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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.taxon;
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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.assertTrue;
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import java.util.Set;
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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.BeforeClass;
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import org.junit.Ignore;
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import org.junit.Test;
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import eu.etaxonomy.cdm.model.agent.Person;
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import eu.etaxonomy.cdm.model.common.DefaultTermInitializer;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.name.BotanicalName;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.ZoologicalName;
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//import eu.etaxonomy.cdm.model.reference.Book;
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import eu.etaxonomy.cdm.model.reference.ReferenceBase;
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
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import eu.etaxonomy.cdm.test.unit.EntityTestBase;
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public class TaxonTest extends EntityTestBase {
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private static final Logger logger = Logger.getLogger(TaxonTest.class);
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private ReferenceBase sec;
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private ReferenceBase misSec;
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private ZoologicalName name1;
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private BotanicalName name2;
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private Taxon rootT;
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private Taxon child1;
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private Taxon child2;
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private Synonym syn1;
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private Synonym syn2;
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private BotanicalName name3;
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private BotanicalName name4;
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private Taxon freeT;
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private Taxon misTaxon1;
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private Taxon misTaxon2;
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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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@Before
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public void setUp() throws Exception {
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ReferenceFactory refFactory = ReferenceFactory.newInstance();
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Person linne =new Person("Carl", "Linné", "L.");
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sec= refFactory.newBook();
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sec.setAuthorTeam(linne);
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sec.setTitleCache("Schönes saftiges Allgäu", true);
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misSec = refFactory.newBook();
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misSec.setTitleCache("Stupid book", true);
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name1 = ZoologicalName.NewInstance(Rank.SPECIES(),"Panthera",null,"onca",null,linne,null,"p.1467", null);
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name2 = BotanicalName.NewInstance(Rank.SPECIES(),"Abies",null,"alba",null,linne,null,"p.317", null);
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name3 = BotanicalName.NewInstance(Rank.SUBSPECIES(),"Polygala",null,"vulgaris","alpina",linne,null,"p.191", null);
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name4 = BotanicalName.NewInstance(Rank.SPECIES(),"Cichoria",null,"carminata",null,linne,null,"p.14", null);
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rootT = Taxon.NewInstance(name1,sec);
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freeT = Taxon.NewInstance(name4,sec);
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// taxonomic children
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child1 = Taxon.NewInstance(name2,sec);
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child2 = Taxon.NewInstance(name3,sec);
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rootT.addTaxonomicChild(child1, sec, "p.998");
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rootT.addTaxonomicChild(child2, sec, "p.987");
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// synonymy
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syn1=Synonym.NewInstance(name1,sec);
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syn2=Synonym.NewInstance(name2,sec);
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child1.addSynonym(syn1, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF());
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child2.addSynonym(syn2, SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF());
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//misaplication
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misTaxon1 = Taxon.NewInstance(name4, misSec);
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misTaxon2 = Taxon.NewInstance(name4, misSec);
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rootT.addMisappliedName(misTaxon1, null, "99");
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child1.addMisappliedName(misTaxon2, null, "44");
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}
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@Test
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public void testGenerateTitle() {
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assertTrue(rootT.generateTitle().startsWith(rootT.getName().getTitleCache()));
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}
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@Test
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public void testAddTaxonomicChild() {
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rootT.addTaxonomicChild(freeT, null, null);
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Assert.assertEquals(Integer.valueOf(3), Integer.valueOf(rootT.getTaxonomicChildren().size()));
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}
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@Test
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public void testGetTaxonomicParent() {
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assertEquals(rootT, child2.getTaxonomicParent());
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}
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@Test
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public void testSetTaxonomicParent() {
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child2.setTaxonomicParent(child1, null, null);
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assertEquals(child1, child2.getTaxonomicParent());
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}
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@Test
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public void testGetTaxonomicChildren() {
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Set<Taxon> kids=rootT.getTaxonomicChildren();
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assertTrue(kids.size()==2 && kids.contains(child1) && kids.contains(child2));
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}
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@Test
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public void testHasTaxonomicChildren() {
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assertFalse(child2.hasTaxonomicChildren());
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assertTrue(rootT.hasTaxonomicChildren());
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rootT.removeTaxonomicChild(child1);
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assertTrue(rootT.hasTaxonomicChildren());
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rootT.removeTaxonomicChild(child2);
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assertFalse(rootT.hasTaxonomicChildren());
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}
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@Test
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public void testGetTaxonomicChildrenCount() {
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assertEquals(0, child2.getTaxonomicChildrenCount());
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assertEquals(2, rootT.getTaxonomicChildrenCount());
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rootT.removeTaxonomicChild(child1);
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assertEquals(1, rootT.getTaxonomicChildrenCount());
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rootT.removeTaxonomicChild(child2);
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assertEquals(0, rootT.getTaxonomicChildrenCount());
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}
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@Test
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public void testIsMisappliedName() {
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assertFalse(child2.isMisappliedName());
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assertFalse(rootT.isMisappliedName());
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assertTrue(misTaxon1.isMisappliedName());
