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// $Id$
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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.io.excel.stream;
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import static org.junit.Assert.assertEquals;
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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.net.URISyntaxException;
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import java.net.URL;
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import java.util.List;
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import java.util.Set;
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import org.apache.log4j.Logger;
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import org.junit.Before;
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import org.junit.Test;
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import org.unitils.dbunit.annotation.DataSet;
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import org.unitils.spring.annotation.SpringBeanByName;
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import org.unitils.spring.annotation.SpringBeanByType;
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import eu.etaxonomy.cdm.api.service.IClassificationService;
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import eu.etaxonomy.cdm.api.service.IDescriptionService;
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import eu.etaxonomy.cdm.api.service.INameService;
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import eu.etaxonomy.cdm.api.service.ITaxonService;
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import eu.etaxonomy.cdm.api.service.ITermService;
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import eu.etaxonomy.cdm.io.common.CdmApplicationAwareDefaultImport;
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import eu.etaxonomy.cdm.io.common.IImportConfigurator;
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import eu.etaxonomy.cdm.io.common.events.LoggingIoObserver;
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import eu.etaxonomy.cdm.model.common.Annotation;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.IdentifiableSource;
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import eu.etaxonomy.cdm.model.common.LanguageString;
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import eu.etaxonomy.cdm.model.description.CommonTaxonName;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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import eu.etaxonomy.cdm.model.description.Distribution;
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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.name.NomenclaturalCode;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.test.integration.CdmTransactionalIntegrationTest;
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/**
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* @author a.mueller
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* @created 24.05.2013
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*/
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public class ExcelStreamImportTest extends CdmTransactionalIntegrationTest{
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(ExcelStreamImportTest.class);
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@SpringBeanByName
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CdmApplicationAwareDefaultImport defaultImport;
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@SpringBeanByType
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INameService nameService;
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@SpringBeanByType
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ITaxonService taxonService;
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@SpringBeanByType
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ITermService termService;
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@SpringBeanByType
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IClassificationService classificationService;
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@SpringBeanByType
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IDescriptionService descriptionService;
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private IImportConfigurator configurator;
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private IImportConfigurator uuidConfigurator;
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@Before
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public void setUp() throws URISyntaxException {
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//TODO create own test file
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String inputFile = "/eu/etaxonomy/cdm/io/excel/stream/ExcelStreamImport-TestInput.xls";
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URL url = this.getClass().getResource(inputFile);
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assertNotNull("URL for the test file '" + inputFile + "' does not exist", url);
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configurator = ExcelStreamImportConfigurator.NewInstance(url.toURI(), null, NomenclaturalCode.ICNAFP, null);
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assertNotNull("Configurator could not be created", configurator);
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configurator.addObserver(new LoggingIoObserver());
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inputFile = "/eu/etaxonomy/cdm/io/excel/taxa/NormalExplicitImportTest.testUuid-input.xls";
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url = this.getClass().getResource(inputFile);
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assertNotNull("URL for the test file '" + inputFile + "' does not exist", url);
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uuidConfigurator = ExcelStreamImportConfigurator.NewInstance(url.toURI(), null, NomenclaturalCode.ICNAFP, null);
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assertNotNull("Configurator could not be created", configurator);
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}
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@Test
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public void testInit() {
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assertNotNull("normalExplicitImport should not be null", defaultImport);
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assertNotNull("nameService should not be null", nameService);
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}
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@Test
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@DataSet
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public void testDoInvoke() {
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// printDataSet(System.out, new String[]{"ANNOTATION"});
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boolean result = defaultImport.invoke(configurator);
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assertTrue("Return value for import.invoke should be true", result);
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commitAndStartNewTransaction(new String[]{"TAXONNAMEBASE", "ANNOTATION"});
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assertEquals("Number of TaxonNames should be 10", 10 /*TODO */, nameService.count(null));
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List<Classification> treeList = classificationService.list(null, null,null,null,null);
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assertEquals("Number of classifications should be 1", 1, treeList.size());
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Classification tree = treeList.get(0);
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List<TaxonNode> rootNodes = tree.getChildNodes();
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assertEquals("Number of root nodes should be 1", 1, rootNodes.size());
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TaxonNode rootNode = rootNodes.iterator().next();
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// printDataSet(System.out, new String[]{"ANNOTATION"});
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Set<Annotation> annotationSet = rootNode.getTaxon().getAnnotations();
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assertTrue("Annotation is set for first Taxon", !annotationSet.isEmpty());
