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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 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.BeforeClass;
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import org.junit.Test;
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import eu.etaxonomy.cdm.model.common.DefaultTermInitializer;
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import eu.etaxonomy.cdm.model.common.TimePeriod;
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import eu.etaxonomy.cdm.model.name.BotanicalName;
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import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
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import eu.etaxonomy.cdm.model.name.NonViralName;
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import eu.etaxonomy.cdm.model.name.Rank;
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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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* @created 04.03.2016
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*/
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public class HomotypicGroupTaxonComparatorTest {
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(HomotypicGroupTaxonComparatorTest.class);
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private Reference<?> sec;
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private Reference<?> ref1;
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private Reference<?> ref2;
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private Reference<?> ref3;
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private Calendar cal1;
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private Calendar cal2;
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private Calendar cal3;
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private BotanicalName botName1;
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private BotanicalName botName2;
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private BotanicalName botName3;
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private BotanicalName botName4;
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private BotanicalName botName5;
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private List<TaxonBase<?>> list;
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private Taxon taxon1;
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private Synonym synonym2;
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private Synonym synonym3;
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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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/**
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* @throws java.lang.Exception
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*/
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@Before
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public void setUp() throws Exception {
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sec = ReferenceFactory.newBook();
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ref1 = ReferenceFactory.newBook();
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ref2 = ReferenceFactory.newBook();
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ref3 = ReferenceFactory.newBook();
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cal1 = Calendar.getInstance();
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cal2 = Calendar.getInstance();
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cal3 = Calendar.getInstance();
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cal1.set(1856, 3, 2);
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cal2.set(1943, 3, 2);
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cal3.set(1945, 3, 2);
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ref1.setDatePublished(TimePeriod.NewInstance(cal1));
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ref2.setDatePublished(TimePeriod.NewInstance(cal2));
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ref3.setDatePublished(TimePeriod.NewInstance(cal3));
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botName1 = BotanicalName.NewInstance(Rank.SPECIES());
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botName2 = BotanicalName.NewInstance(Rank.SPECIES());
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botName3 = BotanicalName.NewInstance(Rank.SPECIES());
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botName4 = BotanicalName.NewInstance(Rank.SPECIES());
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botName5 = BotanicalName.NewInstance(Rank.SPECIES());
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setNameParts(botName1, "Aaa", "aaa");
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setNameParts(botName2, "Bbb", "bbb");
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setNameParts(botName3, "Ccc", "ccc");
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setNameParts(botName4, "Ddd", "ddd");
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setNameParts(botName5, "Eee", "eee");
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// zooName1.setPublicationYear(1823);
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list = new ArrayList<TaxonBase<?>>();
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taxon1 = Taxon.NewInstance(botName1, sec);
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}
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private void setNameParts(NonViralName<?> name, String genus, String speciesEpi) {
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name.setGenusOrUninomial(genus);
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name.setSpecificEpithet(speciesEpi);
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name.getTitleCache();
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}
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/******************** TESTS *****************************************************/
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@Test
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public void testCompare_BasionymGroupsTogether() {
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//2 basionym groups
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HomotypicalGroup homotypicalGroup = botName2.getHomotypicalGroup();
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taxon1.addHeterotypicSynonymName(botName3);
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taxon1.addHeterotypicSynonymName(botName5, homotypicalGroup, null, null);
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botName3.addBasionym(botName5);
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synonym2 = taxon1.addHeterotypicSynonymName(botName2).getSynonym();
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taxon1.addHeterotypicSynonymName(botName4, homotypicalGroup, null, null);
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botName2.addBasionym(botName4);
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list.addAll(taxon1.getSynonyms());
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Collections.sort(list, new HomotypicGroupTaxonComparator(null));