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assertTrue(misTaxon2.isMisappliedName());
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}
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@Test
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public void testGetSynonyms() {
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assertTrue(child1.getSynonyms().contains(syn1));
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assertTrue(child2.getSynonyms().contains(syn2));
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assertTrue(rootT.getSynonyms().isEmpty());
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}
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@Test
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public void testGetSynonymNames() {
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assertTrue(child1.getSynonymNames().contains(name1));
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assertTrue(child2.getSynonymNames().contains(name2));
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assertTrue(rootT.getSynonymNames().isEmpty());
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}
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@Test
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public void testAddSynonym() {
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freeT.addSynonym(syn1, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF());
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assertTrue(freeT.getSynonyms().contains(syn1));
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assertTrue(syn1.getAcceptedTaxa().contains(freeT));
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assertFalse(freeT.getSynonyms().contains(syn2));
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}
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@Test
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public void testAddAndRemoveDescriptionTaxonDescription() {
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TaxonDescription desc = TaxonDescription.NewInstance();
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rootT.addDescription(desc); //test if reflection method in addDescription() works
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assertTrue("The description has not properly been added to the taxon", rootT.getDescriptions().contains(desc));
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assertEquals("The taxon has not properly been added to the description", rootT, desc.getTaxon());
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rootT.removeDescription(desc); //test if reflection method in removeDescription() works
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assertFalse("The description has not properly been removed from the taxon", rootT.getDescriptions().contains(desc));
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assertEquals("The taxon has not properly been removed from the description", null, desc.getTaxon());
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}
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/**
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* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#NewInstance(eu.etaxonomy.cdm.model.name.TaxonNameBase, eu.etaxonomy.cdm.model.reference.ReferenceBase)}.
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*/
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@Test
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public void testNewInstance() {
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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.taxon.Taxon#Taxon()}.
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*/
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@Test
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public void testTaxon() {
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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.taxon.Taxon#Taxon(eu.etaxonomy.cdm.model.name.TaxonNameBase, eu.etaxonomy.cdm.model.reference.ReferenceBase)}.
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*/
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@Test
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public void testTaxonTaxonNameBaseReferenceBase() {
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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.taxon.Taxon#getDescriptions()}.
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*/
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@Test
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public void testGetDescriptions() {
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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.taxon.Taxon#setDescriptions(java.util.Set)}.
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*/
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@Test
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public void testSetDescriptions() {
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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.taxon.Taxon#addDescription(eu.etaxonomy.cdm.model.description.TaxonDescription)}.
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*/
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@Test
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public void testAddDescription() {
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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.taxon.Taxon#removeDescription(eu.etaxonomy.cdm.model.description.TaxonDescription)}.
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*/
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@Test
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public void testRemoveDescription() {
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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.taxon.Taxon#getSynonymRelations()}.
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*/
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@Test
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public void testGetSynonymRelations() {
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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.taxon.Taxon#setSynonymRelations(java.util.Set)}.
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*/
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@Test
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public void testSetSynonymRelations() {
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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.taxon.Taxon#addSynonymRelation(eu.etaxonomy.cdm.model.taxon.SynonymRelationship)}.
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*/
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@Test
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public void testAddSynonymRelation() {
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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.taxon.Taxon#removeSynonymRelation(eu.etaxonomy.cdm.model.taxon.SynonymRelationship)}.
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*/
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@Test
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public void testRemoveSynonymRelation() {
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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.taxon.Taxon#getRelationsFromThisTaxon()}.
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*/
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@Test
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public void testGetRelationsFromThisTaxon() {
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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.taxon.Taxon#setRelationsFromThisTaxon(java.util.Set)}.
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*/
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@Test
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public void testSetRelationsFromThisTaxon() {
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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.taxon.Taxon#getRelationsToThisTaxon()}.
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*/
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@Test
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public void testGetRelationsToThisTaxon() {
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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.taxon.Taxon#setRelationsToThisTaxon(java.util.Set)}.
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*/
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@Test
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public void testSetRelationsToThisTaxon() {
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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.taxon.Taxon#getTaxonRelations()}.
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*/
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@Test
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public void testGetTaxonRelations() {
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Taxon taxon = Taxon.NewInstance(null, null);
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taxon.addTaxonRelation(Taxon.NewInstance(null, null), TaxonRelationshipType.CONTRADICTION(), null, null);
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Set<TaxonRelationship> relationships = taxon.getTaxonRelations();
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assertTrue("There should be exactly one relationship", relationships.size() == 1);
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}
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/**
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* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#removeTaxonRelation(eu.etaxonomy.cdm.model.taxon.TaxonRelationship)}.
