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/**
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* Copyright (C) 2009 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.api.service;
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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 java.io.FileNotFoundException;
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import java.util.List;
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import java.util.UUID;
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import org.apache.log4j.Level;
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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.spring.annotation.SpringBeanByType;
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import eu.etaxonomy.cdm.api.service.config.FindTaxaAndNamesConfiguratorImpl;
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import eu.etaxonomy.cdm.api.service.config.IFindTaxaAndNamesConfigurator;
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import eu.etaxonomy.cdm.api.service.pager.Pager;
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import eu.etaxonomy.cdm.api.service.search.ICdmMassIndexer;
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import eu.etaxonomy.cdm.common.UTF8;
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.description.CommonTaxonName;
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import eu.etaxonomy.cdm.model.description.Distribution;
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import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
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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.location.Country;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.name.IBotanicalName;
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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.Reference;
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
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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.SynonymType;
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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.TaxonRelationshipType;
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import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
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import eu.etaxonomy.cdm.persistence.query.MatchMode;
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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.kohlbecker
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* @since 04.02.2009
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*/
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public class TaxonServiceSearchTaxaAndNamesTest extends CdmTransactionalIntegrationTest {
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private static Logger logger = Logger.getLogger(TaxonServiceSearchTaxaAndNamesTest.class);
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private static final String ABIES_BALSAMEA_UUID = "f65d47bd-4f49-4ab1-bc4a-bc4551eaa1a8";
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private static final String ABIES_ALBA_UUID = "7dbd5810-a3e5-44b6-b563-25152b8867f4";
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private static final String CLASSIFICATION_UUID = "2a5ceebb-4830-4524-b330-78461bf8cb6b";
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private static final String CLASSIFICATION_ALT_UUID = "d7c741e3-ae9e-4a7d-a566-9e3a7a0b51ce";
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private static final String D_ABIES_BALSAMEA_UUID = "900108d8-e6ce-495e-b32e-7aad3099135e";
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private static final String D_ABIES_ALBA_UUID = "ec8bba03-d993-4c85-8472-18b14942464b";
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// private static final String D_ABIES_KAWAKAMII_SEC_KOMAROV_UUID = "e9d8c2fd-6409-46d5-9c2e-14a2bbb1b2b1";
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@SpringBeanByType
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private ITaxonService taxonService;
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@SpringBeanByType
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private ITermService termService;
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@SpringBeanByType
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private IClassificationService classificationService;
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@SpringBeanByType
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private IReferenceService referenceService;
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@SpringBeanByType
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private IDescriptionService descriptionService;
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@SpringBeanByType
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private INameService nameService;
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@SpringBeanByType
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private ICdmMassIndexer indexer;
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@SpringBeanByType
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private ITaxonNodeService nodeService;
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private NamedArea germany;
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// private NamedArea france ;
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private NamedArea russia ;
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private NamedArea canada ;
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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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germany = Country.GERMANY();
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// france = Country.FRANCEFRENCHREPUBLIC();
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russia = Country.RUSSIANFEDERATION();
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canada = Country.CANADA();
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}
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@Test
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public void testDbUnitUsageTest() throws Exception {
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assertNotNull("taxonService should exist", taxonService);
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assertNotNull("nameService should exist", nameService);
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}
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/**
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* This test permutes through all search mode combinations.
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*
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* 7 Accepted Taxa
