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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.strategy.cache.taxon;
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import static org.junit.Assert.assertEquals;
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import org.apache.logging.log4j.LogManager;import org.apache.logging.log4j.Logger;
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import org.joda.time.DateTime;
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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 eu.etaxonomy.cdm.common.URI;
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import eu.etaxonomy.cdm.model.agent.Person;
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import eu.etaxonomy.cdm.model.agent.Team;
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import eu.etaxonomy.cdm.model.name.IBotanicalName;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
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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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import eu.etaxonomy.cdm.model.reference.ReferenceType;
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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.TaxonBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
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import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
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import eu.etaxonomy.cdm.strategy.parser.TimePeriodParser;
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import eu.etaxonomy.cdm.test.TermTestBase;
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/**
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* @author a.mueller
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* @since 21.09.2009
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*/
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public class TaxonBaseDefaultCacheStrategyTest extends TermTestBase {
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@SuppressWarnings("unused")
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private static final Logger logger = LogManager.getLogger(TaxonBaseDefaultCacheStrategyTest.class);
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private final String expectedNameTitleCache = "Abies alba (L.) Mill.";
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private final String expectedNameCache = "Abies alba";
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private IBotanicalName name;
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private Reference sec;
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@Before
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public void setUp() throws Exception {
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name = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
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name.setGenusOrUninomial("Abies");
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name.setSpecificEpithet("alba");
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Person combinationAuthor = Person.NewInstance();
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combinationAuthor.setNomenclaturalTitle("Mill.");
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Person basionymAuthor = Person.NewInstance();
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basionymAuthor.setNomenclaturalTitle("L.");
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name.setCombinationAuthorship(combinationAuthor);
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name.setBasionymAuthorship(basionymAuthor);
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assertEquals("Namecache should be Abies alba", expectedNameCache, name.getNameCache());
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assertEquals("Titlecache should be Abies alba (Mill.) L.", expectedNameTitleCache, name.getTitleCache());
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sec = ReferenceFactory.newBook();
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sec.setTitle("Sp.Pl.");
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}
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//******************************* TESTS ********************************************************
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@Test
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public void testGetTitleCache() {
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Taxon taxon = Taxon.NewInstance(name, sec);
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assertEquals("Taxon titlecache is wrong", expectedNameTitleCache + " sec. Sp.Pl.", taxon.getTitleCache());
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//without sec.
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taxon.setSec(null);
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assertEquals("Taxon titlecache is wrong", expectedNameTitleCache + " sec. ???", taxon.getTitleCache());
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//appended phrase without sec.
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String appendedPhrase = "aff. 'schippii'";
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taxon.setAppendedPhrase(appendedPhrase);
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assertEquals("Taxon titlecache is wrong", expectedNameTitleCache + " aff. 'schippii'", taxon.getTitleCache());
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//appended phrase with sec.
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taxon.setSec(sec);
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assertEquals("Taxon titlecache is wrong", expectedNameTitleCache + " aff. 'schippii' sec. Sp.Pl.", taxon.getTitleCache());
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//use name cache
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taxon.setUseNameCache(true);
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assertEquals("Taxon titlecache is wrong", expectedNameCache + " aff. 'schippii' sec. Sp.Pl.", taxon.getTitleCache());
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taxon.setDoubtful(true);
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assertEquals("Taxon titlecache is wrong", "?" + expectedNameCache + " aff. 'schippii' sec. Sp.Pl.", taxon.getTitleCache());
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//with nom status
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taxon.setAppendedPhrase(null);
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taxon.setUseNameCache(false);
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taxon.setDoubtful(false);
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name.addStatus(NomenclaturalStatusType.ILLEGITIMATE(), null, null);
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assertEquals("Taxon titlecache is wrong", expectedNameTitleCache + ", nom. illeg., sec. Sp.Pl.", taxon.getTitleCache());
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}
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@Test
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public void testGetTitleCacheWithNameUsedInSource() {
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Taxon taxon = Taxon.NewInstance(name, sec);
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TaxonName nameUsedInSource = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
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nameUsedInSource.setGenusOrUninomial("Pinus");
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nameUsedInSource.setSpecificEpithet("blanca");
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taxon.getSecSource().setNameUsedInSource(nameUsedInSource);
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assertEquals("Taxon titlecache is wrong", expectedNameTitleCache + " sec. Sp.Pl. (sub Pinus blanca)", taxon.getTitleCache());
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}
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//same as for accepted taxa but with syn. sec. instead of sec.
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@Test
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public void testSynSec() {
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Synonym syn = Synonym.NewInstance(name, sec);
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assertEquals("Taxon titlecache is wrong", expectedNameTitleCache + " syn. sec. Sp.Pl.", syn.getTitleCache());
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//without sec.
