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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.api.service;
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import static org.junit.Assert.assertFalse;
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import static org.junit.Assert.assertNull;
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import static org.junit.Assert.assertTrue;
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import java.io.FileNotFoundException;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Set;
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import java.util.UUID;
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import org.junit.Assert;
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import org.junit.Before;
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import org.junit.Test;
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import org.unitils.spring.annotation.SpringBeanByType;
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import eu.etaxonomy.cdm.api.service.exception.HomotypicalGroupChangeException;
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import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
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import eu.etaxonomy.cdm.model.name.INonViralName;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.SynonymType;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
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import eu.etaxonomy.cdm.test.integration.CdmIntegrationTest;
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/**
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* This test checks of all the business logic methods do what they are expected to do.
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*
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* @author n.hoffmann
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* @since Dec 16, 2010
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*/
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public class TaxonServiceImplBusinessTest extends CdmIntegrationTest {
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private Synonym s1;
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private Synonym s2;
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private Taxon t2;
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private Taxon t1;
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@SpringBeanByType
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private ITaxonService service;
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@SpringBeanByType
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private INameService nameService;
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private String referenceDetail;
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private Reference reference;
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private SynonymType homoTypicSynonymType;
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private SynonymType heteroTypicSynonymType;
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private INonViralName s1n;
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private INonViralName t2n;
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private INonViralName t1n;
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private TaxonName s2n;
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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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//service = new TaxonServiceImpl();
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//nameService = new NameServiceImpl();
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t1n = TaxonNameFactory.NewNonViralInstance(null);
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t1 = Taxon.NewInstance(t1n, reference);
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t2n = TaxonNameFactory.NewNonViralInstance(null);
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t2 = Taxon.NewInstance(t2n, reference);
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s1n = TaxonNameFactory.NewNonViralInstance(null);
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s1 = Synonym.NewInstance(s1n, reference);
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s2n = TaxonNameFactory.NewNonViralInstance(null);
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s2 = Synonym.NewInstance(s2n, reference);
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// referencing
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homoTypicSynonymType = SynonymType.HOMOTYPIC_SYNONYM_OF();
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heteroTypicSynonymType = SynonymType.HETEROTYPIC_SYNONYM_OF();
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reference = ReferenceFactory.newGeneric();
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referenceDetail = "test";
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}
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/**
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* Test method for {@link eu.etaxonomy.cdm.api.service.TaxonServiceImpl#swapSynonymAndAcceptedTaxon(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.taxon.Taxon)}.
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*/
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@Test
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public final void testSwapSynonymAndAcceptedTaxon() {
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t1.addSynonym(s1, homoTypicSynonymType);
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UpdateResult result = service.swapSynonymAndAcceptedTaxon(s1, t1, true);
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Synonym syn = (Synonym)service.load(s1.getUuid());
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Assert.assertNull(syn);
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TaxonName name = nameService.load(s1n.getUuid());
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Assert.assertNotNull(name);
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//The name of the new accepted taxon should be the same as from the former synonym
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Assert.assertEquals(((Taxon)result.getCdmEntity()).getName(), name);
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}
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/**
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* Test method for {@link eu.etaxonomy.cdm.api.service.TaxonServiceImpl#changeSynonymToAcceptedTaxon(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.taxon.Taxon)}.
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*/
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@Test
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public final void testChangeSynonymToAcceptedTaxon() {
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t1.addSynonym(s1, homoTypicSynonymType);
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HomotypicalGroup oldGroup = s1.getName().getHomotypicalGroup();
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Assert.assertEquals("Homotypical group of new accepted taxon should contain exactly 2 names", 2, oldGroup.getTypifiedNames().size());
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boolean deleteSynonym = false;
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Taxon taxon = null;
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UpdateResult result;
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try {
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result = service.changeSynonymToAcceptedTaxon(s1, t1, deleteSynonym);
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Assert.assertTrue("Change must fail for synonym and taxon in same homotypical group",result.isAbort());
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} catch (HomotypicalGroupChangeException e1) {
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// TODO Auto-generated catch block
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e1.printStackTrace();
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}
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t1.addSynonym(s2, heteroTypicSynonymType);
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Assert.assertEquals("Homotypical group of old accepted taxon should still contain exactly 2 names", 2, oldGroup.getTypifiedNames().size());
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Assert.assertTrue("Old accepted taxon should now have 2 synonyms", t1.getSynonyms().size() == 2);
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try {
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taxon = (Taxon)service.changeSynonymToAcceptedTaxon(s2, t1, deleteSynonym).getCdmEntity();
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} catch (HomotypicalGroupChangeException e) {
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Assert.fail("Change must not throw exception for heterotypic synonym change");
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}
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Assert.assertTrue("Former accepted taxon should still have 1 synonym", t1.getSynonyms().size() == 1);
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Assert.assertNotNull(taxon);
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Assert.assertEquals(s2n, taxon.getName());
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HomotypicalGroup newGroup = taxon.getName().getHomotypicalGroup();
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Assert.assertEquals("Homotypical group of new accepted taxon should contain exactly one name", 1, newGroup.getTypifiedNames().size());
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}
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/**
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* Test method for {@link eu.etaxonomy.cdm.api.service.TaxonServiceImpl#changeSynonymToAcceptedTaxon(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.taxon.Taxon)}.