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*/
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@Test
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public void testRemoveTaxonRelation() {
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Taxon taxon = Taxon.NewInstance(null, null);
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taxon.addTaxonRelation(Taxon.NewInstance(null, null), TaxonRelationshipType.CONTRADICTION(), null, null);
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assertTrue("There should be exactly one taxon relationship", taxon.getTaxonRelations().size() == 1);
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TaxonRelationship relationship = (TaxonRelationship) taxon.getTaxonRelations().toArray()[0];
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assertNotNull("Relationship should not be null", relationship);
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taxon.removeTaxonRelation(relationship);
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assertTrue("There should be no taxon relationships", taxon.getTaxonRelations().size() == 0);
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}
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/**
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* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#addTaxonRelation(eu.etaxonomy.cdm.model.taxon.TaxonRelationship)}.
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*
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* FIXME addTaxonRelation(TaxonRelationship) is not working at the moment
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*/
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//@Ignore
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@Test
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public void testAddTaxonRelationTaxonRelationship() {
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Taxon taxon = Taxon.NewInstance(null, null);
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taxon.addTaxonRelation(Taxon.NewInstance(null, null), TaxonRelationshipType.CONTRADICTION(), null, null);
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assertTrue("There should be exactly one taxon relationship", taxon.getTaxonRelations().size() == 1);
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TaxonRelationship relationship = (TaxonRelationship) taxon.getTaxonRelations().toArray()[0];
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assertNotNull("Relationship should not be null", relationship);
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taxon.removeTaxonRelation(relationship);
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assertTrue("There should be no taxon relationships", taxon.getTaxonRelations().size() == 0);
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taxon.addTaxonRelation(relationship);
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assertEquals("There should be exactly one taxon relationships", 1, taxon.getTaxonRelations().size());
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}
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/**
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349
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* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#addRelationship(eu.etaxonomy.cdm.model.common.RelationshipBase)}.
|
|
350
|
*/
|
|
351
|
@Test
|
|
352
|
public void testAddRelationship() {
|
|
353
|
logger.warn("Not yet implemented");
|
|
354
|
}
|
|
355
|
|
|
356
|
/**
|
|
357
|
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#addTaxonRelation(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType, eu.etaxonomy.cdm.model.reference.ReferenceBase, java.lang.String)}.
|
|
358
|
*/
|
|
359
|
@Test
|
|
360
|
public void testAddTaxonRelationTaxonTaxonRelationshipTypeReferenceBaseString() {
|
|
361
|
logger.warn("Not yet implemented");
|
|
362
|
}
|
|
363
|
|
|
364
|
/**
|
|
365
|
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#addMisappliedName(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.reference.ReferenceBase, java.lang.String)}.
|
|
366
|
*/
|
|
367
|
@Test
|
|
368
|
public void testAddMisappliedName() {
|
|
369
|
logger.warn("Not yet implemented");
|
|
370
|
}
|
|
371
|
|
|
372
|
|
|
373
|
/**
|
|
374
|
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#hasSynonyms()}.
|
|
375
|
*/
|
|
376
|
@Test
|
|
377
|
public void testHasSynonyms() {
|
|
378
|
logger.warn("Not yet implemented");
|
|
379
|
}
|
|
380
|
|
|
381
|
/**
|
|
382
|
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#getMisappliedNames()}.
|
|
383
|
*/
|
|
384
|
@Test
|
|
385
|
public void testGetMisappliedNames() {
|
|
386
|
logger.warn("Not yet implemented");
|
|
387
|
}
|
|
388
|
|
|
389
|
|
|
390
|
/**
|
|
391
|
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#getSynonymsSortedByType()}.
|
|
392
|
*/
|
|
393
|
@Test
|
|
394
|
public void testGetSynonymsSortedByType() {
|
|
395
|
logger.warn("Not yet implemented");
|
|
396
|
}
|
|
397
|
|
|
398
|
/**
|
|
399
|
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#addSynonym(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType)}.
|
|
400
|
*/
|
|
401
|
@Test
|
|
402
|
public void testAddSynonymSynonymSynonymRelationshipType() {
|
|
403
|
logger.warn("Not yet implemented");
|
|
404
|
}
|
|
405
|
|
|
406
|
/**
|
|
407
|
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#addSynonym(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType, eu.etaxonomy.cdm.model.reference.ReferenceBase, java.lang.String)}.
|
|
408
|
*/
|
|
409
|
@Test
|
|
410
|
public void testAddSynonymSynonymSynonymRelationshipTypeReferenceBaseString() {
|
|
411
|
logger.warn("Not yet implemented");
|
|
412
|
}
|
|
413
|
|
|
414
|
/**
|
|
415
|
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#addSynonymName(eu.etaxonomy.cdm.model.name.TaxonNameBase, eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType)}.