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* 1 Synonym
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* 1 misapplied which is also in the set of accepted
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* 2 Names without taxa
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*
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*/
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@Test
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@DataSet
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public final void testFindTaxaAndNames() {
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IFindTaxaAndNamesConfigurator conf = FindTaxaAndNamesConfiguratorImpl.NewInstance();
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conf.setTitleSearchString("Abies*");
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conf.setMatchMode(MatchMode.BEGINNING);
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// ---------------------------------------------------------
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setTaxaAndNamesModes(conf, true, true, true, true, true);
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@SuppressWarnings("rawtypes")
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Pager<IdentifiableEntity> pager = taxonService.findTaxaAndNames(conf);
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logSearchResults(pager, Level.DEBUG);
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assertEquals(10, pager.getRecords().size());
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setTaxaAndNamesModes(conf, false, true, true, true, true);
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pager = taxonService.findTaxaAndNames(conf);
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assertEquals(4, pager.getRecords().size());
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setTaxaAndNamesModes(conf, true, false, true, true, true);
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pager = taxonService.findTaxaAndNames(conf);
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assertEquals(9, pager.getRecords().size());
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setTaxaAndNamesModes(conf, false, false, true, true, true);
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pager = taxonService.findTaxaAndNames(conf);
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//logSearchResults(pager, Level.DEBUG);
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assertEquals(3, pager.getRecords().size());
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// ---------------------------------------------------------
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setTaxaAndNamesModes(conf, true, true, false, true, true);
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pager = taxonService.findTaxaAndNames(conf);
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logSearchResults(pager, Level.DEBUG);
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assertEquals(10, pager.getRecords().size());
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setTaxaAndNamesModes(conf, false, true, false, true, true);
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pager = taxonService.findTaxaAndNames(conf);
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assertEquals("one synonym, two names without taxa and a misapplied name", 4, pager.getRecords().size());
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setTaxaAndNamesModes(conf, true, false, false, true, true);
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pager = taxonService.findTaxaAndNames(conf);
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assertEquals(9, pager.getRecords().size());
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setTaxaAndNamesModes(conf, false, false, false, true, true);
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pager = taxonService.findTaxaAndNames(conf);
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assertEquals(3, pager.getRecords().size());
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// =========================================================
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setTaxaAndNamesModes(conf, true, true, true, false, true);
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pager = taxonService.findTaxaAndNames(conf);
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// logSearchResults(pager, Level.DEBUG);
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assertEquals(10, pager.getRecords().size());
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setTaxaAndNamesModes(conf, false, true, true, false, true);
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pager = taxonService.findTaxaAndNames(conf);
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logSearchResults(pager, Level.DEBUG);
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assertEquals(3, pager.getRecords().size());
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setTaxaAndNamesModes(conf, true, false, true, false, true);
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pager = taxonService.findTaxaAndNames(conf);
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logSearchResults(pager, Level.DEBUG);
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assertEquals(9, pager.getRecords().size());
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setTaxaAndNamesModes(conf, false, false, true, false, true);
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pager = taxonService.findTaxaAndNames(conf);
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logSearchResults(pager, Level.DEBUG);
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assertEquals(2, pager.getRecords().size());
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// ---------------------------------------------------------
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setTaxaAndNamesModes(conf, true, true, false, false, true);
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pager = taxonService.findTaxaAndNames(conf);
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logSearchResults(pager, Level.DEBUG);
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assertEquals(10, pager.getRecords().size());
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setTaxaAndNamesModes(conf, false, true, false, false, true);
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pager = taxonService.findTaxaAndNames(conf);
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logSearchResults(pager, Level.DEBUG);
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assertEquals(3, pager.getRecords().size());
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setTaxaAndNamesModes(conf, true, false, false, false, true);
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pager = taxonService.findTaxaAndNames(conf);