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*/
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@Test
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public final void testChangeSynonymWithMultipleSynonymsInHomotypicalGroupToAcceptedTaxon() {
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t1.addSynonym(s1, heteroTypicSynonymType);
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TaxonName otherHeteroSynonymName = TaxonNameFactory.NewNonViralInstance(null);
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t1.addHeterotypicSynonymName(otherHeteroSynonymName);
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TaxonName homotypicSynonymName = TaxonNameFactory.NewNonViralInstance(null);
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Synonym homotypicSynonym = Synonym.NewInstance(homotypicSynonymName, t1.getSec());
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t1.addHomotypicSynonym(homotypicSynonym);
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HomotypicalGroup group = s1.getHomotypicGroup();
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Reference citation1 = ReferenceFactory.newBook();
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String microReference1 = "p. 55";
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Synonym s2 = t1.addHeterotypicSynonymName(s2n, citation1, microReference1, group);
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HomotypicalGroup homoGroup2 = s1.getHomotypicGroup();
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Assert.assertEquals("Homotypical group must be the same group as for the old synonym", group, homoGroup2);
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//run
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Taxon newTaxon = null;
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try {
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newTaxon = (Taxon)service.changeSynonymToAcceptedTaxon(s1, t1, false).getCdmEntity();
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} catch (HomotypicalGroupChangeException e1) {
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Assert.fail("Invocation of change method should not throw an exception");
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}
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Assert.assertEquals("Former accepted taxon should now have 2 synonyms left", 2, t1.getSynonyms().size());
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Assert.assertEquals("Former accepted taxon should now have 1 heterotypic synonym group left", 1, t1.getHeterotypicSynonymyGroups().size());
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Assert.assertNotNull(newTaxon);
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Assert.assertEquals(s1n, newTaxon.getName());
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Assert.assertEquals("New accepted taxon should have 1 synonym", 1, newTaxon.getSynonyms().size());
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Assert.assertEquals("The new synonym must be the homotypic synonym of the old synonym", s2, newTaxon.getSynonyms().iterator().next());
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HomotypicalGroup homoGroup = newTaxon.getHomotypicGroup();
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Assert.assertEquals("Homotypical group must be the same group as for the old synonym", group, homoGroup);
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List<Synonym> synonymsInNewTaxonsGroup = newTaxon.getSynonymsInGroup(homoGroup);
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String message = "New accepted taxon should have 1 synonym in its homotypic group: s2. The old synonym may still exist (or not) but not as a synonym of the new taxon";
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Assert.assertEquals(message, 1, synonymsInNewTaxonsGroup.size());
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Assert.assertTrue("The old synonym's homotypic 'partner' must be a synonym of the new accepted taxon, too.", synonymsInNewTaxonsGroup.contains(s2));
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Assert.assertTrue("The old synonym must be in the new accepted taxons homotypic group as it has not been deleted ", newTaxon.getName().getHomotypicalGroup().equals(s2.getName().getHomotypicalGroup()));
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boolean iWasHere = false;
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for (Synonym syn : synonymsInNewTaxonsGroup){
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if (syn.equals(s2) ){
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Assert.assertEquals("s2 relationship needs to have the same citation as the former relation to the given accepted taxon.", citation1, s2.getSec());
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iWasHere = true;
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}
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}
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Assert.assertTrue("Relationship to s2 must have been concidered in 'for'-loop", iWasHere);
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try {
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UpdateResult result = service.changeSynonymToAcceptedTaxon(homotypicSynonym, t1, false);
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Assert.assertTrue("The method should throw an exception when invoked on taxa in the same homotypical group", !result.getExceptions().isEmpty());
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} catch (HomotypicalGroupChangeException e) {
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//OK
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}
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// Assert.assertNull("Synonym should not be used in a name anymore", s1.getName());
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}
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/**
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* Test method for {@link eu.etaxonomy.cdm.api.service.TaxonServiceImpl#changeSynonymToRelatedTaxon(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType, eu.etaxonomy.cdm.model.reference.Reference, java.lang.String)}.