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Assert.assertEquals("basionym for first group should come first", botName4, list.get(0).getName());
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Assert.assertEquals(botName2, list.get(1).getName());
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Assert.assertEquals(botName5, list.get(2).getName());
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Assert.assertEquals(botName3, list.get(3).getName());
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//add replaced synonym relation between basionyms
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botName4.addReplacedSynonym(botName5, null, null, null);
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Collections.sort(list, new HomotypicGroupTaxonComparator(null));
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Assert.assertEquals("basionym of second group should come first now as it is the replaced synonym",
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botName5, list.get(0).getName());
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Assert.assertEquals(botName3, list.get(1).getName());
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Assert.assertEquals("replacement name should come after replaced synonym but first in basionym group",
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botName4, list.get(2).getName());
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Assert.assertEquals(botName2, list.get(3).getName());
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//set a name as first name
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Collections.sort(list, new HomotypicGroupTaxonComparator(synonym2));
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Assert.assertEquals("name2 should come first now",
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botName2, list.get(0).getName());
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Assert.assertEquals("name2 should be followed by its basionym", botName4, list.get(1).getName());
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Assert.assertEquals("other basionym group should come later but with basionym first",
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botName5, list.get(2).getName());
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Assert.assertEquals(botName3, list.get(3).getName());
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}
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@Test
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public void testCompare_BasionymGroupsSeparated() {
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//2 basionym groups in 2 homotypic groups
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synonym3 = taxon1.addHeterotypicSynonymName(botName3).getSynonym();
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taxon1.addHeterotypicSynonymName(botName5);
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botName3.addBasionym(botName5); //also merges homotypic groups
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taxon1.addHeterotypicSynonymName(botName2).getSynonym();
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taxon1.addHeterotypicSynonymName(botName4);
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botName2.addBasionym(botName4);
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list.addAll(taxon1.getSynonyms());
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UUID uuidFirst = UUID.fromString("000000972-d164-4cb5-9a1e-d6216cc858f6");
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UUID uuidSecond = UUID.fromString("ffffff972-d164-4cb5-9a1e-d6216cc858f6");
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Assert.assertTrue(uuidFirst.toString().compareTo(uuidSecond.toString())<-1);
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botName4.getHomotypicalGroup().setUuid(uuidFirst);
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botName5.getHomotypicalGroup().setUuid(uuidSecond);
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//start test
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Collections.sort(list, new HomotypicGroupTaxonComparator(null));
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Assert.assertEquals("basionym for first group should come first", botName4, list.get(0).getName());
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Assert.assertEquals(botName2, list.get(1).getName());
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Assert.assertEquals(botName5, list.get(2).getName());
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Assert.assertEquals(botName3, list.get(3).getName());
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//set a name as first name
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//TODO
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//first taxon in group should have an impact only for the homotypic group to which it belongs
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//but this is still under discussion and may change in future
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Collections.sort(list, new HomotypicGroupTaxonComparator(synonym3));
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Assert.assertEquals(botName4, list.get(0).getName());
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Assert.assertEquals(botName2, list.get(1).getName());
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Assert.assertEquals(botName3, list.get(2).getName());
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Assert.assertEquals(botName5, list.get(3).getName());
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}
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@Test
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public void testCompare_BasionymGroupsSomeWithYears() {
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//2 basionym groups, 1 new combination with year (botName2) and 1 basionym with year (botName5)
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//The later should come first according to the rules, though alphabetically being
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//basionym botName4
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botName2.setNomenclaturalReference(ref2);
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botName5.setNomenclaturalReference(ref3);
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HomotypicalGroup homotypicalGroup = botName2.getHomotypicalGroup();
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taxon1.addHeterotypicSynonymName(botName3);
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taxon1.addHeterotypicSynonymName(botName5, homotypicalGroup, null, null);
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botName3.addBasionym(botName5);
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synonym2 = taxon1.addHeterotypicSynonymName(botName2).getSynonym();
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taxon1.addHeterotypicSynonymName(botName4, homotypicalGroup, null, null);
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botName2.addBasionym(botName4);
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list.addAll(taxon1.getSynonyms());
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Collections.sort(list, new HomotypicGroupTaxonComparator(null));
