()}.
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*/
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@Test
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public void testGetRelationsFromThisName() {
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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.TaxonNameBase#getRelationsToThisName()}.
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*/
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@Test
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public void testGetRelationsToThisName() {
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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.TaxonNameBase#getStatus()}.
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* and for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#addStatus(eu.etaxonomy.cdm.model.name.NomenclaturalStatus)}.
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* and for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#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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/**
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* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#isOriginalCombination()}.
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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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/**
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* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#getBasionym()}.
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*/
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@Test
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public void testGetBasionym() {
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TaxonNameBase name1 = BotanicalName.NewInstance(null);
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TaxonNameBase basionym1 = BotanicalName.NewInstance(null);
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TaxonNameBase basionym2 = BotanicalName.NewInstance(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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TaxonNameBase 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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/**
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* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#addBasionym(eu.etaxonomy.cdm.model.name.TaxonNameBase)}.
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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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/**
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* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#addBasionym(eu.etaxonomy.cdm.model.name.TaxonNameBase, java.lang.String)}.
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*/
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@Test
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public void testAddBasionymTString() {
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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.TaxonNameBase#getCacheStrategy()}.
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*/
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@Test
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public void testGetCacheStrategy() {
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//is abstract
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}
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/**
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* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#setCacheStrategy(eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy)}.
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*/
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@Test
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public void testSetCacheStrategy() {
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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.TaxonNameBase#getRank()}.
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*/
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@Test
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public void testGetRank() {
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TaxonNameBase<?,?> name1 = BotanicalName.NewInstance(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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/**
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* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#getNomenclaturalReference()}.
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*/
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@Test
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public void testGetSetNomenclaturalReference() {
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INomenclaturalReference nr = (INomenclaturalReference) 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 = (INomenclaturalReference) nameBase1.getNomenclaturalReference();
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assertNotNull("Nomenclatural Reference shall not be null", nr);
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}
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/**
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* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#getAppendedPhrase()}.
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*/
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@Test
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public void testGetAppendedPhrase() {
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TaxonNameBase<?,?> name1 = BotanicalName.NewInstance(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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/**
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* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#getNomenclaturalMicroReference()}.
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*/
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@Test
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public void testGetSetNomenclaturalMicroReference() {
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TaxonNameBase<?,?> name1 = BotanicalName.NewInstance(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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/**
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* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#getHasProblem()}.
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*/
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@Test
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public void testGetSetHasProblem() {
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TaxonNameBase<?,?> name1 = BotanicalName.NewInstance(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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/**
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* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#getNameTypeDesignations()}.
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*/
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@Test
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public void testGetNameTypeDesignations() {
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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.TaxonNameBase#setNameTypeDesignations(java.util.Set)}.
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*/
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@Test
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public void testSetNameTypeDesignations() {
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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.TaxonNameBase#addNameTypeDesignation(eu.etaxonomy.cdm.model.name.TaxonNameBase, eu.etaxonomy.cdm.model.reference.Reference, java.lang.String, java.lang.String, boolean, boolean)}.
|
408
|
*/
|
409
|
@Test
|
410
|
public void testAddNameTypeDesignation() {
|
411
|
logger.warn("not yet implemented");
|
412
|
}
|
413
|
|
414
|
/**
|
415
|
* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#removeNameTypeDesignation(eu.etaxonomy.cdm.model.name.NameTypeDesignation)}.
|
416
|
*/
|
417
|
@Test
|
418
|
public void testRemoveNameTypeDesignation() {
|
419
|
logger.warn("not yet implemented");
|
420
|
}
|
421
|
|
422
|
/**
|
423
|
* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#getSpecimenTypeDesignations()}.
|
424
|
*/
|
425
|
@Test
|
426
|
public void testGetSpecimenTypeDesignations() {
|
427
|
logger.warn("not yet implemented");
|
428
|
}
|
429
|
|
430
|
/**
|
431
|
* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#setSpecimenTypeDesignations(java.util.Set)}.
|
432
|
*/
|
433
|
@Test
|
434
|
public void testSetSpecimenTypeDesignations() {
|
435
|
logger.warn("not yet implemented");
|
436
|
}
|
437
|
|
438
|
/**
|
439
|
* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#getSpecimenTypeDesignationsOfHomotypicalGroup()}.