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*/
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@Test
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public final void testChangeSynonymToRelatedTaxon() {
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t1.addSynonym(s1, homoTypicSynonymType);
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t1.addSynonym(s2, homoTypicSynonymType);
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Set<TaxonBase> newInstances = new HashSet<>();
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newInstances.add(s1);
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newInstances.add(t1);
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newInstances.add(t2);
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service.save(newInstances);
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TaxonName synonymName = s1.getName();
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UUID synNameUUID = synonymName.getUuid();
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Taxon newTaxon = (Taxon) service.changeSynonymToRelatedTaxon(s1, t2, TaxonRelationshipType.CONGRUENT_OR_EXCLUDES(), reference, referenceDetail).getCdmEntity();
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//check removeTaxonBase()
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//UUID s1UUID = service.update(s1);
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UUID newTaxonUUID = service.save(newTaxon).getUuid();
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s1 =(Synonym)service.find(s1.getUuid());
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newTaxon = (Taxon)service.find(newTaxonUUID);
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assertNull(s1);
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synonymName = nameService.find(synNameUUID);
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assertFalse(synonymName.getTaxonBases().contains(s1));
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assertTrue(synonymName.getTaxonBases().contains(newTaxon));
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synonymName = s2.getName();
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newTaxon = (Taxon)service.changeSynonymToRelatedTaxon(s2, t1, TaxonRelationshipType.MISAPPLIED_NAME_FOR(), reference, referenceDetail).getCdmEntity();
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//check removeTaxonBase()
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//UUID s1UUID = service.update(s1);
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newTaxonUUID = service.save(newTaxon).getUuid();
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s2 =(Synonym)service.find(s2.getUuid());
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newTaxon = (Taxon)service.find(newTaxonUUID);
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assertNull(s2);
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assertFalse(synonymName.getTaxonBases().contains(s2));
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assertTrue(synonymName.getTaxonBases().contains(newTaxon));
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}
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@Test
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public void changeHomotypicalGroupOfSynonym(){
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//s1 - Heterotypic
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t1.addSynonym(s1, heteroTypicSynonymType);
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//s2 - heterotypic
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TaxonName otherHeteroSynonymName = TaxonNameFactory.NewNonViralInstance(null);
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Synonym s2 = Synonym.NewInstance(otherHeteroSynonymName, t1.getSec());
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t1.addSynonym(s2, heteroTypicSynonymType);
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TaxonName otherHeteroSynonymNameB = TaxonNameFactory.NewNonViralInstance(null);
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otherHeteroSynonymName.addBasionym(otherHeteroSynonymNameB);
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Synonym s2b = Synonym.NewInstance(otherHeteroSynonymNameB, t1.getSec());
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t1.addSynonym(s2b, heteroTypicSynonymType);
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//homotypic
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TaxonName homotypicSynonymName = TaxonNameFactory.NewNonViralInstance(null);
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Synonym homotypicSynonym = Synonym.NewInstance(homotypicSynonymName, t1.getSec());
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t1.addHomotypicSynonym(homotypicSynonym);
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t1.getName().addBasionym(homotypicSynonymName);
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//Preconditions test
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Assert.assertFalse("s2 must not be in s1 homotypic group", s2.getHomotypicGroup().equals(s1.getHomotypicGroup()));
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Assert.assertFalse("s2 must not be in t1 homotypic group", s2.getHomotypicGroup().equals(t1.getHomotypicGroup()));
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Assert.assertNotNull("s2 must have exactly 1 synonym relationship/ must have accepted taxon", s2.getAcceptedTaxon());
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Assert.assertEquals("s2 must have heterotypic relationship type", heteroTypicSynonymType, s2.getType());
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Assert.assertEquals("s2 must have exactly 1 basionym relationships", 1, s2.getName().getBasionyms().size());
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//do it
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service.changeHomotypicalGroupOfSynonym(s2, s1.getHomotypicGroup(), t1, true);
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//postconditions
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Assert.assertEquals("s2 must be in s1 homotypic group", s2.getHomotypicGroup(), s1.getHomotypicGroup());