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logSearchResults(pager, Level.DEBUG);
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assertEquals(9, pager.getRecords().size());
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// only names without taxa
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// - Abies borisii-regis
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// - Abies lasio
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setTaxaAndNamesModes(conf, false, false, false, false, true);
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pager = taxonService.findTaxaAndNames(conf);
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logSearchResults(pager, Level.DEBUG);
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assertEquals(2, pager.getRecords().size());
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// =========================================================
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setTaxaAndNamesModes(conf, true, true, true, true, false);
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pager = taxonService.findTaxaAndNames(conf);
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logSearchResults(pager, Level.DEBUG);
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assertEquals(8, pager.getRecords().size());
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setTaxaAndNamesModes(conf, false, true, true, true, false);
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pager = taxonService.findTaxaAndNames(conf);
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logSearchResults(pager, Level.DEBUG);
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assertEquals("one synonym and a misapplied name", 2, pager.getRecords().size());
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setTaxaAndNamesModes(conf, true, false, true, true, false);
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pager = taxonService.findTaxaAndNames(conf);
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logSearchResults(pager, Level.DEBUG);
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assertEquals(7, pager.getRecords().size());
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setTaxaAndNamesModes(conf, false, false, true, true, false);
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pager = taxonService.findTaxaAndNames(conf);
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logSearchResults(pager, Level.DEBUG);
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assertEquals(1, pager.getRecords().size());
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// ---------------------------------------------------------
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setTaxaAndNamesModes(conf, true, true, false, true, false);
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pager = taxonService.findTaxaAndNames(conf);
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logSearchResults(pager, Level.DEBUG);
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assertEquals(8, pager.getRecords().size());
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setTaxaAndNamesModes(conf, false, true, false, true, false);
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pager = taxonService.findTaxaAndNames(conf);
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logSearchResults(pager, Level.DEBUG);
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assertEquals(2, pager.getRecords().size());
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setTaxaAndNamesModes(conf, true, false, false, true, false);
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pager = taxonService.findTaxaAndNames(conf);
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logSearchResults(pager, Level.DEBUG);
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assertEquals(7, pager.getRecords().size());
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// only misapplied names
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// - Abies kawakamii sec. Komarov, V. L., Flora SSSR 29
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setTaxaAndNamesModes(conf, false, false, false, true, false);
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pager = taxonService.findTaxaAndNames(conf);
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logSearchResults(pager, Level.DEBUG);
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assertEquals(1, pager.getRecords().size());
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// =========================================================
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setTaxaAndNamesModes(conf, true, true, true, false, false);
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pager = taxonService.findTaxaAndNames(conf);
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logSearchResults(pager, Level.DEBUG);
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assertEquals(8, pager.getRecords().size());
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setTaxaAndNamesModes(conf, false, true, true, false, false);
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pager = taxonService.findTaxaAndNames(conf);
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logSearchResults(pager, Level.DEBUG);
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assertEquals(1, pager.getRecords().size());
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setTaxaAndNamesModes(conf, true, false, true, false, false);
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pager = taxonService.findTaxaAndNames(conf);
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logSearchResults(pager, Level.DEBUG);
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assertEquals(7, pager.getRecords().size());
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setTaxaAndNamesModes(conf, false, false, true, false, false);
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pager = taxonService.findTaxaAndNames(conf);
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logSearchResults(pager, Level.DEBUG);
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assertEquals(0, pager.getRecords().size());
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// ---------------------------------------------------------
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setTaxaAndNamesModes(conf, true, true, false, false, false);
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pager = taxonService.findTaxaAndNames(conf);
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logSearchResults(pager, Level.DEBUG);
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assertEquals(8, pager.getRecords().size());
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setTaxaAndNamesModes(conf, false, true, false, false, false);