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syn.setSec(null);
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assertEquals("Taxon titlecache is wrong", expectedNameTitleCache + " syn. sec. ???", syn.getTitleCache());
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//appended phrase without sec.
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String appendedPhrase = "aff. 'schippii'";
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syn.setAppendedPhrase(appendedPhrase);
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assertEquals("Taxon titlecache is wrong", expectedNameTitleCache + " aff. 'schippii'", syn.getTitleCache());
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//appended phrase with sec.
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syn.setSec(sec);
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assertEquals("Taxon titlecache is wrong", expectedNameTitleCache + " aff. 'schippii' syn. sec. Sp.Pl.", syn.getTitleCache());
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//use name cache
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syn.setUseNameCache(true);
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assertEquals("Taxon titlecache is wrong", expectedNameCache + " aff. 'schippii' syn. sec. Sp.Pl.", syn.getTitleCache());
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syn.setDoubtful(true);
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assertEquals("Taxon titlecache is wrong", "?" + expectedNameCache + " aff. 'schippii' syn. sec. Sp.Pl.", syn.getTitleCache());
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//with nom status
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syn.setAppendedPhrase(null);
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syn.setUseNameCache(false);
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syn.setDoubtful(false);
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name.addStatus(NomenclaturalStatusType.ILLEGITIMATE(), null, null);
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assertEquals("Taxon titlecache is wrong", expectedNameTitleCache + ", nom. illeg., syn. sec. Sp.Pl.", syn.getTitleCache());
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}
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@Test
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public void testGetTitleCacheWithoutName() {
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Taxon taxon = Taxon.NewInstance(null, sec);
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assertEquals("Taxon titlecache is wrong", "??? sec. Sp.Pl.", taxon.getTitleCache());
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}
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//test missing "&" in title cache #3822
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@Test
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public void testAndInTitleCache() {
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Taxon taxon = Taxon.NewInstance(name, sec);
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Team team = Team.NewInstance();
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team.addTeamMember((Person)name.getCombinationAuthorship());
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team.addTeamMember((Person)name.getBasionymAuthorship());
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name.setCombinationAuthorship(team);
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// System.out.println(taxonBase.generateTitle());
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assertEquals("Abies alba (L.) Mill. \u0026 L. sec. Sp.Pl.", taxon.generateTitle());
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name = TaxonNameFactory.NewBotanicalInstance(null);
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NonViralNameParserImpl.NewInstance().parseFullName(name, "Cichorium glandulosum Boiss. \u0026 A. Huet", null, true);
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Taxon taxon2 = Taxon.NewInstance(name, sec);
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assertEquals("Cichorium glandulosum Boiss. \u0026 A. Huet sec. Sp.Pl.", taxon2.getTitleCache());
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}
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@Test
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public void testProtectedTitleCache(){
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Taxon taxon = Taxon.NewInstance(name, sec);
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taxon.setTitleCache("abc", true);
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taxon.setDoubtful(true);
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Assert.assertEquals("abc", taxon.getTitleCache());
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}
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@Test
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public void testProtectedSecTitleCache(){
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Taxon taxon = Taxon.NewInstance(name, sec);
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sec.setTitleCache("My protected sec ref", true);
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taxon.setDoubtful(true);
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taxon.setSecMicroReference("123");
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Assert.assertEquals("?Abies alba (L.) Mill. sec. My protected sec ref: 123", taxon.getTitleCache());
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}
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@Test
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public void testMicroReference(){
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Taxon taxon = Taxon.NewInstance(name, sec);
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String secMicroRef = "p. 553";
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//not atomized
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taxon.setSecMicroReference(secMicroRef);
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assertEquals("Taxon titlecache is wrong", expectedNameTitleCache + " sec. Sp.Pl.: p. 553",
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taxon.getTitleCache());
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//atomized
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sec.setAuthorship(Team.NewTitledInstance("Team", "T."));
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sec.setDatePublished(TimePeriodParser.parseStringVerbatim("1798"));
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taxon.setTitleCache(null, false);
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assertEquals("Taxon titlecache is wrong", expectedNameTitleCache + " sec. Team 1798: p. 553",
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taxon.getTitleCache());
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}
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@Test
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public void testWebPageSec(){
