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/**
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* Copyright (C) 2015 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.taxeditor.operation;
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import java.util.ArrayList;
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import java.util.Iterator;
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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.apache.logging.log4j.LogManager;
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import org.apache.logging.log4j.Logger;
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import org.eclipse.core.commands.ExecutionException;
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import org.junit.Assert;
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import org.junit.Ignore;
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import org.junit.Test;
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import org.unitils.dbunit.annotation.DataSet;
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import eu.etaxonomy.cdm.api.service.ITaxonNodeService;
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import eu.etaxonomy.cdm.api.service.ITaxonService;
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import eu.etaxonomy.cdm.api.service.UpdateResult;
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import eu.etaxonomy.cdm.model.common.Annotation;
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import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.description.TextData;
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import eu.etaxonomy.cdm.model.metadata.SecReferenceHandlingSwapEnum;
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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.NameTypeDesignation;
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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.OriginalSourceType;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.taxeditor.editor.name.operation.CreateSynonymInExistingHomotypicalGroupOperation;
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import eu.etaxonomy.taxeditor.store.CdmStore;
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/**
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* @author cmathew
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* @date 3 Feb 2015
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*/
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@DataSet
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public class TaxonEditorTest extends BaseOperationTest {
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@SuppressWarnings("unused")
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private static final Logger logger = LogManager.getLogger();
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private ITaxonNodeService taxonNodeService = getRemoteApplicationController().getTaxonNodeService();
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private ITaxonService taxonService = getRemoteApplicationController().getTaxonService();
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@Test
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public void testAddHomotypicSynonym() throws ExecutionException {
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UUID taxonNodeUuid = UUID.fromString("ce54c396-3694-47f2-abb0-1d7b7e057985");
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TaxonNode taxonNode = taxonNodeService.load(taxonNodeUuid);
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Taxon taxon = taxonNode.getTaxon();
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HomotypicalGroup group = taxon.getHomotypicGroup();
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TaxonName newSynonymName = TaxonNameFactory.NewBotanicalInstance(null);
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newSynonymName.setTitleCache("New Synonym", true);
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operation = new CreateSynonymInExistingHomotypicalGroupOperation("Create Synonym In Existing Homotypical Group",
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undoContext, taxon, group, newSynonymName, postOperation);
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operation.execute(monitor, info);
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taxonNodeService.merge(taxonNode);
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Assert.assertEquals(taxon.getHomotypicGroup().getTypifiedNames().size(), 2);
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Assert.assertEquals(taxon.getSynonyms().size(), 1);
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Iterator<Synonym> synonymItr = taxon.getSynonyms().iterator();
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Synonym synonym = synonymItr.next();
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Assert.assertTrue(taxon.getHomotypicGroup().getTypifiedNames().contains(synonym.getName()));
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}
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@Test
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public void addHeterotypicSynonym() throws ExecutionException {
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UUID taxonNodeUuid = UUID.fromString("ce54c396-3694-47f2-abb0-1d7b7e057985");
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TaxonNode taxonNode = taxonNodeService.load(taxonNodeUuid);
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Taxon taxon = taxonNode.getTaxon();
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HomotypicalGroup group = taxon.getHomotypicGroup();
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TaxonName newSynonymName = TaxonNameFactory.NewBotanicalInstance(null);
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newSynonymName.setTitleCache("New Synonym", true);
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operation = new CreateSynonymInExistingHomotypicalGroupOperation("Create Synonym In Existing Homotypical Group",
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undoContext, taxon, group, newSynonymName, postOperation);
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operation.execute(monitor, info);
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taxonNodeService.merge(taxonNode);
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}