|
440
|
*/
|
441
|
@Test
|
442
|
public void testGetSpecimenTypeDesignationsOfHomotypicalGroup() {
|
443
|
logger.warn("not yet implemented");
|
444
|
}
|
445
|
|
446
|
/**
|
447
|
* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#addSpecimenTypeDesignation(eu.etaxonomy.cdm.model.occurrence.Specimen, eu.etaxonomy.cdm.model.name.TypeDesignationStatus, eu.etaxonomy.cdm.model.reference.Reference, java.lang.String, java.lang.String, boolean)}.
|
448
|
*/
|
449
|
@Test
|
450
|
public void testAddSpecimenTypeDesignationSpecimenTypeDesignationStatusReferenceBaseStringStringBoolean() {
|
451
|
logger.warn("not yet implemented");
|
452
|
}
|
453
|
|
454
|
/**
|
455
|
* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#addSpecimenTypeDesignation(eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation)}.
|
456
|
*/
|
457
|
@Test
|
458
|
public void testAddSpecimenTypeDesignationSpecimenTypeDesignation() {
|
459
|
logger.warn("not yet implemented");
|
460
|
}
|
461
|
|
462
|
/**
|
463
|
* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#removeSpecimenTypeDesignation(eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation)}.
|
464
|
*/
|
465
|
@Test
|
466
|
public void testRemoveSpecimenTypeDesignation() {
|
467
|
logger.warn("not yet implemented");
|
468
|
}
|
469
|
|
470
|
/**
|
471
|
* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#removeTypeDesignation(eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation)}.
|
472
|
*/
|
473
|
@Test
|
474
|
public void testRemoveTypeDesignation() {
|
475
|
logger.warn("not yet implemented");
|
476
|
}
|
477
|
|
478
|
/**
|
479
|
* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#getHomotypicalGroup()}.
|
480
|
*/
|
481
|
@Test
|
482
|
public void testGetHomotypicalGroup() {
|
483
|
logger.warn("not yet implemented");
|
484
|
}
|
485
|
|
486
|
/**
|
487
|
* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#setHomotypicalGroup(eu.etaxonomy.cdm.model.name.HomotypicalGroup)}.
|
488
|
*/
|
489
|
@Test
|
490
|
public void testSetHomotypicalGroup() {
|
491
|
logger.warn("not yet implemented");
|
492
|
}
|
493
|
|
494
|
/**
|
495
|
* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#getCitation()}.
|
496
|
*/
|
497
|
@Test
|
498
|
public void testGetCitation() {
|
499
|
logger.warn("not yet implemented");
|
500
|
}
|
501
|
|
502
|
/**
|
503
|
* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#getCitationString()}.
|
504
|
*/
|
505
|
@Test
|
506
|
public void testGetCitationString() {
|
507
|
logger.warn("not yet implemented");
|
508
|
}
|
509
|
|
510
|
/**
|
511
|
* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#getReferenceYear()}.
|
512
|
*/
|
513
|
@Test
|
514
|
public void testGetReferenceYear() {
|
515
|
logger.warn("not yet implemented");
|
516
|
}
|
517
|
|
518
|
/**
|
519
|
* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#addTaxonBase(eu.etaxonomy.cdm.model.taxon.TaxonBase)}.
|
520
|
*/
|
521
|
@Test
|
522
|
public void testAddTaxonBase() {
|
523
|
Taxon taxon = Taxon.NewInstance(null, null);
|
524
|
nameBase2.addTaxonBase(taxon); //test if reflection method addTaxonBase() works
|
525
|
assertTrue("The taxon has not properly been added to the taxonName", nameBase2.getTaxonBases().contains(taxon));
|
526
|
assertEquals("The taxon name has not properly been added to the taxon", nameBase2, taxon.getName());
|
527
|
nameBase2.removeTaxonBase(taxon); //test if reflection method in removeTaxonBase() works
|
528
|
assertFalse("The taxon has not properly been removed from the taxon name", nameBase2.getTaxonBases().contains(taxon));
|
529
|
assertEquals("The taxon name has not properly been removed from the taxon", null, taxon.getName());
|
530
|
}
|
531
|
|
532
|
|
533
|
@Test
|
534
|
public void testAddAndRemoveDescriptionTaxonNameDescription() {
|
535
|
TaxonNameDescription description = TaxonNameDescription.NewInstance();
|
536
|
nameBase2.addDescription(description); //test if reflection method in addDescription() works
|
537
|
assertTrue("The description has not properly been added to the taxonName", nameBase2.getDescriptions().contains(description));
|
538
|
assertEquals("The taxon name has not properly been added to the description", nameBase2, description.getTaxonName());
|
539
|
nameBase2.removeDescription(description); //test if reflection method in removeDescription() works
|
540
|
assertFalse("The description has not properly been removed from the taxon name", nameBase2.getDescriptions().contains(description));
|
541
|
assertEquals("The taxon name has not properly been removed from the description", null, description.getTaxonName());
|
542
|
}
|
543
|
|
544
|
/**
|
545
|
* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#getTaxa()}.
