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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 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.Logger;
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import org.junit.Assert;
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import org.junit.Test;
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import org.unitils.database.annotations.Transactional;
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import org.unitils.database.util.TransactionMode;
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import org.unitils.dbunit.annotation.DataSet;
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import org.unitils.dbunit.annotation.ExpectedDataSet;
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import org.unitils.spring.annotation.SpringBeanByType;
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import eu.etaxonomy.cdm.api.service.dto.IdentifiedEntityDTO;
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import eu.etaxonomy.cdm.api.service.dto.MarkedEntityDTO;
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import eu.etaxonomy.cdm.api.service.pager.Pager;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.Identifier;
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import eu.etaxonomy.cdm.model.common.MarkerType;
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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.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.TaxonNode;
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import eu.etaxonomy.cdm.model.term.DefinedTerm;
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import eu.etaxonomy.cdm.model.term.TermVocabulary;
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import eu.etaxonomy.cdm.model.term.VocabularyEnum;
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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.persistence.query.TaxonTitleType;
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import eu.etaxonomy.cdm.test.integration.CdmTransactionalIntegrationTest;
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/**
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* @author a.mueller
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*
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*/
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@Transactional(TransactionMode.DISABLED)
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public class IdentifiableServiceBaseTest extends CdmTransactionalIntegrationTest {
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(IdentifiableServiceBaseTest.class);
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@SpringBeanByType
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private INameService nameService;
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@SpringBeanByType
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private ITermService termService;
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@SpringBeanByType
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private IVocabularyService vocService;
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@SpringBeanByType
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private ITaxonService taxonService;
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@SpringBeanByType
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private IReferenceService referenceService;
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@SpringBeanByType
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private IClassificationService classificationService;
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/****************** TESTS *****************************/
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@Test
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public final void voidTestSeriveExists(){
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Assert.assertNotNull("Service shoulb be initialized", nameService);
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}
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@Test
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@DataSet
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@ExpectedDataSet
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public final void testUpdateTitleCache() {
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Assert.assertEquals("There should be 5 TaxonNames in the data set", 5, nameService.count(TaxonName.class));
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Class<TaxonName> clazz = TaxonName.class;
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int stepSize = 2;
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nameService.updateCaches(clazz, stepSize, null, null);
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commit();
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// commitAndStartNewTransaction(new String[]{"TaxonName","TaxonName_AUD"});
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}
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@Test
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@DataSet(value="IdentifiableServiceBaseTest.testFindByIdentifierOrMarker.xml")
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public final void testFindByIdentifier(){
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UUID uuidIdentifierType1 = UUID.fromString("02bb62db-a229-4eeb-83e6-a9a093943d5e");
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UUID uuidIdentifierType2 = UUID.fromString("ef6e960f-5289-456c-b25c-cff7f4de2f63");
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DefinedTerm it1 = (DefinedTerm)termService.find(uuidIdentifierType1);
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Assert.assertNotNull("identifier type must not be null", it1);
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boolean includeEntity = true;
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Pager<IdentifiedEntityDTO<Taxon>> taxonPager = taxonService.findByIdentifier(Taxon.class, "ext-1234", it1, null, includeEntity, null, null, null);
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Assert.assertTrue("Result should not be empty", taxonPager.getCount() == 1);
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IdentifiedEntityDTO<Taxon>.CdmEntity entity = taxonPager.getRecords().get(0).getCdmEntity();
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Taxon taxon = entity.getEntity();
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Assert.assertEquals(UUID.fromString("888cded1-cadc-48de-8629-e32927919879"), taxon.getUuid());
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Assert.assertEquals(UUID.fromString("888cded1-cadc-48de-8629-e32927919879"), entity.getUuid());
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Assert.assertEquals("Taxon should have 1 identifier", 1, taxon.getIdentifiers().size());
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Identifier<?> identifier = taxon.getIdentifiers().get(0);
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DefinedTerm type = CdmBase.deproxy(identifier.getType(), DefinedTerm.class);
