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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.taxa;
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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.io.FileNotFoundException;
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import java.net.URISyntaxException;
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import java.net.URL;
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import java.util.ArrayList;
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import java.util.HashSet;
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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.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.Test;
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import org.unitils.dbunit.annotation.DataSet;
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import org.unitils.dbunit.annotation.DataSets;
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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.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.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.Language;
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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.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.name.NomenclaturalCode;
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import eu.etaxonomy.cdm.model.name.NonViralName;
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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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.cdm.test.integration.CdmTransactionalIntegrationTest;
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import eu.etaxonomy.cdm.test.unitils.CleanSweepInsertLoadStrategy;
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/**
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* @author a.mueller
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* @created 26.08.2009
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*/
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public class NormalExplicitImportTest extends CdmTransactionalIntegrationTest{
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(NormalExplicitImportTest.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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private IImportConfigurator configurator;
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private IImportConfigurator uuidConfigurator;
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private IImportConfigurator configuratorXslx;
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@Before
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public void setUp() throws URISyntaxException {
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String inputFile = "/eu/etaxonomy/cdm/io/excel/taxa/NormalExplicitImportTest-input.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 = NormalExplicitImportConfigurator.NewInstance(url.toURI(), null, NomenclaturalCode.ICNAFP, null);
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assertNotNull("Configurator could not be created", configurator);
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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 = NormalExplicitImportConfigurator.NewInstance(url.toURI(), null, NomenclaturalCode.ICNAFP, null);
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assertNotNull("Configurator could be created", configurator);
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String inputFileXslx = "/eu/etaxonomy/cdm/io/excel/taxa/NormalExplicitImportTest-input.xlsx";
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url = this.getClass().getResource(inputFileXslx);
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assertNotNull("URL for the test file '" + inputFileXslx + "' does not exist", url);
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configuratorXslx = NormalExplicitImportConfigurator.NewInstance(url.toURI(), null, NomenclaturalCode.ICNAFP, null);
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assertNotNull("Configurator could not be created", configuratorXslx);
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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);
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boolean result = defaultImport.invoke(configurator).isSuccess();
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assertTrue("Return value for import.invoke should be true", result);
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assertEquals("Number of TaxonNames should be 9", 9, 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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assertEquals("Root taxon name should be Animalia", "Animalia", rootNode.getTaxon().getName().getTitleCache());
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TaxonNode arthropodaNode = rootNode.getChildNodes().iterator().next();
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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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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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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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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", 1, synonyms.size());
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Synonym synonym = synonyms.iterator().next();
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assertEquals("Synonym name should be ", "Noctua atlantica", ((NonViralName<?>)synonym.getName()).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
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public void testDoInvokeXslx() {
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//printDataSet(System.out);
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boolean result = defaultImport.invoke(configuratorXslx).isSuccess();
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assertTrue("Return value for import.invoke should be true", result);
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assertEquals("Number of TaxonNames should be 9", 9, 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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assertEquals("Root taxon name should be Animalia", "Animalia", rootNode.getTaxon().getName().getTitleCache());
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TaxonNode arthropodaNode = rootNode.getChildNodes().iterator().next();
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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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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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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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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", 1, synonyms.size());
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Synonym synonym = synonyms.iterator().next();
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assertEquals("Synonym name should be ", "Noctua atlantica", ((NonViralName<?>)synonym.getName()).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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@DataSets({
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@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="/eu/etaxonomy/cdm/io/ClearDB_with_Terms_DataSet.xml"),
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@DataSet(value="/eu/etaxonomy/cdm/io/TermsDataSet-with_auditing_info.xml"),
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@DataSet(value="NormalExplicitImportTest.testUuid.xml"),
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})
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public void testUUID(){
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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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//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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//import
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boolean result = defaultImport.invoke(uuidConfigurator).isSuccess();
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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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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.getAuthorship().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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//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.getAuthorship().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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* 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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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.test.integration.CdmIntegrationTest#createTestData()
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*/
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@Override
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public void createTestDataSet() throws FileNotFoundException {
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// TODO Auto-generated method stub
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}
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}
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