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assertEquals("Root taxon name should be Metazoa", "Metazoa", rootNode.getTaxon().getName().getTitleCache());
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TaxonNode secondTaxon = rootNode.getChildNodes().iterator().next();
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Set<Annotation> secondAnnotation = secondTaxon.getTaxon().getAnnotations();
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assertTrue("Annotation is empty for second Taxon", secondAnnotation.isEmpty());
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Set<TaxonDescription> taxonSet = secondTaxon.getTaxon().getDescriptions();
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assertTrue("Description is not Empty", !taxonSet.isEmpty());
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assertEquals("Number of Distributions should be 7", 7, descriptionService.listDescriptionElements(null, null, Distribution.class, null, null, null).size());
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// assertEquals("Number of Vernecular Names should be 7", 6, descriptionService.listDescriptionElements(null, null, CommonTaxonName.class, null, null, null).size());
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List<DescriptionElementBase> list = descriptionService.listDescriptionElements(null, null, CommonTaxonName.class, null, null, null);
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for(DescriptionElementBase db : list){
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System.out.println(db.toString());
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}
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//TODO: write test for Refences Sources
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Set<IdentifiableSource> sourcesSet = secondTaxon.getTaxon().getSources();
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assertTrue("Sources are set for second Taxon", !sourcesSet.isEmpty());
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for(IdentifiableSource s : sourcesSet){
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System.out.println("ID: "+ s.getId());
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System.out.println("External ID: " +s.getIdInSource());
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System.out.println("Namespace: " + s.getIdNamespace());
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System.out.println("Reference: " + s.getCitation().toString());
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}
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// assertEquals("Arthropoda node taxon name should be Arthropoda", "Arthropoda", arthropodaNode.getTaxon().getName().getTitleCache());
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// TaxonNode insectaNode = arthropodaNode.getChildNodes().iterator().next();
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// TaxonNode lepidopteraNode = insectaNode.getChildNodes().iterator().next();
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// TaxonNode noctuidaeNode = lepidopteraNode.getChildNodes().iterator().next();
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// TaxonNode noctuaNode = noctuidaeNode.getChildNodes().iterator().next();
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// assertEquals("Number of child nodes of noctuca should be 2", 2, noctuaNode.getChildNodes().size());
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//
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// Iterator<TaxonNode> it = noctuaNode.getChildNodes().iterator();
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// TaxonNode childNode1 = it.next();
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// TaxonNode childNode2 = it.next();
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//
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// TaxonNode noctuaPronubaNode;
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// if (childNode1.getTaxon().getName().getTitleCache().startsWith("Noctua pronuba")){
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// noctuaPronubaNode = childNode1;
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// }else{
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// noctuaPronubaNode = childNode2;
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// }
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//
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// assertEquals("Noctua pronuba taxon name should be ", "Noctua pronuba", noctuaPronubaNode.getTaxon().getName().getTitleCache());
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// Taxon noctuaPronubaTaxon = noctuaPronubaNode.getTaxon();
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// Set<Synonym> synonyms = noctuaPronubaTaxon.getSynonyms();
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// assertEquals("Number of synonyms should be 1", 3 /*TODO*/, synonyms.size());
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// Synonym synonym = synonyms.iterator().next();
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// assertEquals("Synonym name should be ", "Noctua atlantica", (CdmBase.deproxy(synonym.getName(), NonViralName.class )).getNameCache());
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// Set<TaxonDescription> descriptions = noctuaPronubaTaxon.getDescriptions();
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// Assert.assertEquals("Number of descriptions should be 1", 1, descriptions.size());
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// TaxonDescription taxonDescription = descriptions.iterator().next();
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// Set<DescriptionElementBase> elements = taxonDescription.getElements();
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// List<CommonTaxonName> commonNames = new ArrayList<CommonTaxonName>();
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// for (DescriptionElementBase element : elements){
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// if (element.isInstanceOf(CommonTaxonName.class)){
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// commonNames.add((CommonTaxonName)element);
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// }
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// }
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// Assert.assertEquals("Number of common names should be 2", 2, commonNames.size());
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// Set<String> commonNameStrings = new HashSet<String>();
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// commonNameStrings.add(commonNames.get(0).getName());
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// commonNameStrings.add(commonNames.get(1).getName());
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// Assert.assertTrue("Common names must include Yellow Underwing", commonNameStrings.contains("Large Sunshine Underwing"));
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// Assert.assertTrue("Common names must include Yellow Underwing", commonNameStrings.contains("Yellow Underwing"));
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}
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// @Test
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// @DataSet(value="NormalExplicitImportTest.testUuid.xml")
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// public void testUUID() throws URISyntaxException{
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// UUID taxonUuid = UUID.fromString("aafce7fe-0c5f-42ed-814b-4c7c2c715660");
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// UUID synonymUuid = UUID.fromString("fc4a995b-37a9-4984-afe6-e352c6c04d92");
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//
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//
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// //test data set
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// assertEquals("Number of taxon bases should be 2", 2, taxonService.count(null));
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// Taxon taxon = (Taxon)taxonService.find(taxonUuid);
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// assertNotNull("Taxon with given uuid should exist", taxon);
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// assertEquals("Taxon should have no description", 0, taxon.getDescriptions().size());
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// Synonym synonym = (Synonym)taxonService.find(synonymUuid);