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Assert.assertEquals(uuidIdentifierType1, type.getUuid());
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Pager<IdentifiedEntityDTO<TaxonName>> names = nameService.findByIdentifier(
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TaxonName.class, "ext-1234", null, null, includeEntity, null, null, null);
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Assert.assertTrue("Identifier does not exist for TaxonName", names.getCount() == 0);
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taxonPager = taxonService.findByIdentifier(null, "ext-1234", null, null, includeEntity, null, null, null);
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Assert.assertEquals("Result size for 'ext-1234' should be 1", 1, taxonPager.getRecords().size());
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taxonPager = taxonService.findByIdentifier(Taxon.class, null, null, null, includeEntity, null, null, null);
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Assert.assertEquals("Result should not be empty", 2 , taxonPager.getRecords().size());
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//includeEntity
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includeEntity = false;
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taxonPager = taxonService.findByIdentifier(Taxon.class, "ext-1234", it1, null, includeEntity, null, null, null);
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entity = taxonPager.getRecords().get(0).getCdmEntity();
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Assert.assertNull("Taxon must not be returned with includeEntity = false", entity.getEntity());
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//Matchmode
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includeEntity = false;
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MatchMode matchmode = null;
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taxonPager = taxonService.findByIdentifier(Taxon.class, "123", null, matchmode, includeEntity, null, null, null);
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Assert.assertTrue("Result size for '123' should be 0", taxonPager.getCount() == 0);
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taxonPager = taxonService.findByIdentifier(Taxon.class, "123", null, MatchMode.EXACT, includeEntity, null, null, null);
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Assert.assertTrue("Result size for '123' should be 0", taxonPager.getCount() == 0);
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taxonPager = taxonService.findByIdentifier(Taxon.class, "123", null, MatchMode.ANYWHERE, includeEntity, null, null, null);
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Assert.assertTrue("Result size for '123' should be 1", taxonPager.getCount() == 1);
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taxonPager = taxonService.findByIdentifier(Taxon.class, "123", null, MatchMode.BEGINNING, includeEntity, null, null, null);
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Assert.assertTrue("Result size for '123' should be 0", taxonPager.getCount() == 0);
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taxonPager = taxonService.findByIdentifier(Taxon.class, "ext", null, MatchMode.BEGINNING, includeEntity, null, null, null);
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Assert.assertTrue("Result size for 'ext' should be 1", taxonPager.getCount() == 2);
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//Paging
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taxonPager = taxonService.findByIdentifier(null, "ext", null, MatchMode.BEGINNING, includeEntity, null, null, null);
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Assert.assertEquals("Total result size for starts with 'ext' should be 4", 4, taxonPager.getRecords().size());
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taxonPager = taxonService.findByIdentifier(null, "ext", null, MatchMode.BEGINNING, includeEntity, 2, 1, null);
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Assert.assertEquals("Total result size for starts with 'ext' should be 4", Long.valueOf(4), taxonPager.getCount());
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Assert.assertEquals("Result size for starts with 'ext' second page should be 2", Integer.valueOf(2), taxonPager.getPageSize());
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Assert.assertEquals("The third taxon (first on second page) should be ext-syn1", "ext-syn1", taxonPager.getRecords().get(0).getIdentifier().getIdentifier());
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taxonPager = taxonService.findByIdentifier(Taxon.class, "ext", null, MatchMode.BEGINNING, includeEntity, null, null, null);
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Assert.assertTrue("Result size for 'ext' should be 2", taxonPager.getCount() == 2);
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}
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@Test
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@DataSet(value="IdentifiableServiceBaseTest.testFindByIdentifierOrMarker.xml")
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public final void testFindByIdentifierClassification(){
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//classification Filter
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Classification classification = classificationService.find(5000);
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TaxonNode rootNode = classification.getRootNode();
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Pager<IdentifiedEntityDTO<Taxon>> taxonPager = taxonService.findByIdentifier(Taxon.class, "ext-1234", null, rootNode, MatchMode.EXACT, false, null, null, null);
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Assert.assertEquals("Result size for 'ext' should be 1", Long.valueOf(1), taxonPager.getCount());
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Assert.assertEquals("Result size for 'ext' should be 1", 1, taxonPager.getRecords().size());
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Pager<IdentifiedEntityDTO<Taxon>> taxPager = taxonService.findByIdentifier(Taxon.class, "ext-cache1", null, rootNode, MatchMode.EXACT, false, null, null, null);
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Assert.assertEquals("Result size for 'ext' should be 0", Long.valueOf(0), taxPager.getCount());
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Assert.assertEquals("Result size for 'ext' should be 0", 0, taxPager.getRecords().size());
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rootNode = null; //check against missing filter
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taxPager = taxonService.findByIdentifier(Taxon.class, "ext-cache1", null, rootNode, MatchMode.EXACT, false, null, null, null);
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Assert.assertEquals("Result size for 'ext-cache1' without filter should be 1", Long.valueOf(1), taxPager.getCount());
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Assert.assertEquals("Result size for 'ext-cache1' without filter should be 1", 1, taxPager.getRecords().size());