|
546
|
*/
|
547
|
@Test
|
548
|
public void testGetTaxa() {
|
549
|
logger.warn("not yet implemented");
|
550
|
}
|
551
|
|
552
|
/**
|
553
|
* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#getSynonyms()}.
|
554
|
*/
|
555
|
@Test
|
556
|
public void testGetSynonyms() {
|
557
|
logger.warn("not yet implemented");
|
558
|
}
|
559
|
|
560
|
@Test
|
561
|
public void testMergeHomotypicGroups() {
|
562
|
TaxonNameBase<?,?> name1 = BotanicalName.NewInstance(null);
|
563
|
TaxonNameBase<?,?> name2 = BotanicalName.NewInstance(null);
|
564
|
TaxonNameBase<?,?> name3 = BotanicalName.NewInstance(null);
|
565
|
TaxonNameBase<?,?> name4 = BotanicalName.NewInstance(null);
|
566
|
|
567
|
assertFalse(name1.getHomotypicalGroup().equals(name2.getHomotypicalGroup()));
|
568
|
int numberOfTypifiedNames = name1.getHomotypicalGroup().getTypifiedNames().size();
|
569
|
assertEquals(1, numberOfTypifiedNames);
|
570
|
|
571
|
name1.mergeHomotypicGroups(name2);
|
572
|
assertEquals(name1.getHomotypicalGroup(), name2.getHomotypicalGroup());
|
573
|
assertSame(name1.getHomotypicalGroup(), name2.getHomotypicalGroup());
|
574
|
numberOfTypifiedNames = name1.getHomotypicalGroup().getTypifiedNames().size();
|
575
|
assertEquals(2, numberOfTypifiedNames);
|
576
|
numberOfTypifiedNames = name2.getHomotypicalGroup().getTypifiedNames().size();
|
577
|
assertEquals(2, numberOfTypifiedNames);
|
578
|
assertTrue(name1.getHomotypicalGroup().getTypifiedNames().contains(name2));
|
579
|
assertTrue(name2.getHomotypicalGroup().getTypifiedNames().contains(name1));
|
580
|
|
581
|
name3.mergeHomotypicGroups(name2);
|
582
|
assertEquals(name1.getHomotypicalGroup(), name3.getHomotypicalGroup());
|
583
|
assertSame(name1.getHomotypicalGroup(), name3.getHomotypicalGroup());
|
584
|
numberOfTypifiedNames = name1.getHomotypicalGroup().getTypifiedNames().size();
|
585
|
assertEquals(3, numberOfTypifiedNames);
|
586
|
numberOfTypifiedNames = name2.getHomotypicalGroup().getTypifiedNames().size();
|
587
|
assertEquals(3, numberOfTypifiedNames);
|
588
|
numberOfTypifiedNames = name3.getHomotypicalGroup().getTypifiedNames().size();
|
589
|
assertEquals(3, numberOfTypifiedNames);
|
590
|
assertTrue(name1.getHomotypicalGroup().getTypifiedNames().contains(name2));
|
591
|
assertTrue(name2.getHomotypicalGroup().getTypifiedNames().contains(name1));
|
592
|
assertTrue(name1.getHomotypicalGroup().getTypifiedNames().contains(name3));
|
593
|
assertTrue(name3.getHomotypicalGroup().getTypifiedNames().contains(name1));
|
594
|
assertTrue(name2.getHomotypicalGroup().getTypifiedNames().contains(name3));
|
595
|
assertTrue(name3.getHomotypicalGroup().getTypifiedNames().contains(name2));
|
596
|
|
597
|
|
598
|
}
|
599
|
|
600
|
|
601
|
@Test
|
602
|
public void testIsBasionymFor() {
|
603
|
TaxonNameBase name1 = BotanicalName.NewInstance(null);
|
604
|
TaxonNameBase name2 = BotanicalName.NewInstance(null);
|
605
|
TaxonNameBase<?,?> name3 = BotanicalName.NewInstance(null);
|
606
|
TaxonNameBase<?,?> name4 = BotanicalName.NewInstance(null);
|
607
|
|
608
|
assertFalse(name2.isBasionymFor(name1));
|
609
|
assertFalse(name1.isBasionymFor(name2));
|
610
|
name1.addBasionym(name2);
|
611
|
assertTrue(name2.isBasionymFor(name1));
|
612
|
assertFalse(name1.isBasionymFor(name2));
|
613
|
}
|
614
|
|
615
|
/**
|
616
|
* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#isHomotypic(eu.etaxonomy.cdm.model.name.TaxonNameBase)}.