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@Test
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public void addDeleteAddHomotypicSynonym() throws ExecutionException {
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UUID taxonNodeUuid = UUID.fromString("ce54c396-3694-47f2-abb0-1d7b7e057985");
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TaxonNode taxonNode = taxonNodeService.load(taxonNodeUuid);
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Taxon taxon = taxonNode.getTaxon();
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HomotypicalGroup group = taxon.getHomotypicGroup();
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TaxonName newSynonymName = TaxonNameFactory.NewBotanicalInstance(null);
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newSynonymName.setTitleCache("New Synonym", true);
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operation = new CreateSynonymInExistingHomotypicalGroupOperation("Create Synonym In Existing Homotypical Group",
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undoContext, taxon, group, newSynonymName, postOperation);
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operation.execute(monitor, info);
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taxonNodeService.merge(taxonNode);
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Assert.assertEquals(taxon.getHomotypicGroup().getTypifiedNames().size(), 2);
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Set<Synonym> synonyms = taxon.getSynonyms();
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for(Synonym synonym : synonyms) {
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taxonService.deleteSynonym(synonym.getUuid(), null);
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}
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taxonNodeService.merge(taxonNode, true);
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newSynonymName = TaxonNameFactory.NewBotanicalInstance(null);
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newSynonymName.setTitleCache("Another New Synonym", true);
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operation = new CreateSynonymInExistingHomotypicalGroupOperation("Create Synonym In Existing Homotypical Group",
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undoContext, taxon, group, newSynonymName, postOperation);
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operation.execute(monitor, info);
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taxonNodeService.merge(taxonNode, true);
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}
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@Test
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public void addDeleteAddHomotypicSynonymWithAnnotations() throws ExecutionException {
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UUID taxonNodeUuid = UUID.fromString("ce54c396-3694-47f2-abb0-1d7b7e057985");
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TaxonNode taxonNode = taxonNodeService.load(taxonNodeUuid);
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Taxon taxon = taxonNode.getTaxon();
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HomotypicalGroup group = taxon.getHomotypicGroup();
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TaxonName newSynonymName = TaxonNameFactory.NewBotanicalInstance(null);
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newSynonymName.setTitleCache("New Synonym", true);
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operation = new CreateSynonymInExistingHomotypicalGroupOperation("Create Synonym In Existing Homotypical Group",
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undoContext, taxon, group, newSynonymName, postOperation);
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operation.execute(monitor, info);
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taxonNodeService.merge(taxonNode);
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boolean includeUnpublished = true;
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Synonym syn = taxonService.findBestMatchingSynonym("New Synonym", includeUnpublished);
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if (syn != null){
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syn.addAnnotation(Annotation.NewDefaultLanguageInstance("TEst"));
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taxonService.merge(syn);
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}
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Assert.assertEquals(taxon.getHomotypicGroup().getTypifiedNames().size(), 2);
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Set<Synonym> synonyms = taxon.getSynonyms();
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for(Synonym synonym : synonyms) {
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Assert.assertEquals(syn.getUuid(), synonym.getUuid());
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taxonService.deleteSynonym(synonym.getUuid(), null);
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}
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taxonNodeService.merge(taxonNode);
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newSynonymName = TaxonNameFactory.NewBotanicalInstance(null);
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newSynonymName.setTitleCache("Another New Synonym", true);
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operation = new CreateSynonymInExistingHomotypicalGroupOperation("Create Synonym In Existing Homotypical Group",
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undoContext, taxon, group, newSynonymName, postOperation);
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operation.execute(monitor, info);
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taxonNodeService.merge(taxonNode);
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}
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@Test
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@Ignore
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public void swapSynonymWithAcceptedTaxon() {
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List<TaxonNode> rootEntities = new ArrayList<TaxonNode>();
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UUID taxonNodeUuid = UUID.fromString("d425a971-1abe-4895-9e1f-1e5c8ff1c84c");
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TaxonNode taxonNode = taxonNodeService.load(taxonNodeUuid);