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pager = taxonService.findTaxaAndNames(conf);
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logSearchResults(pager, Level.DEBUG);
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assertEquals(1, pager.getRecords().size());
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setTaxaAndNamesModes(conf, true, false, false, false, false);
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pager = taxonService.findTaxaAndNames(conf);
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logSearchResults(pager, Level.DEBUG);
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assertEquals(7, pager.getRecords().size());
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setTaxaAndNamesModes(conf, false, false, false, false, false);
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pager = taxonService.findTaxaAndNames(conf);
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logSearchResults(pager, Level.DEBUG);
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assertEquals(0, pager.getRecords().size());
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}
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/**
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* This test permutes through all search mode combinations with classification filter
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*
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* 1 accepted taxon
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* 1 Synonym
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* 1 misapplied
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* 2 names without taxa
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*
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*/
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@Test
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@DataSet
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330
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public final void testFindTaxaAndNames_with_classification() {
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331
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IFindTaxaAndNamesConfigurator conf = FindTaxaAndNamesConfiguratorImpl.NewInstance();
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conf.setTitleSearchString("Abies*");
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conf.setClassification(classificationService.load(UUID.fromString(CLASSIFICATION_UUID)));
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conf.setMatchMode(MatchMode.BEGINNING);
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336
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// ---------------------------------------------------------
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setTaxaAndNamesModes(conf, true, true, true, true, true);
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340
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@SuppressWarnings("rawtypes")
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341
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Pager<IdentifiableEntity> pager = taxonService.findTaxaAndNames(conf);
|
|
342
|
logSearchResults(pager, Level.DEBUG);
|
|
343
|
assertEquals(5, pager.getRecords().size());
|
|
344
|
|
|
345
|
|
|
346
|
setTaxaAndNamesModes(conf, false, true, true, true, true);
|
|
347
|
pager = taxonService.findTaxaAndNames(conf);
|
|
348
|
logSearchResults(pager, Level.DEBUG);
|
|
349
|
assertEquals(4, pager.getRecords().size());
|
|
350
|
|
|
351
|
setTaxaAndNamesModes(conf, true, false, true, true, true);
|
|
352
|
pager = taxonService.findTaxaAndNames(conf);
|
|
353
|
assertEquals(4, pager.getRecords().size());
|
|
354
|
|
|
355
|
setTaxaAndNamesModes(conf, false, false, true, true, true);
|
|
356
|
pager = taxonService.findTaxaAndNames(conf);
|
|
357
|
//logSearchResults(pager, Level.DEBUG);
|
|
358
|
assertEquals(3, pager.getRecords().size());
|
|
359
|
|
|
360
|
// ---------------------------------------------------------
|
|
361
|
|
|
362
|
setTaxaAndNamesModes(conf, true, true, false, true, true);
|
|
363
|
pager = taxonService.findTaxaAndNames(conf);
|
|
364
|
assertEquals(5, pager.getRecords().size());
|
|
365
|
|
|
366
|
setTaxaAndNamesModes(conf, false, true, false, true, true);
|
|
367
|
pager = taxonService.findTaxaAndNames(conf);
|
|
368
|
assertEquals(4, pager.getRecords().size());
|
|
369
|
|
|
370
|
setTaxaAndNamesModes(conf, true, false, false, true, true);
|
|
371
|
pager = taxonService.findTaxaAndNames(conf);
|
|
372
|
assertEquals(4, pager.getRecords().size());
|
|
373
|
|
|
374
|
setTaxaAndNamesModes(conf, false, false, false, true, true);
|
|
375
|
pager = taxonService.findTaxaAndNames(conf);
|
|
376
|
assertEquals(3, pager.getRecords().size());
|
|
377
|
|
|
378
|
// =========================================================
|
|
379
|
|
|
380
|
setTaxaAndNamesModes(conf, true, true, true, false, true);
|
|
381
|
pager = taxonService.findTaxaAndNames(conf);
|
|
382
|
// logSearchResults(pager, Level.DEBUG);
|
|
383
|
assertEquals(4, pager.getRecords().size());
|
|
384
|
|
|
385
|
|
|
386
|
setTaxaAndNamesModes(conf, false, true, true, false, true);
|
|
387
|
pager = taxonService.findTaxaAndNames(conf);
|
|
388
|
logSearchResults(pager, Level.DEBUG);
|
|
389
|
assertEquals(3, pager.getRecords().size());
|
|
390
|
|
|
391
|
setTaxaAndNamesModes(conf, true, false, true, false, true);
|
|
392
|
pager = taxonService.findTaxaAndNames(conf);
|
|
393
|
logSearchResults(pager, Level.DEBUG);
|
|
394
|
assertEquals(3, pager.getRecords().size());
|
|
395
|
|
|
396
|
setTaxaAndNamesModes(conf, false, false, true, false, true);
|
|
397
|
pager = taxonService.findTaxaAndNames(conf);
|
|
398
|
logSearchResults(pager, Level.DEBUG);
|
|
399
|
assertEquals(2, pager.getRecords().size());
|
|
400
|
|
|
401
|
// ---------------------------------------------------------
|
|
402
|
|
|
403
|
setTaxaAndNamesModes(conf, true, true, false, false, true);
|
|
404
|
pager = taxonService.findTaxaAndNames(conf);
|
|
405
|
logSearchResults(pager, Level.DEBUG);
|
|
406
|
assertEquals(4, pager.getRecords().size());
|
|
407
|
|
|
408
|
setTaxaAndNamesModes(conf, false, true, false, false, true);
|
|
409
|
pager = taxonService.findTaxaAndNames(conf);
|
|
410
|
logSearchResults(pager, Level.DEBUG);
|
|
411
|
assertEquals(3, pager.getRecords().size());
|
|
412
|
|
|
413
|
setTaxaAndNamesModes(conf, true, false, false, false, true);
|
|
414
|
pager = taxonService.findTaxaAndNames(conf);
|
|
415
|
logSearchResults(pager, Level.DEBUG);
|
|
416
|
assertEquals(3, pager.getRecords().size());
|
|
417
|
|
|
418
|
// only names without taxa
|
|
419
|
// - Abies borisii-regis
|
|
420
|
// - Abies lasio
|
|
421
|
setTaxaAndNamesModes(conf, false, false, false, false, true);
|
|
422
|