|
617
|
*/
|
618
|
@Test
|
619
|
public void testIsHomotypic() {
|
620
|
TaxonNameBase<?,?> name1 = BotanicalName.NewInstance(null);
|
621
|
TaxonNameBase<?,?> name2 = BotanicalName.NewInstance(null);
|
622
|
TaxonNameBase<?,?> name3 = BotanicalName.NewInstance(null);
|
623
|
TaxonNameBase<?,?> name4 = BotanicalName.NewInstance(null);
|
624
|
name1.mergeHomotypicGroups(name2);
|
625
|
name2.mergeHomotypicGroups(name4);
|
626
|
|
627
|
assertTrue(name1.isHomotypic(name4));
|
628
|
assertTrue(name4.isHomotypic(name1));
|
629
|
assertFalse(name1.isHomotypic(name3));
|
630
|
assertFalse(name3.isHomotypic(name1));
|
631
|
assertTrue(name2.isHomotypic(name1));
|
632
|
|
633
|
}
|
634
|
|
635
|
@Test
|
636
|
public void testMakeGroupsBasionym(){
|
637
|
TaxonNameBase<?,?> name1 = BotanicalName.NewInstance(null);
|
638
|
TaxonNameBase<?,?> name2 = BotanicalName.NewInstance(null);
|
639
|
TaxonNameBase<?,?> name3 = BotanicalName.NewInstance(null);
|
640
|
TaxonNameBase<?,?> name4 = BotanicalName.NewInstance(null);
|
641
|
|
642
|
name1.mergeHomotypicGroups(name2);
|
643
|
name1.mergeHomotypicGroups(name3);
|
644
|
name2.mergeHomotypicGroups(name4);
|
645
|
|
646
|
name1.makeGroupsBasionym();
|
647
|
|
648
|
assertEquals(1, name2.getBasionyms().size());
|
649
|
assertEquals(1, name3.getBasionyms().size());
|
650
|
assertEquals(1, name4.getBasionyms().size());
|
651
|
assertEquals(name1, name4.getBasionym());
|
652
|
|
653
|
}
|
654
|
|
655
|
@Test
|
656
|
public void testIsGroupsBasionym(){
|
657
|
TaxonNameBase<?,?> name1 = BotanicalName.NewInstance(null);
|
658
|
TaxonNameBase<?,?> name2 = BotanicalName.NewInstance(null);
|
659
|
TaxonNameBase<?,?> name3 = BotanicalName.NewInstance(null);
|
660
|
TaxonNameBase<?,?> name4 = BotanicalName.NewInstance(null);
|
661
|
|
662
|
assertFalse(name1.isGroupsBasionym());
|
663
|
|
664
|
name1.mergeHomotypicGroups(name2);
|
665
|
name2.mergeHomotypicGroups(name4);
|
666
|
|
667
|
name1.makeGroupsBasionym();
|
668
|
|
669
|
assertTrue(name1.isGroupsBasionym());
|
670
|
assertFalse(name2.isGroupsBasionym());
|
671
|
name1.mergeHomotypicGroups(name3);
|
672
|
assertFalse(name1.isGroupsBasionym());
|
673
|
}
|
674
|
|
675
|
|
676
|
|
677
|
@Test
|
678
|
public void testRemoveBasionyms(){
|
679
|
TaxonNameBase name1 = BotanicalName.NewInstance(null);
|
680
|
TaxonNameBase basionym = BotanicalName.NewInstance(null);
|
681
|
TaxonNameBase name3 = BotanicalName.NewInstance(null);
|
682
|
|
683
|
name1.addBasionym(basionym);
|
684
|
assertEquals(1, name1.getBasionyms().size());
|
685
|
name1.addBasionym(name3);
|
686
|
assertEquals(2, name1.getBasionyms().size());
|
687
|
name1.removeBasionyms();
|
688
|
assertEquals(0, name1.getBasionyms().size());
|
689
|
}
|
690
|
|
691
|
/**
|
692
|
* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#isSupraGeneric()}.