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rootEntities.add(taxonNode);
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UUID taxonUuid = UUID.fromString("9763e5f0-6cd4-4d96-b8a4-4420854f7727");
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Taxon taxon = (Taxon)taxonService.load(taxonUuid);
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TaxonName taxonName = taxon.getName();
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UUID synonymUuid = UUID.fromString("1eb173bd-b174-4162-8ff5-5136d8f1e746");
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Synonym synonym = (Synonym)taxonService.load(synonymUuid);
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TaxonName synonymName = synonym.getName();
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UpdateResult result = taxonService.swapSynonymAndAcceptedTaxon(synonym.getUuid(), taxon.getUuid(), false, false, SecReferenceHandlingSwapEnum.KeepOrWarn, null, null);
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taxon = (Taxon)result.getCdmEntity();
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Set<TaxonName> synNames = taxon.getSynonymNames();
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Iterator<TaxonName> iterator = synNames.iterator();
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if(iterator.hasNext()){
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Assert.assertEquals(taxonName, iterator.next());
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}else{
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Assert.fail();
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}
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Assert.assertEquals(synonymName, taxon.getName());
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}
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@Test
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public void addTaxon() {
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INonViralName taxonName = TaxonNameFactory.NewNonViralInstance(null);
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Taxon taxon = Taxon.NewInstance(taxonName, null);
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taxon = (Taxon)taxonService.merge(taxon);
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taxon.getName().addTypeDesignation(NameTypeDesignation.NewInstance(), true);
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}
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@Ignore
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@Test
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public void addDescription() {
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UUID taxonNodeUuid = UUID.fromString("ce54c396-3694-47f2-abb0-1d7b7e057985");
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TaxonNode taxonNode = taxonNodeService.load(taxonNodeUuid);
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Taxon taxon = taxonNode.getTaxon();
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TaxonDescription description = TaxonDescription.NewInstance(taxon);
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TextData textData = TextData.NewInstance();
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textData.setFeature(Feature.ECOLOGY());
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description.addElement(textData);
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DescriptionElementSource descriptionElementSource = DescriptionElementSource.NewInstance(OriginalSourceType.PrimaryTaxonomicSource);
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textData.addSource(descriptionElementSource);
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CdmStore.getService(ITaxonNodeService.class).merge(taxonNode);
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description.getId();
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}
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@Test
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public void addTaxonNodeCascadeProblem() {
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UUID taxonNodeUuid = UUID.fromString("ce54c396-3694-47f2-abb0-1d7b7e057985");
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TaxonNode taxonNode = taxonNodeService.load(taxonNodeUuid);
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Taxon childTaxon = Taxon.NewInstance(null, null);
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TaxonNode childTaxonNode = taxonNode.addChildTaxon(childTaxon, null, null);
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CdmStore.getService(ITaxonNodeService.class).merge(childTaxonNode, true);
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Taxon grandChildTaxon = Taxon.NewInstance(null, null);
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TaxonNode grandChildTaxonNode = childTaxonNode.addChildTaxon(grandChildTaxon, null, null);
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CdmStore.getService(ITaxonNodeService.class).merge(grandChildTaxonNode, true);
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Assert.assertEquals(taxonNode.getChildNodes().get(0).getId(), childTaxonNode.getId());
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Assert.assertTrue(childTaxonNode.treeIndex() != null);
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Assert.assertEquals(taxonNode.getChildNodes().get(0).treeIndex(), childTaxonNode.treeIndex());
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Assert.assertFalse(childTaxon.getId() == 0);
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Assert.assertEquals(taxonNode.getChildNodes().get(0).getTaxon().getId(), childTaxon.getId());
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Assert.assertTrue(grandChildTaxonNode.treeIndex() != null);
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Assert.assertEquals(taxonNode.getChildNodes().get(0).getChildNodes().get(0).getId(), grandChildTaxonNode.getId());
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Assert.assertFalse(grandChildTaxon.getId() == 0);
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Assert.assertEquals(taxonNode.getChildNodes().get(0).getChildNodes().get(0).getTaxon().getId(), grandChildTaxon.getId());
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}
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}
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