pager = taxonService.findTaxaAndNames(conf);
|
|
423
|
logSearchResults(pager, Level.DEBUG);
|
|
424
|
assertEquals(2, pager.getRecords().size());
|
|
425
|
|
|
426
|
// =========================================================
|
|
427
|
|
|
428
|
setTaxaAndNamesModes(conf, true, true, true, true, false);
|
|
429
|
pager = taxonService.findTaxaAndNames(conf);
|
|
430
|
logSearchResults(pager, Level.DEBUG);
|
|
431
|
assertEquals(3, pager.getRecords().size());
|
|
432
|
|
|
433
|
|
|
434
|
setTaxaAndNamesModes(conf, false, true, true, true, false);
|
|
435
|
pager = taxonService.findTaxaAndNames(conf);
|
|
436
|
logSearchResults(pager, Level.DEBUG);
|
|
437
|
assertEquals(2, pager.getRecords().size());
|
|
438
|
|
|
439
|
setTaxaAndNamesModes(conf, true, false, true, true, false);
|
|
440
|
pager = taxonService.findTaxaAndNames(conf);
|
|
441
|
logSearchResults(pager, Level.DEBUG);
|
|
442
|
assertEquals(2, pager.getRecords().size());
|
|
443
|
|
|
444
|
setTaxaAndNamesModes(conf, false, false, true, true, false);
|
|
445
|
pager = taxonService.findTaxaAndNames(conf);
|
|
446
|
logSearchResults(pager, Level.DEBUG);
|
|
447
|
assertEquals(1, pager.getRecords().size());
|
|
448
|
|
|
449
|
// ---------------------------------------------------------
|
|
450
|
|
|
451
|
setTaxaAndNamesModes(conf, true, true, false, true, false);
|
|
452
|
pager = taxonService.findTaxaAndNames(conf);
|
|
453
|
logSearchResults(pager, Level.DEBUG);
|
|
454
|
assertEquals(3, pager.getRecords().size());
|
|
455
|
|
|
456
|
setTaxaAndNamesModes(conf, false, true, false, true, false);
|
|
457
|
pager = taxonService.findTaxaAndNames(conf);
|
|
458
|
logSearchResults(pager, Level.DEBUG);
|
|
459
|
assertEquals(2, pager.getRecords().size());
|
|
460
|
|
|
461
|
setTaxaAndNamesModes(conf, true, false, false, true, false);
|
|
462
|
pager = taxonService.findTaxaAndNames(conf);
|
|
463
|
logSearchResults(pager, Level.DEBUG);
|
|
464
|
assertEquals(2, pager.getRecords().size());
|
|
465
|
|
|
466
|
// only misapplied names
|
|
467
|
// - Abies kawakamii sec. Komarov, V. L., Flora SSSR 29
|
|
468
|
setTaxaAndNamesModes(conf, false, false, false, true, false);
|
|
469
|
pager = taxonService.findTaxaAndNames(conf);
|
|
470
|
logSearchResults(pager, Level.DEBUG);
|
|
471
|
assertEquals(1, pager.getRecords().size());
|
|
472
|
|
|
473
|
// =========================================================
|
|
474
|
|
|
475
|
setTaxaAndNamesModes(conf, true, true, true, false, false);
|
|
476
|
pager = taxonService.findTaxaAndNames(conf);
|
|
477
|
logSearchResults(pager, Level.DEBUG);
|
|
478
|
assertEquals(2, pager.getRecords().size());
|
|
479
|
|
|
480
|
|
|
481
|
setTaxaAndNamesModes(conf, false, true, true, false, false);
|
|
482
|
pager = taxonService.findTaxaAndNames(conf);
|
|
483
|
logSearchResults(pager, Level.DEBUG);
|
|
484
|
assertEquals(1, pager.getRecords().size());
|
|
485
|
|
|
486
|
setTaxaAndNamesModes(conf, true, false, true, false, false);
|
|
487
|
pager = taxonService.findTaxaAndNames(conf);
|
|
488
|
logSearchResults(pager, Level.DEBUG);
|
|
489
|
assertEquals(1, pager.getRecords().size());
|
|
490
|
|
|
491
|
setTaxaAndNamesModes(conf, false, false, true, false, false);
|
|
492
|
pager = taxonService.findTaxaAndNames(conf);
|
|
493
|
logSearchResults(pager, Level.DEBUG);
|
|
494
|
assertEquals(0, pager.getRecords().size());
|
|
495
|
|
|
496
|
// ---------------------------------------------------------
|
|
497
|
|
|
498
|
setTaxaAndNamesModes(conf, true, true, false, false, false);
|
|
499
|
pager = taxonService.findTaxaAndNames(conf);
|
|
500
|
logSearchResults(pager, Level.DEBUG);
|
|
501
|
assertEquals(2, pager.getRecords().size());
|
|
502
|
|
|
503
|
setTaxaAndNamesModes(conf, false, true, false, false, false);
|
|
504
|
pager = taxonService.findTaxaAndNames(conf);
|
|
505
|
logSearchResults(pager, Level.DEBUG);
|
|
506
|
assertEquals(1, pager.getRecords().size());
|
|
507
|
|
|
508
|
setTaxaAndNamesModes(conf, true, false, false, false, false);
|
|
509
|
pager = taxonService.findTaxaAndNames(conf);
|
|
510
|
logSearchResults(pager, Level.DEBUG);
|
|
511
|
assertEquals(1, pager.getRecords().size());
|
|
512
|
|
|
513
|
setTaxaAndNamesModes(conf, false, false, false, false, false);
|
|
514
|
pager = taxonService.findTaxaAndNames(conf);
|
|
515
|
logSearchResults(pager, Level.DEBUG);
|
|
516
|
assertEquals(0, pager.getRecords().size());
|
|
517
|
}
|
|
518
|
|
|
519
|
@Test
|
|
520
|
@DataSet
|
|
521
|
public final void testFindTaxaAndNames_CommonName() {
|
|
522
|
// pass 1
|
|
523
|
IFindTaxaAndNamesConfigurator configurator = FindTaxaAndNamesConfiguratorImpl.NewInstance();
|
|
524
|
configurator.setMatchMode(MatchMode.BEGINNING);
|
|
525
|
configurator.setDoTaxa(true);
|
|
526
|
configurator.setDoSynonyms(true);
|
|
527
|
configurator.setDoNamesWithoutTaxa(true);
|
|
528
|
configurator.setDoTaxaByCommonNames(true);
|
|
529
|
configurator.setTitleSearchString("Balsam-Tanne");
|
|
530
|
|
|
531
|
@SuppressWarnings("rawtypes")
|
|
532
|
Pager<IdentifiableEntity> pager = taxonService.findTaxaAndNames(configurator);
|
|
533
|
|
|
534
|
@SuppressWarnings("rawtypes")
|
|
535
|
List<IdentifiableEntity> list = pager.getRecords();
|
|
536
|
assertEquals(1, list.size());
|
|
537
|
configurator.setTitleSearchString("Abies*");
|
|
538
|
configurator.setDoTaxa(false);
|
|
539
|
configurator.setDoSynonyms(false);
|
|
540
|
configurator.setDoNamesWithoutTaxa(false);
|
|
541
|
configurator.setDoTaxaByCommonNames(true);
|
|
542
|
configurator.setDoMisappliedNames(true);
|
|
543
|
configurator.setClassification(classificationService.load(UUID.fromString(CLASSIFICATION_UUID)));
|
|
544
|
pager = taxonService.findTaxaAndNames(configurator);
|
|
545
|
list = pager.getRecords();
|
|
546
|
assertEquals(1, list.size());
|
|
547
|
|
|
548
|
}
|
|
549
|
|
|
550
|
@Test
|
|
551
|
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class)
|
|
552
|
public final void testFindTaxaAndNamesWithHybridFormula() {
|
|
553
|
|
|
554
|
// pass 1
|
|
555
|
IFindTaxaAndNamesConfigurator configurator = FindTaxaAndNamesConfiguratorImpl.NewInstance();
|
|
556
|
configurator.setTitleSearchString("Achillea*");
|
|
557
|
configurator.setMatchMode(MatchMode.BEGINNING);
|
|
558
|
configurator.setDoTaxa(true);
|
|
559
|
configurator.setDoSynonyms(true);
|
|
560
|
configurator.setDoNamesWithoutTaxa(true);
|
|
561
|
configurator.setDoTaxaByCommonNames(true);
|
|
562
|
|
|
563
|
@SuppressWarnings("rawtypes")
|
|
564
|
Pager<IdentifiableEntity> pager = taxonService.findTaxaAndNames(configurator);
|
|
565
|
// Assert.assertEquals("Expecting one taxon",1,pager.getRecords().size());
|
|
566
|
|
|
567
|
}
|
|
568
|
|
|
569
|
/**
|
|
570
|
* Test method for
|
|
571
|
* {@link eu.etaxonomy.cdm.api.service.TaxonServiceImpl#searchByName(java.lang.String, eu.etaxonomy.cdm.model.reference.Reference)}
|
|
572
|
* .