|
693
|
*/
|
694
|
@Test
|
695
|
public void testIsSupraGeneric() {
|
696
|
nameBase1.setRank(Rank.FAMILY());
|
697
|
assertTrue(nameBase1.isSupraGeneric());
|
698
|
nameBase1.setRank(Rank.GENUS());
|
699
|
assertFalse(nameBase1.isSupraGeneric());
|
700
|
nameBase1.setRank(Rank.FORM());
|
701
|
assertFalse(nameBase1.isSupraGeneric());
|
702
|
nameBase1.setRank(null);
|
703
|
assertFalse(nameBase1.isSupraGeneric());
|
704
|
}
|
705
|
|
706
|
@Test
|
707
|
public void testRemoveTaxonBases(){
|
708
|
|
709
|
Taxon newTaxon = new Taxon(nameBase1, null);
|
710
|
assertEquals(1, nameBase1.getTaxonBases().size());
|
711
|
|
712
|
|
713
|
nameBase1.removeTaxonBase(newTaxon);
|
714
|
assertEquals(0, nameBase1.getTaxonBases().size());
|
715
|
|
716
|
}
|
717
|
/**
|
718
|
* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#isGenus()}.
|
719
|
*/
|
720
|
@Test
|
721
|
public void testIsGenus() {
|
722
|
nameBase1.setRank(Rank.FAMILY());
|
723
|
assertFalse(nameBase1.isGenus());
|
724
|
nameBase1.setRank(Rank.GENUS());
|
725
|
assertTrue(nameBase1.isGenus());
|
726
|
nameBase1.setRank(Rank.FORM());
|
727
|
assertFalse(nameBase1.isGenus());
|
728
|
nameBase1.setRank(null);
|
729
|
assertFalse(nameBase1.isGenus());
|
730
|
}
|
731
|
|
732
|
/**
|
733
|
* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#isInfraGeneric()}.
|
734
|
*/
|
735
|
@Test
|
736
|
public void testIsInfraGeneric() {
|
737
|
nameBase1.setRank(Rank.FAMILY());
|
738
|
assertFalse(nameBase1.isInfraGeneric());
|
739
|
nameBase1.setRank(Rank.GENUS());
|
740
|
assertFalse(nameBase1.isInfraGeneric());
|
741
|
nameBase1.setRank(Rank.SUBGENUS());
|
742
|
assertTrue(nameBase1.isInfraGeneric());
|
743
|
nameBase1.setRank(Rank.SPECIES());
|
744
|
assertFalse(nameBase1.isInfraGeneric());
|
745
|
nameBase1.setRank(Rank.FORM());
|
746
|
assertFalse(nameBase1.isInfraGeneric());
|
747
|
nameBase1.setRank(Rank.INFRAGENERICTAXON());
|
748
|
assertTrue(nameBase1.isInfraGeneric());
|
749
|
nameBase1.setRank(null);
|
750
|
assertFalse(nameBase1.isInfraGeneric());
|
751
|
}
|
752
|
|
753
|
/**
|
754
|
* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#isSpecies()}.
|
755
|
*/
|
756
|
@Test
|
757
|
public void testIsSpecies() {
|
758
|
nameBase1.setRank(Rank.FAMILY());
|
759
|
assertFalse(nameBase1.isSpecies());
|
760
|
nameBase1.setRank(Rank.GENUS());
|
761
|
assertFalse(nameBase1.isSpecies());
|
762
|
nameBase1.setRank(Rank.SUBGENUS());
|
763
|
assertFalse(nameBase1.isSpecies());
|
764
|
nameBase1.setRank(Rank.SPECIES());
|
765
|
assertTrue(nameBase1.isSpecies());
|
766
|
nameBase1.setRank(Rank.FORM());
|
767
|
assertFalse(nameBase1.isSpecies());
|
768
|
nameBase1.setRank(null);
|
769
|
assertFalse(nameBase1.isSpecies());
|
770
|
}
|
771
|
|
772
|
/**
|
773
|
* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#isInfraSpecific()}.