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// assertNotNull("Synonym with given uuid should exist", synonym);
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// assertEquals("Synonym should have 1 accepted taxon", 1, synonym.getAcceptedTaxa().size());
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//
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// //import
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// boolean result = defaultImport.invoke(uuidConfigurator);
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// //test result
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// assertTrue("Return value for import.invoke should be true", result);
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// assertEquals("Number of taxon names should be 2", 2, nameService.count(null));
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// assertEquals("Number of taxa should be 2", 2, taxonService.count(null));
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// taxon = (Taxon)taxonService.find(taxonUuid);
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// assertEquals("Taxon should have 1 description", 1, taxon.getDescriptions().size());
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// TaxonDescription description = taxon.getDescriptions().iterator().next();
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// assertEquals("Number of description elements should be 2", 2, description.getElements().size());
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//
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// String expectedText = "Description for the first taxon";
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// TextData textData = getTextElement(description, expectedText);
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// assertNotNull("The element should exists", textData);
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// Feature feature = textData.getFeature();
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// assertEquals("Unexpected feature", Feature.DESCRIPTION(), feature);
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// assertEquals("There should be exactly 1 language", 1,textData.getMultilanguageText().size());
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// Language language = textData.getMultilanguageText().keySet().iterator().next();
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// assertEquals("Language should be German", Language.GERMAN(), language);
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// String text = textData.getText(language);
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// assertEquals("Unexpected description text", expectedText, text);
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// assertEquals("Number of source elements should be 1", 1, textData.getSources().size());
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// DescriptionElementSource source = textData.getSources().iterator().next();
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// Reference ref = source.getCitation();
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// assertNotNull("Citation should not be null", ref);
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// assertNotNull("Authorship should not be null", ref.getAuthorship());
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// assertEquals("Source author should be 'Meyer et. al.'", "Meyer et. al.",ref.getAuthorTeam().getTitleCache());
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// assertEquals("Publication title should be 'My first book'", "My first book", ref.getTitle());
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// assertEquals("Publication year should be '1987'", "1987", ref.getYear());
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// TaxonNameBase nameUsedInSource = source.getNameUsedInSource();
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// assertNotNull("Name used in source should not be null", nameUsedInSource);
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// assertEquals("Name used in source title should be ", "Abies", nameUsedInSource.getTitleCache());
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//
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//
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// //synonym
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// expectedText = "A synonym description";
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// textData = getTextElement(description, expectedText);
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// assertNotNull("The element should exists", textData);
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// feature = textData.getFeature();
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// assertEquals("Unexpected feature", Feature.DESCRIPTION(), feature);
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// assertEquals("There should be exactly 1 language", 1,textData.getMultilanguageText().size());
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// language = textData.getMultilanguageText().keySet().iterator().next();
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// assertEquals("Language should be Spanish", Language.SPANISH_CASTILIAN(), language);
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// text = textData.getText(language);
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// assertEquals("Unexpected description text", expectedText, text);
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// assertEquals("Number of source elements should be 1", 1, textData.getSources().size());
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// source = textData.getSources().iterator().next();
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// ref = source.getCitation();
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// assertNotNull("Citation should not be null", ref);
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// assertNotNull("Authorship should not be null", ref.getAuthorship());
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// assertEquals("Source author should be 'Theys, A.'", "Theys, A.",ref.getAuthorTeam().getTitleCache());
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// assertEquals("Publication title should be 'The ultimate book'", "The ultimate book", ref.getTitle());
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// assertEquals("Publication year should be '2011'", "2011", ref.getYear());
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// nameUsedInSource = source.getNameUsedInSource();
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// assertNotNull("Name used in source should not be null", nameUsedInSource);
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// assertEquals("Name used in source title should be Pinus", "Pinus", nameUsedInSource.getTitleCache());
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//
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// }
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/**
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* Returns description element for record id 1
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* @param description
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* @return
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*/
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private TextData getTextElement(TaxonDescription description, String descriptionText) {
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for (DescriptionElementBase element : description.getElements()){
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if (element.isInstanceOf(TextData.class)){
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TextData textData = CdmBase.deproxy(element, TextData.class);
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for (LanguageString ls :textData.getMultilanguageText().values()){
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if (ls.getText().equals(descriptionText)){
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return textData;
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}
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}
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}
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}
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return null;
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}
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}
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