|
|
573
|
*/
|
|
574
|
@Test
|
|
575
|
@DataSet
|
|
576
|
public final void testfindTaxaAndNamesForEditor() {
|
|
577
|
IFindTaxaAndNamesConfigurator configurator = FindTaxaAndNamesConfiguratorImpl.NewInstance();
|
|
578
|
configurator.setTitleSearchString("Abies bor*");
|
|
579
|
configurator.setMatchMode(MatchMode.BEGINNING);
|
|
580
|
configurator.setDoTaxa(true);
|
|
581
|
configurator.setDoSynonyms(false);
|
|
582
|
configurator.setDoNamesWithoutTaxa(true);
|
|
583
|
configurator.setDoTaxaByCommonNames(false);
|
|
584
|
|
|
585
|
@SuppressWarnings("rawtypes")
|
|
586
|
List<UuidAndTitleCache<? extends IdentifiableEntity>> list = taxonService.findTaxaAndNamesForEditor(configurator);
|
|
587
|
|
|
588
|
Assert.assertEquals("Expecting one entity", 1, list.size());
|
|
589
|
|
|
590
|
configurator.setTitleSearchString("silver fir");
|
|
591
|
configurator.setMatchMode(MatchMode.BEGINNING);
|
|
592
|
configurator.setDoTaxa(false);
|
|
593
|
configurator.setDoSynonyms(false);
|
|
594
|
configurator.setDoNamesWithoutTaxa(true);
|
|
595
|
configurator.setDoTaxaByCommonNames(true);
|
|
596
|
|
|
597
|
list = taxonService.findTaxaAndNamesForEditor(configurator);
|
|
598
|
|
|
599
|
Assert.assertEquals("Expecting one entity", 1, list.size());
|
|
600
|
|
|
601
|
}
|
|
602
|
|
|
603
|
|
|
604
|
/**
|
|
605
|
*
|
|
606
|
* @param conf
|
|
607
|
* @param doTaxa
|
|
608
|
* @param doSynonyms
|
|
609
|
* @param doCommonNames
|
|
610
|
* @param doMisappliedNames
|
|
611
|
* @param doNamesWithoutTaxa
|
|
612
|
* @return
|
|
613
|
*/
|
|
614
|
protected IFindTaxaAndNamesConfigurator setTaxaAndNamesModes(
|
|
615
|
IFindTaxaAndNamesConfigurator conf,
|
|
616
|
boolean doTaxa,
|
|
617
|
boolean doSynonyms,
|
|
618
|
boolean doCommonNames,
|
|
619
|
boolean doMisappliedNames,
|
|
620
|
boolean doNamesWithoutTaxa){
|
|
621
|
|
|
622
|
conf.setDoTaxa(doTaxa);
|
|
623
|
conf.setDoSynonyms(doSynonyms);
|
|
624
|
conf.setDoTaxaByCommonNames(doCommonNames);
|
|
625
|
conf.setDoMisappliedNames(doMisappliedNames);
|
|
626
|
conf.setDoNamesWithoutTaxa(doNamesWithoutTaxa);
|
|
627
|
|
|
628
|
return conf;
|
|
629
|
}
|
|
630
|
|
|
631
|
/**
|
|
632
|
* @param pager
|
|
633
|
*/
|
|
634
|
protected void logSearchResults(@SuppressWarnings("rawtypes") Pager<IdentifiableEntity> pager, Level level) {
|
|
635
|
@SuppressWarnings("rawtypes")
|
|
636
|
List<IdentifiableEntity> list = pager.getRecords();
|
|
637
|
logger.debug("number of taxa: " + list.size());
|
|
638
|
|
|
639
|
if (logger.isDebugEnabled()) {
|
|
640
|
for (int i = 0; i < list.size(); i++) {
|
|
641
|
String nameCache = "";
|
|
642
|
if (list.get(i) instanceof TaxonName) {
|
|
643
|
nameCache = ((TaxonName)list.get(i)).getNameCache();
|
|
644
|
} else if (list.get(i) instanceof TaxonBase) {
|
|
645
|
TaxonName taxonName = ((TaxonBase<?>) list.get(i)).getName();
|
|
646
|
nameCache = taxonName.getNameCache();
|
|
647
|
} else {
|
|
648
|
}
|
|
649
|
logger.log(level, list.get(i).getClass() + "(" + i + ")" + ": Name Cache = " + nameCache + ", Title Cache = "
|
|
650
|
+ list.get(i).getTitleCache());
|
|
651
|
}
|
|
652
|
}
|
|
653
|
}
|
|
654
|
|
|
655
|
/**
|
|
656
|
* uncomment @Test annotation to create the dataset for this test
|
|
657
|
*/
|
|
658
|
@Override
|
|
659
|
// @Test
|
|
660
|
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="ClearDBDataSet.xml")
|
|
661
|
public final void createTestDataSet() throws FileNotFoundException {
|
|
662
|
|
|
663
|
Classification europeanAbiesClassification = Classification.NewInstance("European Abies");
|
|
664
|
europeanAbiesClassification.setUuid(UUID.fromString(CLASSIFICATION_UUID));
|
|
665
|
classificationService.save(europeanAbiesClassification);
|
|
666
|
|
|
667
|
Classification alternativeClassification = Classification.NewInstance("Abies alternative");