|
|
416
|
*/
|
|
417
|
@Test
|
|
418
|
public void testAddSynonymNameTaxonNameBaseSynonymRelationshipType() {
|
|
419
|
logger.warn("Not yet implemented");
|
|
420
|
}
|
|
421
|
|
|
422
|
/**
|
|
423
|
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#addSynonymName(eu.etaxonomy.cdm.model.name.TaxonNameBase, eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType, eu.etaxonomy.cdm.model.reference.ReferenceBase, java.lang.String)}.
|
|
424
|
*/
|
|
425
|
@Test
|
|
426
|
public void testAddSynonymNameTaxonNameBaseSynonymRelationshipTypeReferenceBaseString() {
|
|
427
|
logger.warn("Not yet implemented");
|
|
428
|
}
|
|
429
|
|
|
430
|
/**
|
|
431
|
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#addHeterotypicSynonymName(eu.etaxonomy.cdm.model.name.TaxonNameBase)}.
|
|
432
|
*/
|
|
433
|
@Test
|
|
434
|
public void testAddHeterotypicSynonymNameTaxonNameBase() {
|
|
435
|
logger.warn("Not yet implemented");
|
|
436
|
}
|
|
437
|
|
|
438
|
/**
|
|
439
|
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#addHeterotypicSynonymName(eu.etaxonomy.cdm.model.name.TaxonNameBase, eu.etaxonomy.cdm.model.name.HomotypicalGroup, eu.etaxonomy.cdm.model.reference.ReferenceBase, java.lang.String)}.
|
|
440
|
*/
|
|
441
|
@Test
|
|
442
|
public void testAddHeterotypicSynonymNameTaxonNameBaseHomotypicalGroupReferenceBaseString() {
|
|
443
|
logger.warn("Not yet implemented");
|
|
444
|
}
|
|
445
|
|
|
446
|
/**
|
|
447
|
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#addHomotypicSynonymName(eu.etaxonomy.cdm.model.name.TaxonNameBase, eu.etaxonomy.cdm.model.reference.ReferenceBase, java.lang.String)}.
|
|
448
|
*/
|
|
449
|
@Test
|
|
450
|
public void testAddHomotypicSynonymName() {
|
|
451
|
logger.warn("Not yet implemented");
|
|
452
|
}
|
|
453
|
|
|
454
|
/**
|
|
455
|
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#addHomotypicSynonym(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.reference.ReferenceBase, java.lang.String)}.
|
|
456
|
*/
|
|
457
|
@Test
|
|
458
|
public void testAddHomotypicSynonym() {
|
|
459
|
logger.warn("Not yet implemented");
|
|
460
|
}
|
|
461
|
|
|
462
|
/**
|
|
463
|
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#removeSynonym(eu.etaxonomy.cdm.model.taxon.Synonym)}.
|
|
464
|
*/
|
|
465
|
@Test
|
|
466
|
public void testRemoveSynonym() {
|
|
467
|
logger.warn("Not yet implemented");
|
|
468
|
}
|
|
469
|
|
|
470
|
/**
|
|
471
|
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#iterator()}.
|
|
472
|
*/
|
|
473
|
@Test
|
|
474
|
public void testIterator() {
|
|
475
|
logger.warn("Not yet implemented");
|
|
476
|
}
|
|
477
|
|
|
478
|
/**
|
|
479
|
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#getHomotypicSynonymsByHomotypicGroup()}.
|
|
480
|
*/
|
|
481
|
@Test
|
|
482
|
public void testGetHomotypicSynonymsByHomotypicGroup() {
|
|
483
|
logger.warn("Not yet implemented");
|
|
484
|
}
|
|
485
|
|
|
486
|
/**
|
|
487
|
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#getHomotypicSynonymsByHomotypicRelationship()}.
|
|
488
|
*/
|
|
489
|
@Test
|
|
490
|
public void testGetHomotypicSynonymsByHomotypicRelationship() {
|
|
491
|
logger.warn("Not yet implemented");
|
|
492
|
}
|
|
493
|
|
|
494
|
/**
|
|
495
|
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#getHomotypicSynonymyGroups()}.
|
|
496
|
*/
|
|
497
|
@Test
|
|
498
|
public void testGetHomotypicSynonymyGroups() {
|
|
499
|
logger.warn("Not yet implemented");
|
|
500
|
}
|
|
501
|
|
|
502
|
/**
|
|
503
|
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#getHeterotypicSynonymyGroups()}.
|
|
504
|
*/
|
|
505
|
@Test
|
|
506
|
public void testGetHeterotypicSynonymyGroups() {
|
|
507
|
logger.warn("Not yet implemented");
|
|
508
|
}
|
|
509
|
|
|
510
|
}
|