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Assert.assertEquals("basionym with date should comes first", botName5, list.get(0).getName());
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Assert.assertEquals(botName3, list.get(1).getName());
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Assert.assertEquals(botName4, list.get(2).getName());
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Assert.assertEquals(botName2, list.get(3).getName());
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//even with nom. illeg. the name with date should come first
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NomenclaturalStatus illegStatus = NomenclaturalStatus.NewInstance(NomenclaturalStatusType.ILLEGITIMATE());
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botName5.addStatus(illegStatus);
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Assert.assertEquals("basionym with date should comes first", botName5, list.get(0).getName());
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Assert.assertEquals(botName3, list.get(1).getName());
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Assert.assertEquals(botName4, list.get(2).getName());
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Assert.assertEquals(botName2, list.get(3).getName());
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//add replaced synonym relation between basionyms
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botName5.addReplacedSynonym(botName4, null, null, null);
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Collections.sort(list, new HomotypicGroupTaxonComparator(null));
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Assert.assertEquals("basionym of second group should come first now as it is the replaced synonym",
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botName4, list.get(0).getName());
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Assert.assertEquals(botName2, list.get(1).getName());
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Assert.assertEquals("replacement name should come after replaced synonym but first in basionym group",
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botName5, list.get(2).getName());
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Assert.assertEquals(botName3, list.get(3).getName());
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}
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@Test
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public void testCompare_BasionymGroupsWithRanks1() {
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botName2.setRank(Rank.VARIETY());
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botName2.setInfraSpecificEpithet("varbbbb");
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botName3.setRank(Rank.VARIETY());
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botName3.setInfraSpecificEpithet("subspccc");
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botName4.setRank(Rank.SUBSPECIES());
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botName4.setInfraSpecificEpithet("subspddd");
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HomotypicalGroup homotypicalGroup = botName2.getHomotypicalGroup();
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taxon1.addHeterotypicSynonymName(botName3);
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taxon1.addHeterotypicSynonymName(botName5, homotypicalGroup, null, null);
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botName3.addBasionym(botName5);
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synonym2 = taxon1.addHeterotypicSynonymName(botName2).getSynonym();
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taxon1.addHeterotypicSynonymName(botName4, homotypicalGroup, null, null);
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botName2.addBasionym(botName4);
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list.addAll(taxon1.getSynonyms());
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Collections.sort(list, new HomotypicGroupTaxonComparator(null));
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Assert.assertEquals("basionym with rank species should comes first", botName5, list.get(0).getName());
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Assert.assertEquals(botName3, list.get(1).getName());
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Assert.assertEquals(botName4, list.get(2).getName());
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Assert.assertEquals(botName2, list.get(3).getName());
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//add replaced synonym relation between basionyms
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botName5.addReplacedSynonym(botName4, null, null, null);
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Collections.sort(list, new HomotypicGroupTaxonComparator(null));
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Assert.assertEquals("basionym of second group should come first now as it is the replaced synonym",
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botName4, list.get(0).getName());
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Assert.assertEquals(botName2, list.get(1).getName());
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Assert.assertEquals("replacement name should come after replaced synonym but first in basionym group",
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botName5, list.get(2).getName());
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Assert.assertEquals(botName3, list.get(3).getName());
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}
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@Test
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public void testCompare_BasionymGroupsWithRanks2() {
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botName2.setRank(Rank.VARIETY());
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botName2.setInfraSpecificEpithet("varbbbb");
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botName3.setRank(Rank.VARIETY());
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botName3.setInfraSpecificEpithet("subspccc");
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botName4.setRank(Rank.SUBSPECIES());
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botName4.setInfraSpecificEpithet("subspddd");
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botName5.setRank(Rank.VARIETY());
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botName5.setInfraSpecificEpithet("vareee");
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HomotypicalGroup homotypicalGroup = botName2.getHomotypicalGroup();
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taxon1.addHeterotypicSynonymName(botName3);
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taxon1.addHeterotypicSynonymName(botName5, homotypicalGroup, null, null);
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botName3.addBasionym(botName5);
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synonym2 = taxon1.addHeterotypicSynonymName(botName2).getSynonym();
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taxon1.addHeterotypicSynonymName(botName4, homotypicalGroup, null, null);
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botName2.addBasionym(botName5);
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botName4.addBasionym(botName5);