|
774
|
*/
|
775
|
@Test
|
776
|
public void testIsInfraSpecific() {
|
777
|
nameBase1.setRank(Rank.FAMILY());
|
778
|
assertFalse(nameBase1.isInfraSpecific());
|
779
|
nameBase1.setRank(Rank.GENUS());
|
780
|
assertFalse(nameBase1.isInfraSpecific());
|
781
|
nameBase1.setRank(Rank.SUBGENUS());
|
782
|
assertFalse(nameBase1.isInfraSpecific());
|
783
|
nameBase1.setRank(Rank.SPECIES());
|
784
|
assertFalse(nameBase1.isInfraSpecific());
|
785
|
nameBase1.setRank(Rank.FORM());
|
786
|
assertTrue(nameBase1.isInfraSpecific());
|
787
|
nameBase1.setRank(Rank.INFRASPECIFICTAXON());
|
788
|
assertTrue(nameBase1.isInfraSpecific());
|
789
|
nameBase1.setRank(null);
|
790
|
assertFalse(nameBase1.isInfraSpecific());
|
791
|
}
|
792
|
|
793
|
/**
|
794
|
* Test method for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase#getNomenclaturalCode()}.
|
795
|
*/
|
796
|
@Test
|
797
|
public void testGetNomenclaturalCode() {
|
798
|
//is abstract
|
799
|
}
|
800
|
|
801
|
|
802
|
//descriptions, fullTitleCache, homotypicalGroup,
|
803
|
|
804
|
//no changes to: appendedPharse, nomenclaturalReference,
|
805
|
//nomenclaturalMicroReference, parsingProblem, problemEnds, problemStarts
|
806
|
//protectedFullTitleCache
|
807
|
|
808
|
@Test
|
809
|
public void testClone(){
|
810
|
NonViralName taxonNameBase1 = NonViralName.NewInstance(Rank.SPECIES());
|
811
|
NonViralName<?> genusName = NonViralName.NewInstance(Rank.GENUS());
|
812
|
Taxon taxonBase = Taxon.NewInstance(taxonNameBase1, null);
|
813
|
|
814
|
//basionym & homonym
|
815
|
NonViralName<?> basionym = NonViralName.NewInstance(Rank.SPECIES());
|
816
|
NonViralName<?> earlierHomonym = NonViralName.NewInstance(Rank.SPECIES());
|
817
|
taxonNameBase1.addBasionym(basionym);
|
818
|
taxonNameBase1.addRelationshipToName(earlierHomonym, NameRelationshipType.LATER_HOMONYM(), "later homonym rule");
|
819
|
//status
|
820
|
Reference<?> statusReference = ReferenceFactory.newArticle();
|
821
|
NomenclaturalStatus nomStatus = NomenclaturalStatus.NewInstance(NomenclaturalStatusType.CONSERVED(), statusReference, "55");
|
822
|
taxonNameBase1.addStatus(nomStatus);
|
823
|
//typeDesignation
|
824
|
DerivedUnit typeSpecimen = DerivedUnit.NewPreservedSpecimenInstance();
|
825
|
Reference<?> specimenTypeCitation = ReferenceFactory.newArticle();
|
826
|
Reference<?> nameTypeCitation = ReferenceFactory.newArticle();
|
827
|
SpecimenTypeDesignation specimenTypeDesignationOriginal = taxonNameBase1.addSpecimenTypeDesignation(typeSpecimen, SpecimenTypeDesignationStatus.HOLOTYPE(), specimenTypeCitation, null, null, false, false);
|
828
|
NameTypeDesignation nameTypeDesignationOriginal = genusName.addNameTypeDesignation(taxonNameBase1, nameTypeCitation, null, null, NameTypeDesignationStatus.LECTOTYPE(), true, false, false, false);
|
829
|
|
830
|
//description
|
831
|
TaxonNameDescription description = TaxonNameDescription.NewInstance(taxonNameBase1);
|
832
|
TextData textData = TextData.NewInstance(Feature.IMAGE());
|
833
|
textData.putText(Language.DEFAULT(), "My media text data");
|
834
|
Media media = Media.NewInstance();
|
835
|
textData.addMedia(media);
|
836
|
description.addElement(textData);
|
837
|
|
838
|
//CLONE
|
839
|
TaxonNameBase<?,?> clone = (TaxonNameBase)taxonNameBase1.clone();
|
840
|
TaxonNameBase<?,?> genusClone = (TaxonNameBase)genusName.clone();
|
841
|
assertSame("Rank should be same", taxonNameBase1.getRank(), clone.getRank());
|
842
|
assertTrue("TaxonBases should not be cloned", clone.getTaxonBases().isEmpty());
|
843
|
assertEquals("TaxonBases of original name should not be empty", 1, taxonNameBase1.getTaxonBases().size());
|
844
|