|
|
668
|
alternativeClassification.setUuid(UUID.fromString(CLASSIFICATION_ALT_UUID));
|
|
669
|
classificationService.save(alternativeClassification);
|
|
670
|
|
|
671
|
Reference sec = ReferenceFactory.newBook();
|
|
672
|
sec.setTitleCache("Kohlbecker, A., Testcase standart views, 2013", true);
|
|
673
|
Reference sec_sensu = ReferenceFactory.newBook();
|
|
674
|
sec_sensu.setTitleCache("Komarov, V. L., Flora SSSR 29", true);
|
|
675
|
referenceService.save(sec);
|
|
676
|
referenceService.save(sec_sensu);
|
|
677
|
|
|
678
|
IBotanicalName n_abies = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());
|
|
679
|
n_abies.setNameCache("Abies", true);
|
|
680
|
Taxon t_abies = Taxon.NewInstance(n_abies, sec);
|
|
681
|
taxonService.save(t_abies);
|
|
682
|
|
|
683
|
IBotanicalName n_abies_alba = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
684
|
n_abies_alba.setNameCache("Abies alba", true);
|
|
685
|
Taxon t_abies_alba = Taxon.NewInstance(n_abies_alba, sec);
|
|
686
|
t_abies_alba.setUuid(UUID.fromString(ABIES_ALBA_UUID));
|
|
687
|
taxonService.save(t_abies_alba);
|
|
688
|
|
|
689
|
IBotanicalName n_abies_subalpina = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
690
|
n_abies_subalpina.setNameCache("Abies subalpina", true);
|
|
691
|
Synonym s_abies_subalpina = Synonym.NewInstance(n_abies_subalpina, sec);
|
|
692
|
taxonService.save(s_abies_subalpina);
|
|
693
|
|
|
694
|
IBotanicalName n_abies_balsamea = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
695
|
n_abies_balsamea.setNameCache("Abies balsamea", true);
|
|
696
|
Taxon t_abies_balsamea = Taxon.NewInstance(n_abies_balsamea, sec);
|
|
697
|
t_abies_balsamea.setUuid(UUID.fromString(ABIES_BALSAMEA_UUID));
|
|
698
|
t_abies_balsamea.addSynonym(s_abies_subalpina, SynonymType.SYNONYM_OF());
|
|
699
|
taxonService.save(t_abies_balsamea);
|
|
700
|
|
|
701
|
IBotanicalName n_abies_grandis = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
702
|
n_abies_grandis.setNameCache("Abies grandis", true);
|
|
703
|
Taxon t_abies_grandis = Taxon.NewInstance(n_abies_grandis, sec);
|
|
704
|
taxonService.save(t_abies_grandis);
|
|
705
|
|
|
706
|
IBotanicalName n_abies_kawakamii = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
707
|
n_abies_kawakamii.setNameCache("Abies kawakamii", true);
|
|
708
|
Taxon t_abies_kawakamii = Taxon.NewInstance(n_abies_kawakamii, sec);
|
|
709
|
t_abies_kawakamii.getTitleCache();
|
|
710
|
taxonService.save(t_abies_kawakamii);
|
|
711
|
|
|
712
|
//
|
|
713
|
// 1 Misapplied Name
|
|
714
|
//
|
|
715
|
// abies_kawakamii_sensu_komarov as missapplied name for t_abies_balsamea
|
|
716
|
Taxon t_abies_kawakamii_sensu_komarov = Taxon.NewInstance(n_abies_kawakamii, sec_sensu);
|
|
717
|
taxonService.save(t_abies_kawakamii_sensu_komarov);
|
|
718
|
t_abies_kawakamii_sensu_komarov.addTaxonRelation(t_abies_balsamea, TaxonRelationshipType.MISAPPLIED_NAME_FOR(), null, null);
|
|
719
|
taxonService.saveOrUpdate(t_abies_kawakamii_sensu_komarov);
|
|
720
|
|
|
721
|
IBotanicalName n_abies_lasiocarpa = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
722
|
n_abies_lasiocarpa.setNameCache("Abies lasiocarpa", true);
|
|
723
|
Taxon t_abies_lasiocarpa = Taxon.NewInstance(n_abies_lasiocarpa, sec);
|
|
724
|
taxonService.save(t_abies_lasiocarpa);
|
|
725
|
|
|
726
|
// add 3 taxa to classifications
|
|
727
|
europeanAbiesClassification.addChildTaxon(t_abies_balsamea, null, null);
|
|
728
|
alternativeClassification.addChildTaxon(t_abies_lasiocarpa, null, null);
|
|
729
|
classificationService.saveOrUpdate(europeanAbiesClassification);
|
|
730
|
classificationService.saveOrUpdate(alternativeClassification);
|
|
731
|
|
|
732
|
//
|
|
733
|
// 2 Names without taxa
|
|