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list.addAll(taxon1.getSynonyms());
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Collections.sort(list, new HomotypicGroupTaxonComparator(null));
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Assert.assertEquals("basionym should comes first", botName5, list.get(0).getName());
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Assert.assertEquals("subspecies should come next", botName4, list.get(1).getName());
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Assert.assertEquals("variety with b should come next", botName2, list.get(2).getName());
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Assert.assertEquals("variety with c should come last", botName3, list.get(3).getName());
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}
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@Test
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public void testCompare_BasionymGroupsWithNomIlleg() {
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NomenclaturalStatus illegStatus = NomenclaturalStatus.NewInstance(NomenclaturalStatusType.ILLEGITIMATE());
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botName4.addStatus(illegStatus);
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//2 basionym groups
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HomotypicalGroup homotypicalGroup = botName2.getHomotypicalGroup();
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taxon1.addHeterotypicSynonymName(botName3);
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taxon1.addHeterotypicSynonymName(botName5, homotypicalGroup, null, null);
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botName3.addBasionym(botName5);
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synonym2 = taxon1.addHeterotypicSynonymName(botName2).getSynonym();
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taxon1.addHeterotypicSynonymName(botName4, homotypicalGroup, null, null);
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// botName2.addBasionym(botName4);
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list.addAll(taxon1.getSynonyms());
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Collections.sort(list, new HomotypicGroupTaxonComparator(null));
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Assert.assertEquals("basionym for non nom. illeg. group should come first", botName2, list.get(0).getName());
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Assert.assertEquals(botName5, list.get(1).getName());
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Assert.assertEquals(botName3, list.get(2).getName());
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Assert.assertEquals("Nom illeg should come last", botName4, list.get(3).getName());
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//name having a nom. illeg. as basionym should stay in its basionym group
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//NOTE: this is dirty data as nom. illeg. is not allowed as basionym by the code
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botName2.addBasionym(botName4);
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Collections.sort(list, new HomotypicGroupTaxonComparator(null));
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Assert.assertEquals("basionym for non nom. illeg. group should come first", botName5, list.get(0).getName());
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Assert.assertEquals(botName3, list.get(1).getName());
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Assert.assertEquals("Nom illeg basionym group should come last", botName4, list.get(2).getName());
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Assert.assertEquals("Names with nom. illeg. as basionym should stay in basionym group", botName2, list.get(3).getName());
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//non basionym nom. illeg. should not change the order
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botName4.removeStatus(illegStatus);
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botName2.addStatus(illegStatus);
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Collections.sort(list, new HomotypicGroupTaxonComparator(null));
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Assert.assertEquals("basionym for non nom. illeg. group should come first", botName4, list.get(0).getName());
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Assert.assertEquals(botName2, list.get(1).getName());
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Assert.assertEquals("Nom illeg basionym group should come last", botName5, list.get(2).getName());
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Assert.assertEquals("Names with nom. illeg. as basionym should stay in basionym group", botName3, list.get(3).getName());
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}
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@Test
|
384
|
public void testCompare_NoCircularProblemsWithBasionyms() {
|
385
|
|
386
|
taxon1.addHomotypicSynonymName(botName3, null, null);
|
387
|
taxon1.addHomotypicSynonymName(botName5, null, null);
|
388
|
botName3.addBasionym(botName5);
|
389
|
|
390
|
Assert.assertEquals(botName1.getHomotypicalGroup(), botName5.getHomotypicalGroup());
|
391
|
botName5.addBasionym(botName1);
|
392
|
botName1.addBasionym(botName3);
|
393
|
|
394
|
list.addAll(taxon1.getSynonyms());
|
395
|
list.add(taxon1);
|
396
|
Collections.sort(list, new HomotypicGroupTaxonComparator(null));
|
397
|
|
398
|
Assert.assertEquals(botName1, list.get(0).getName());
|
399
|
Assert.assertEquals(botName3, list.get(1).getName());
|
400
|
Assert.assertEquals(botName5, list.get(2).getName());
|
401
|
|
402
|
//additional basionym for botName3
|
403
|
taxon1.addHomotypicSynonymName(botName2, null, null);
|
404
|
Assert.assertEquals(botName1.getHomotypicalGroup(), botName2.getHomotypicalGroup());
|
405
|
botName3.addBasionym(botName2);
|
406
|
list.clear();
|
407
|
list.addAll(taxon1.getSynonyms());
|
408
|
list.add(taxon1);
|
409
|
Collections.sort(list, new HomotypicGroupTaxonComparator(null));
|
410
|
|
411
|
Assert.assertEquals(botName1, list.get(0).getName());
|
412
|
Assert.assertEquals(botName2, list.get(1).getName());
|
413
|
Assert.assertEquals(botName3, list.get(2).getName());
|
414
|
Assert.assertEquals(botName5, list.get(3).getName());
|
415
|
|
416
|
}
|
417
|
|
418
|
@Test
|
419
|
public void testCompare_NoCircularProblemsWithReplacedSynonyms() {
|
420
|
|
421
|
taxon1.addHomotypicSynonymName(botName3, null, null);
|
422
|
taxon1.addHomotypicSynonymName(botName5, null, null);
|
423
|
botName3.addReplacedSynonym(botName5, null, null, null);
|
424
|
|
425
|
Assert.assertEquals(botName1.getHomotypicalGroup(), botName5.getHomotypicalGroup());
|
426
|
botName5.addReplacedSynonym(botName1, null, null, null);
|
427
|
botName1.addReplacedSynonym(botName3, null, null, null);
|
428
|
|
429
|
list.addAll(taxon1.getSynonyms());
|
430
|
list.add(taxon1);
|
431
|
Collections.sort(list, new HomotypicGroupTaxonComparator(null));
|
432
|
|
433
|
Assert.assertEquals(botName1, list.get(0).getName());
|
434
|
Assert.assertEquals(botName3, list.get(1).getName());
|
435
|
Assert.assertEquals(botName5, list.get(2).getName());
|
436
|
|
437
|
|
438
|
}
|
439
|
|
440
|
}
|