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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.model.taxon;
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import java.util.ArrayList;
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import java.util.Calendar;
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import java.util.Collections;
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import java.util.List;
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import org.apache.log4j.Logger;
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import org.junit.Assert;
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import org.junit.BeforeClass;
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import org.junit.Test;
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import eu.etaxonomy.cdm.model.agent.Person;
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import eu.etaxonomy.cdm.model.common.DefaultTermInitializer;
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import eu.etaxonomy.cdm.model.common.VerbatimTimePeriod;
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import eu.etaxonomy.cdm.model.name.IBotanicalName;
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import eu.etaxonomy.cdm.model.name.IZoologicalName;
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import eu.etaxonomy.cdm.model.name.Rank;
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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.Book;
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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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/**
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* @author a.mueller
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* @since 11.06.2008
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*/
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public class TaxonComparatorTest {
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private static final Logger logger = Logger.getLogger(TaxonComparatorTest.class);
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@BeforeClass
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public static void setUpBeforeClass() {
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DefaultTermInitializer vocabularyStore = new DefaultTermInitializer();
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vocabularyStore.initialize();
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}
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/******************** TESTS *****************************************************/
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/**
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* Test method for {@link eu.etaxonomy.cdm.model.taxon.TaxonComparator#compare(eu.etaxonomy.cdm.model.taxon.TaxonBase, eu.etaxonomy.cdm.model.taxon.TaxonBase)}.
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*/
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@Test
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public void testCompare() {
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List<TaxonBase<?>> list = createTestData();
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Collections.sort(list, new TaxonComparator());
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//Order should be
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// 4: 1823
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// 3: 1943
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// 1: 1945
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// 2:
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Assert.assertEquals(list.get(0).getId(), 3);
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Assert.assertEquals(getYear(list.get(0)), "1759");
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Assert.assertEquals(list.get(1).getId(), 1);
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Assert.assertEquals(getYear(list.get(1)), "1759");
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Assert.assertEquals(list.get(2).getId(), 5);
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Assert.assertEquals(getYear(list.get(2)), "1823");
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Assert.assertEquals(list.get(3).getId(), 4);
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Assert.assertEquals(getYear(list.get(3)), "1943");
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Assert.assertEquals(list.get(4).getId(), 2);
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Assert.assertEquals(getYear(list.get(4)), "");
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}
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/**
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* @return
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*/
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private List<TaxonBase<?>> createTestData() {
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Reference sec = ReferenceFactory.newBook();
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Reference ref1 = ReferenceFactory.newArticle();
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ref1.setAbbrevTitle("Gard. Dict. ed. 7 110, 2 1759");
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Reference ref2 = ReferenceFactory.newBook();
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Reference ref3 = ReferenceFactory.newBook();
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Calendar cal1 = Calendar.getInstance();
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Calendar cal2 = Calendar.getInstance();
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Calendar cal3 = Calendar.getInstance();
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cal1.set(1759, 3, 2);
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cal2.set(1856, 3, 2);
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cal3.set(1943, 3, 2);
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ref1.setDatePublished(VerbatimTimePeriod.NewVerbatimInstance(cal1));
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// ref2.setDatePublished(TimePeriod.NewInstance(cal2));
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ref3.setDatePublished(VerbatimTimePeriod.NewVerbatimInstance(cal3));
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Person author1 = Person.NewTitledInstance("Rehder");
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author1.setNomenclaturalTitle("Rehder");
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Person author4 = Person.NewTitledInstance("Mill.");
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author1.setNomenclaturalTitle("Mill.");
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Person author2 = Person.NewTitledInstance("A.Murray");
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author2.setNomenclaturalTitle("A.Murray");
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Person author3 = Person.NewTitledInstance("Lemmon");
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author3.setNomenclaturalTitle("Lemmon");
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IBotanicalName botName1 = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES(),
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"Abies", null, "procera",null,
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author1, ref1, null, null);
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IBotanicalName botName2 = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES(),
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"Abies", null, "magnifica", null,
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author2, ref2, null, null);
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IBotanicalName botName3 = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS(),
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"Abies", null, null,null,
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author4, ref1, null, null);
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IBotanicalName botName4 = TaxonNameFactory.NewBotanicalInstance(Rank.VARIETY(),
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"Abies", null, "magnifica","shastensis",
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author3, ref3, null, null);
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IZoologicalName zooName1 = TaxonNameFactory.NewZoologicalInstance(null);
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// botName3.setNomenclaturalReference(ref3);
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zooName1.setPublicationYear(1823);
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List<TaxonBase<?>> list = new ArrayList<TaxonBase<?>>();
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Taxon taxon1 = Taxon.NewInstance(botName1, sec);
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Taxon taxon2 = Taxon.NewInstance(botName2, sec);
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Taxon taxon3 = Taxon.NewInstance(botName3, sec);
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Taxon taxon4 = Taxon.NewInstance(botName4, sec);
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Taxon zooTaxon4 = Taxon.NewInstance(zooName1, sec);
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taxon1.setId(1);
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taxon2.setId(2);
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taxon3.setId(3);
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taxon4.setId(4);
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zooTaxon4.setId(5);
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list.add(taxon3);
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list.add(taxon2);
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list.add(taxon1);
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list.add(taxon4);
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list.add(zooTaxon4);
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return list;
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}
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private List<TaxonNode> createTestDataWithTaxonNodes(){
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List<TaxonBase<?>> taxa = createTestData();
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List<TaxonNode> result = new ArrayList();
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TaxonNode node;
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Classification classification = Classification.NewInstance("TestClassification");
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int index = 0;
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for (TaxonBase<?> taxon: taxa){
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if (taxon instanceof Taxon){
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node = classification.addChildTaxon((Taxon)taxon, null, null);
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node.setId(++index);
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result.add(node);
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}
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}
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return result;
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}
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/**
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* @param taxonBase
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* @return
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*/
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private String getYear(TaxonBase<?> taxon) {
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String year = "";
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TaxonName tnb = taxon.getName();
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if (tnb.isZoological()){
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year = String.valueOf(tnb.getPublicationYear());
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}else{
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year = tnb.getNomenclaturalReference().getYear();
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}
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return year;
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}
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@Test
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public void testCompareTaxonNodeByName(){
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List<TaxonNode> list = createTestDataWithTaxonNodes();
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Collections.sort(list, new TaxonNodeByNameComparator());
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for(TaxonNode node: list){
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System.out.println(node.getTaxon().getName().getFullTitleCache());
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}
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//Order should be
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// 5: without rank
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// 1: Genus
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// 2: Species (Abies magnifica A.Murray)
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// 4: subSpecies (Abies magnifica var. shastensis Lemmon)
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// 3: Species (Abies procera Rehder)
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Assert.assertEquals(list.get(0).getId(), 5);
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Assert.assertEquals(list.get(1).getId(), 1);
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Assert.assertEquals(list.get(2).getId(), 2);
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Assert.assertEquals(list.get(3).getId(), 4);
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Assert.assertEquals(list.get(4).getId(), 3);
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}
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}
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