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Assert.assertNotNull("s2 must have exactly 1 synonym relationship/accepted taxon", s2.getAcceptedTaxon());
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Assert.assertEquals("s2 must have heterotypic relationship", heteroTypicSynonymType, s2.getType());
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Assert.assertEquals("s2 must have exactly 0 basionym relationships", 0, s2.getName().getBasionyms().size());
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//Preconditions test
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Assert.assertEquals("'homotypicSynonym' must have exactly 1 basionym relationships", 1, homotypicSynonym.getName().getNameRelations().size());
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Assert.assertEquals("'t1' must have exactly 1 basionym relationships", 1, t1.getName().getBasionyms().size());
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Assert.assertFalse("s2 must not be in t1 homotypic group", s2.getHomotypicGroup().equals(t1.getHomotypicGroup()));
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//do it
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service.changeHomotypicalGroupOfSynonym(s2, homotypicSynonym.getHomotypicGroup(), null, true);
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//postconditions
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Assert.assertEquals("s2 must be in 'homotypicSynonym' homotypic group", s2.getHomotypicGroup(), homotypicSynonym.getHomotypicGroup());
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Assert.assertEquals("s2 must be in 't1' homotypic group", s2.getHomotypicGroup(), t1.getHomotypicGroup());
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Assert.assertNotNull("s2 must have exactly 1 synonym relationship/accepted taxon", s2.getAcceptedTaxon());
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Assert.assertEquals("s2 must have homotypic relationship", this.homoTypicSynonymType, s2.getType());
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Assert.assertEquals("s2 must have exactly 1 basionym relationships", 1, s2.getName().getBasionyms().size());
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Assert.assertEquals("'homotypicSynonym' must have exactly 2 basionym relationships", 2, homotypicSynonym.getName().getNameRelations().size());
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Assert.assertEquals("'t1' must have exactly 1 basionym relationships", 1, t1.getName().getBasionyms().size());
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Assert.assertEquals("'t1' must have exactly 2 homotypic synonyms", 2, t1.getHomotypicSynonymsByHomotypicSynonymType().size());
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Assert.assertEquals("'t1' must have exactly 2 names in homotypic group", 2, t1.getHomotypicSynonymsByHomotypicGroup(null).size());
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Assert.assertEquals("'t1' homotypic group must include 3 names (t1, s2, homotypicSynonym)", 3, t1.getHomotypicGroup().getTypifiedNames().size());
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//do it
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service.changeHomotypicalGroupOfSynonym(s2, t2.getHomotypicGroup(), t2, false);
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//postconditions
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Assert.assertEquals("s2 must be in 't2' homotypic group", t2.getHomotypicGroup(), s2.getHomotypicGroup());
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Assert.assertFalse("s2 must not be in 't1' homotypic group", s2.getHomotypicGroup().equals(t1.getHomotypicGroup()));
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Assert.assertNotNull("s2 must have exactly 1 synonym relationship/accepted taxon", s2.getAcceptedTaxon());
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Assert.assertEquals("s2 must have homotypic relationship", this.homoTypicSynonymType, s2.getType());
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Assert.assertEquals("s2 must have exactly 0 basionym relationships", 0, s2.getName().getBasionyms().size());
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Assert.assertEquals("'homotypicSynonym' must have exactly 1 basionym relationships", 1, homotypicSynonym.getName().getNameRelations().size());
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Assert.assertEquals("'t1' must have exactly 1 basionym relationships", 1, t1.getName().getBasionyms().size());
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Assert.assertEquals("'t1' must have exactly 1 homotypic synonyms", 1, t1.getHomotypicSynonymsByHomotypicSynonymType().size());
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Assert.assertEquals("'t1' must have exactly 1 names in homotypic group", 1, t1.getHomotypicSynonymsByHomotypicGroup().size());
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Assert.assertEquals("'t1' homotypic group must include 2 names (t1, homotypicSynonym)", 2, t1.getHomotypicGroup().getTypifiedNames().size());
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//do it
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service.changeHomotypicalGroupOfSynonym(s2, s1.getHomotypicGroup(), t1, false);
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//postconditions
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Assert.assertEquals("s2 must be in s1 homotypic group", s2.getHomotypicGroup(), s1.getHomotypicGroup());
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337
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Assert.assertFalse("s2 must not be in 't2' homotypic group", t2.getHomotypicGroup().equals(s2.getHomotypicGroup()));
|
338
|
//had 2 accepted taxa when synonym relationships still existed
|
339
|
Assert.assertNotNull("s2 must have accepted taxon", s2.getAcceptedTaxon());
|
340
|
Assert.assertEquals("Both relationships of s2 must be heterotypic", heteroTypicSynonymType, s2.getType());
|
341
|
Assert.assertEquals("s2 must have exactly 0 basionym relationships", 0, s2.getName().getBasionyms().size());
|
342
|
|
343
|
}
|
344
|
|
345
|
|
346
|
@Override
|
347
|
public void createTestDataSet() throws FileNotFoundException {}
|
348
|
|
349
|
}
|