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Reference sec = ReferenceFactory.newWebPage();
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sec.setTitle("My long webpage");
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sec.setAbbrevTitle("MLW");
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sec.setUri(URI.create("https://abc.de"));
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sec.setDatePublished(TimePeriodParser.parseStringVerbatim("2 Jan 1982"));
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TaxonBase<?> taxonBase = Taxon.NewInstance(name, sec);
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Assert.assertEquals("Abies alba (L.) Mill. sec. MLW 1982", taxonBase.getTitleCache());
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sec.setDatePublished(null);
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taxonBase.setTitleCache(null, false);
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Assert.assertEquals("Abies alba (L.) Mill. sec. MLW", taxonBase.getTitleCache());
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sec.setAccessed(DateTime.parse("1983-06-30"));
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taxonBase.setTitleCache(null, false);
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Assert.assertEquals("Abies alba (L.) Mill. sec. MLW 1983", taxonBase.getTitleCache());
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sec.setAbbrevTitle(null);
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taxonBase.setTitleCache(null, false);
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Assert.assertEquals("Abies alba (L.) Mill. sec. My long webpage 1983", taxonBase.getTitleCache());
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sec.setAbbrevTitle("MLW");
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taxonBase.setSecMicroReference("table 1");
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Assert.assertEquals("Abies alba (L.) Mill. sec. MLW 1983: table 1", taxonBase.getTitleCache());
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sec.setType(ReferenceType.Database);
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taxonBase.setSecMicroReference(null);
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Assert.assertEquals("Abies alba (L.) Mill. sec. MLW 1983", taxonBase.getTitleCache());
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sec.setType(ReferenceType.Map);
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taxonBase.setTitleCache(null, false);
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Assert.assertEquals("Abies alba (L.) Mill. sec. MLW 1983", taxonBase.getTitleCache());
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}
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@Test
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public void testMisapplication(){
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//assert default (taxon without relation)
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Taxon man = Taxon.NewInstance(name, sec);
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ITaxonCacheStrategy<Taxon> cacheStrategy = man.cacheStrategy();
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assertEquals("Taxon titlecache must use sec", expectedNameTitleCache + " sec. Sp.Pl.", cacheStrategy.getTitleCache(man));
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//make it a MAN only
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Taxon mainTaxon = Taxon.NewInstance(TaxonNameFactory.NewBacterialInstance(Rank.SPECIES()), ReferenceFactory.newBook() );
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mainTaxon.addMisappliedName(man, null, null);
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assertEquals("Taxon titlecache must use sensu", expectedNameCache + " sensu Sp.Pl., non (L.) Mill.", cacheStrategy.getTitleCache(man));
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man.setSec(null);
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assertEquals("Taxon titlecache must use sensu", expectedNameCache + " auct., non (L.) Mill.", cacheStrategy.getTitleCache(man));
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man.setAppendedPhrase("aucts.");
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assertEquals("Taxon titlecache must use sensu", expectedNameCache + " aucts., non (L.) Mill.", cacheStrategy.getTitleCache(man));
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//reset sec + appendedPhrase
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man.setSec(sec);
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man.setAppendedPhrase(null);
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//add another from relation
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Taxon relatedTaxon = Taxon.NewInstance(TaxonNameFactory.NewBacterialInstance(Rank.SPECIES()), ReferenceFactory.newBook() );
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TaxonRelationship rel = man.addTaxonRelation(relatedTaxon, TaxonRelationshipType.CONGRUENT_TO(), null, null);
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assertEquals("Taxon titlecache must use sec", expectedNameTitleCache + " sec. Sp.Pl.", cacheStrategy.getTitleCache(man));
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man.removeTaxonRelation(rel);
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assertEquals("Taxon titlecache must use sensu", expectedNameCache + " sensu Sp.Pl., non (L.) Mill.", cacheStrategy.getTitleCache(man));
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//add another to relation
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rel = relatedTaxon.addTaxonRelation(man, TaxonRelationshipType.CONGRUENT_TO(), null, null);
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assertEquals("Taxon titlecache must use sec", expectedNameTitleCache + " sec. Sp.Pl.", cacheStrategy.getTitleCache(man));
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man.removeTaxonRelation(rel);
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assertEquals("Taxon titlecache must use sensu", expectedNameCache + " sensu Sp.Pl., non (L.) Mill.", cacheStrategy.getTitleCache(man));
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//add taxon node
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Classification c = Classification.NewInstance("Test");
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TaxonNode tn = c.addChildTaxon(man, null);
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assertEquals("Taxon titlecache must use sec", expectedNameTitleCache + " sec. Sp.Pl.", cacheStrategy.getTitleCache(man));
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man.removeTaxonNode(tn);
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assertEquals("Taxon titlecache must use sensu", expectedNameCache + " sensu Sp.Pl., non (L.) Mill.", cacheStrategy.getTitleCache(man));
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}
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}
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