//Homotypical group - CAUTION: behaviour may be changed in future
|
845
|
//TODO still needs to be discussed
|
846
|
// assertSame("The clone must have the same homotypical group as the original", taxonNameBase1.getHomotypicalGroup(), clone.getHomotypicalGroup());
|
847
|
// assertSame("The genusClone must have the same homotypical group as the original genus", genusName.getHomotypicalGroup(), genusClone.getHomotypicalGroup());
|
848
|
|
849
|
//description
|
850
|
assertEquals("There should be exactly 1 name description", 1, clone.getDescriptions().size());
|
851
|
TaxonNameDescription descriptionClone = (TaxonNameDescription)clone.getDescriptions().iterator().next();
|
852
|
assertEquals("There should be exactly 1 description element", 1, descriptionClone.getElements().size());
|
853
|
TextData textDataClone = (TextData)descriptionClone.getElements().iterator().next();
|
854
|
String text = textDataClone.getText(Language.DEFAULT());
|
855
|
assertEquals("Textdata should be equal", "My media text data", text);
|
856
|
assertEquals("There should be exactly 1 media attached", 1, textDataClone.getMedia().size());
|
857
|
Media mediaClone = textDataClone.getMedia().get(0);
|
858
|
assertSame("Media must be the same", media, mediaClone);
|
859
|
|
860
|
//type designation
|
861
|
assertEquals("There should be exactly 1 specimen type designation", 1, clone.getTypeDesignations().size());
|
862
|
assertNotSame("type designation sets should not be the same", taxonNameBase1.getTypeDesignations(), clone.getTypeDesignations());
|
863
|
SpecimenTypeDesignation specimenTypeDesignationClone = (SpecimenTypeDesignation)clone.getTypeDesignations().iterator().next();
|
864
|
assertNotSame("The specimen type designation should not be the same", specimenTypeDesignationOriginal, specimenTypeDesignationClone);
|
865
|
assertSame("The derived unit of the specimen type designation needs to be the same", specimenTypeDesignationOriginal.getTypeSpecimen(), specimenTypeDesignationClone.getTypeSpecimen());
|
866
|
assertSame("The status of the specimen type designation needs to be the same", specimenTypeDesignationOriginal.getTypeStatus(), specimenTypeDesignationClone.getTypeStatus());
|
867
|
assertEquals("The specimen type designation must have exactly 1 typified name which is 'clone'", 1, specimenTypeDesignationClone.getTypifiedNames().size());
|
868
|
assertTrue("The specimen type designation must have 'clone' as typified name", specimenTypeDesignationClone.getTypifiedNames().contains(clone));
|
869
|
// assertSame("The specimen type designation must have the same homotypical group as the typified name", specimenTypeDesignationClone.getHomotypicalGroup(), clone.getHomotypicalGroup());
|
870
|
|
871
|
assertEquals("There should be exactly 1 name type designation", 1, genusClone.getTypeDesignations().size());
|
872
|
assertNotSame("type designation sets should not be the same", genusName.getTypeDesignations(), genusClone.getTypeDesignations());
|
873
|
NameTypeDesignation nameTypeDesignationClone = (NameTypeDesignation)genusClone.getTypeDesignations().iterator().next();
|
874
|
assertNotSame("The name type designation should not be the same", nameTypeDesignationOriginal, nameTypeDesignationClone);
|
875
|
assertSame("The nyme type of the name type designation needs to be the same", taxonNameBase1, nameTypeDesignationClone.getTypeName());
|
876
|
assertSame("The status of the name type designation needs to be the same", nameTypeDesignationOriginal.getTypeStatus(), nameTypeDesignationClone.getTypeStatus());
|
877
|
assertEquals("The name type designation must have exactly 1 typified name which is 'genusClone'", 1, nameTypeDesignationClone.getTypifiedNames().size());