734
|
//
|
|
735
|
TaxonName n_abies_borisiiregis = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
736
|
n_abies_borisiiregis.setNameCache("Abies borisii-regis", true);
|
|
737
|
nameService.save(n_abies_borisiiregis);
|
|
738
|
|
|
739
|
TaxonName n_abies_lasio = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
740
|
n_abies_lasio.setNameCache("Abies lasio", true);
|
|
741
|
nameService.save(n_abies_lasio);
|
|
742
|
|
|
743
|
// A hybrid name not from Abies
|
|
744
|
IBotanicalName n_abies_millefolium_x_Achillea_nobilis = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
745
|
n_abies_millefolium_x_Achillea_nobilis.setNameCache("Achillea millefolium × Achillea nobilis", true);
|
|
746
|
Taxon t_abies_millefolium_x_Achillea_nobilis = Taxon.NewInstance(n_abies_millefolium_x_Achillea_nobilis, sec);
|
|
747
|
taxonService.save(t_abies_millefolium_x_Achillea_nobilis);
|
|
748
|
|
|
749
|
//
|
|
750
|
// Description
|
|
751
|
//
|
|
752
|
TaxonDescription d_abies_alba = TaxonDescription.NewInstance(t_abies_alba);
|
|
753
|
TaxonDescription d_abies_balsamea = TaxonDescription.NewInstance(t_abies_balsamea);
|
|
754
|
|
|
755
|
d_abies_alba.setUuid(UUID.fromString(D_ABIES_ALBA_UUID));
|
|
756
|
d_abies_balsamea.setUuid(UUID.fromString(D_ABIES_BALSAMEA_UUID));
|
|
757
|
|
|
758
|
|
|
759
|
// CommonTaxonName
|
|
760
|
d_abies_alba.addElement(CommonTaxonName.NewInstance("Wei"+UTF8.SHARP_S+"tanne", Language.GERMAN()));
|
|
761
|
d_abies_alba.addElement(CommonTaxonName.NewInstance("silver fir", Language.ENGLISH()));
|
|
762
|
d_abies_alba.addElement(Distribution
|
|
763
|
.NewInstance(
|
|
764
|
germany,
|
|
765
|
PresenceAbsenceTerm.NATIVE()));
|
|
766
|
d_abies_alba.addElement(Distribution
|
|
767
|
.NewInstance(
|
|
768
|
russia,
|
|
769
|
PresenceAbsenceTerm.ABSENT()));
|
|
770
|
|
|
771
|
// TextData
|
|
772
|
d_abies_balsamea
|
|
773
|
.addElement(TextData
|
|
774
|
.NewInstance(
|
|
775
|
"Die Balsam-Tanne (Abies balsamea) ist eine Pflanzenart aus der Gattung der Tannen (Abies). Sie wächst im nordöstlichen Nordamerika, wo sie sowohl Tief- als auch Bergland besiedelt. Sie gilt als relativ anspruchslos gegenüber dem Standort und ist frosthart. In vielen Teilen des natürlichen Verbreitungsgebietes stellt sie die Klimaxbaumart dar.",
|
|
776
|
Language.GERMAN(), null));
|
|
777
|
d_abies_balsamea
|
|
778
|
.addElement(CommonTaxonName
|
|
779
|
.NewInstance(
|
|
780
|
"Balsam-Tanne",
|
|
781
|
Language.GERMAN(), null));
|
|
782
|
|
|
783
|
d_abies_balsamea
|
|
784
|
.addElement(Distribution
|
|
785
|
.NewInstance(
|
|
786
|
canada,
|
|
787
|
PresenceAbsenceTerm.PRESENT()));
|
|
788
|
|
|
789
|
d_abies_balsamea
|
|
790
|
.addElement(Distribution
|
|
791
|
.NewInstance(
|
|
792
|
germany,
|
|
793
|
PresenceAbsenceTerm.NATIVE()));
|
|
794
|
|
|
795
|
d_abies_balsamea
|
|
796
|
.addElement(TextData
|
|
797
|
.NewInstance(
|
|
798
|
TaxonServiceSearchTestUtf8Constants.RUSSIAN_ABIES_ALBA_LONG,
|
|
799
|
Language.RUSSIAN(), null));
|
|
800
|
d_abies_balsamea
|
|
801
|
.addElement(CommonTaxonName
|
|
802
|
.NewInstance(
|
|
803
|
TaxonServiceSearchTestUtf8Constants.RUSSIAN_ABIES_ALBA_SHORT,
|
|
804
|
Language.RUSSIAN(), null));
|
|
805
|
descriptionService.saveOrUpdate(d_abies_balsamea);
|
|
806
|
|
|
807
|
setComplete();
|
|
808
|
endTransaction();
|
|
809
|
|
|
810
|
|
|
811
|
writeDbUnitDataSetFile(new String[] {
|
|
812
|
"TAXONBASE", "TAXONNAME",
|
|
813
|
"TAXONRELATIONSHIP",
|
|
814
|
"REFERENCE", "DESCRIPTIONELEMENTBASE", "DESCRIPTIONBASE",
|
|
815
|
"AGENTBASE", "HOMOTYPICALGROUP",
|
|
816
|
"CLASSIFICATION", "TAXONNODE",
|
|
817
|
"LANGUAGESTRING", "DESCRIPTIONELEMENTBASE_LANGUAGESTRING",
|
|
818
|
"HIBERNATE_SEQUENCES" // IMPORTANT!!!
|
|
819
|
});
|
|
820
|
|
|
821
|
}
|
|
822
|
|
|
823
|
}
|