|
878
|
assertTrue("The name type designation must have 'genusClone' as typified name", nameTypeDesignationClone.getTypifiedNames().contains(genusClone));
|
879
|
// assertSame("The name type designation must have the same homotypical group as the typified name", nameTypeDesignationClone.getHomotypicalGroup(), genusClone.getHomotypicalGroup());
|
880
|
|
881
|
//status
|
882
|
assertEquals("There should be exactly 1 status", 1, clone.getStatus().size());
|
883
|
assertNotSame("Status sets should not be the same", taxonNameBase1.getStatus(), clone.getStatus());
|
884
|
NomenclaturalStatus cloneStatus = (NomenclaturalStatus)clone.getStatus().iterator().next();
|
885
|
assertSame("The type of the nomStatus needs to be the same", nomStatus.getType(), cloneStatus.getType());
|
886
|
assertSame("The citation of the nomStatus needs to be the same", nomStatus.getCitation(), cloneStatus.getCitation());
|
887
|
assertSame("The rule considered of the nomStatus needs to be the same", nomStatus.getRuleConsidered(), cloneStatus.getRuleConsidered());
|
888
|
//DISCUSS: do we want to reuse the status
|
889
|
// assertSame("The nomStatus needs to be the same", nomStatus, cloneStatus);
|
890
|
|
891
|
|
892
|
// //hybrid parents of clone
|
893
|
// assertEquals("There should be exactly 2 hybrid relationships in which the clone takes the child role", 2, clone.getChildRelationships().size());
|
894
|
// Set<NonViralName> parentSet = new HashSet<NonViralName>();
|
895
|
// Set<NonViralName> childSet = new HashSet<NonViralName>();
|
896
|
// for (Object object : clone.getChildRelationships()){
|
897
|
// HybridRelationship childRelation = (HybridRelationship)object;
|
898
|
// NonViralName relatedFrom = childRelation.getRelatedFrom();
|
899
|
// parentSet.add(relatedFrom);
|
900
|
// NonViralName relatedTo = childRelation.getRelatedTo();
|
901
|
// childSet.add(relatedTo);
|
902
|
// }
|
903
|
// assertTrue("Parent set should contain parent1", parentSet.contains(parent));
|
904
|
// assertTrue("Parent set should contain parent2", parentSet.contains(parent2));
|
905
|
// assertTrue("Child set should contain clone", childSet.contains(clone));
|
906
|
|
907
|
//basionym of clone
|
908
|
assertEquals("There should be exactly 1 relationship in which the clone takes the to role", 1, clone.getRelationsToThisName().size());
|
909
|
NameRelationship nameRelation = (NameRelationship)clone.getRelationsToThisName().iterator().next();
|
910
|
assertSame("Basionym should be from-object in relationship", basionym, nameRelation.getRelatedFrom());
|
911
|
assertSame("Clone should be to-object in relationship", clone, nameRelation.getRelatedTo());
|
912
|
assertSame("Relationship type should be cloned correctly", NameRelationshipType.BASIONYM(), nameRelation.getType());
|
913
|
// assertEquals("Rule should be cloned correctly", "later homonym rule", nameRelation.getRuleConsidered());
|
914
|
|
915
|
|
916
|
//homonym of clone
|
917
|
assertEquals("There should be exactly 1 relationship in which the clone takes the from role", 1, clone.getRelationsFromThisName().size());
|
918
|
nameRelation = (NameRelationship)clone.getRelationsFromThisName().iterator().next();
|
919
|
assertSame("Clone should be from-object in relationship", clone, nameRelation.getRelatedFrom());
|
920
|
assertSame("Homonym should be to-object in relationship", earlierHomonym, nameRelation.getRelatedTo());
|
921
|
assertSame("Relationship type should be cloned correctly", NameRelationshipType.LATER_HOMONYM(), nameRelation.getType());
|
922
|
assertEquals("Rule should be cloned correctly", "later homonym rule", nameRelation.getRuleConsidered());
|
923
|
}
|
924
|
|
925
|
}
|