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//TaxonBase
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rootNode = classification.getRootNode();
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Pager<IdentifiedEntityDTO<TaxonBase>> tbPager = taxonService.findByIdentifier(TaxonBase.class, "ext-1234", null, rootNode, MatchMode.EXACT, false, null, null, null);
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Assert.assertEquals("Result size for 'ext' should be 1", Long.valueOf(1), tbPager.getCount());
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Assert.assertEquals("Result size for 'ext' should be 1", 1, tbPager.getRecords().size());
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tbPager = taxonService.findByIdentifier(TaxonBase.class, "ext-cache1", null, rootNode, MatchMode.EXACT, false, null, null, null);
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Assert.assertEquals("Result size for 'ext' should be 0", Long.valueOf(0), tbPager.getCount());
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Assert.assertEquals("Result size for 'ext' should be 0", 0, tbPager.getRecords().size());
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//Synonym
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Pager<IdentifiedEntityDTO<Synonym>> synPager = taxonService.findByIdentifier(Synonym.class, "ext-syn", null, rootNode, MatchMode.BEGINNING, false, null, null, null);
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Assert.assertEquals("1 Synonym should be linked to the according classification", Long.valueOf(1), synPager.getCount());
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Assert.assertEquals("1 Synonym should be linked to the according classification", 1, synPager.getRecords().size());
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}
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@Test
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@DataSet(value="IdentifiableServiceBaseTest.testFindByIdentifierOrMarker.xml")
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public final void testListByIdentifier(){
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//classification Filter
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List<IdentifiedEntityDTO<Taxon>> taxonPager = taxonService.listByIdentifier(Taxon.class, "ext-1234", null, MatchMode.EXACT, false, null, null);//.listByIdentifier(Taxon.class, "ext-1234", null, rootNode, MatchMode.EXACT, false, null, null);
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Assert.assertEquals("Result size for 'ext' should be 1", 1, taxonPager.size());
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// Assert.assertEquals("Result size for 'ext' should be 1", 1, taxonPager.getRecords().size());
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taxonPager = taxonService.listByIdentifier(Taxon.class, "ext-1234", null, MatchMode.EXACT, true, null, null);//.listByIdentifier(Taxon.class, "ext-1234", null, rootNode, MatchMode.EXACT, false, null, null);
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Assert.assertEquals("Result size for 'ext' should be 1", 1, taxonPager.size());
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IdentifiedEntityDTO<Taxon> identifierDTO = taxonPager.get(0);
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Assert.assertTrue(identifierDTO.getCdmEntity() instanceof UuidAndTitleCache);
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List<IdentifiedEntityDTO<Taxon>> taxPager = taxonService.listByIdentifier(Taxon.class, "ext-cache1", null, MatchMode.EXACT, false, null, null);
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Assert.assertEquals("Result size for 'ext' should be 1", 1, taxPager.size());
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List<IdentifiedEntityDTO<TaxonBase>> tbPager = taxonService.listByIdentifier(TaxonBase.class, "ext-1234", null, MatchMode.EXACT, false, null, null);
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Assert.assertEquals("Result size for 'ext' should be 1",1, tbPager.size());
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//Synonym
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List<IdentifiedEntityDTO<Synonym>> synPager = taxonService.listByIdentifier(Synonym.class, "ext-syn", null, MatchMode.BEGINNING, false, null, null);
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Assert.assertEquals("There should be 2 synonyms with identifier ext-syn", 2, synPager.size());
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List<IdentifiedEntityDTO<Reference>> referenceList = referenceService.listByIdentifier(Reference.class, "123", null, MatchMode.EXACT, false, null, null);//.listByIdentifier(Taxon.class, "ext-1234", null, rootNode, MatchMode.EXACT, false, null, null);
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Assert.assertEquals("Result size for 'ext' should be 1", 1, taxonPager.size());
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referenceList = referenceService.listByIdentifier(Reference.class, "123", null, MatchMode.EXACT, true, null, null);//.listByIdentifier(Taxon.class, "ext-1234", null, rootNode, MatchMode.EXACT, false, null, null);
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Assert.assertEquals("Result size for 'ext' should be 1", 1, referenceList.size());
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IdentifiedEntityDTO<Reference> identifierDTOReference = referenceList.get(0);
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Assert.assertTrue(identifierDTO.getCdmEntity() instanceof UuidAndTitleCache);
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}
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@Test
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@DataSet(value="IdentifiableServiceBaseTest.testFindByIdentifierOrMarker.xml")
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public final void testFindByMarker(){
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//classification Filter
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Classification classification = classificationService.find(5000);
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TaxonNode rootNode = classification.getRootNode();
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Boolean markerValue = true;
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UUID uuidMarkerTypeCompleted = MarkerType.uuidComplete;
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UUID uuidMarkerTypeDoubtful = UUID.fromString("b51325c8-05fe-421a-832b-d86fc249ef6e");
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MarkerType markerType1 = (MarkerType)termService.find(uuidMarkerTypeCompleted);
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MarkerType noMarkerType = null;
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MarkerType markerType2 = (MarkerType)termService.find(uuidMarkerTypeDoubtful);
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Assert.assertNotNull(markerType2);
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TaxonTitleType titleType = TaxonTitleType.TAXON;
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MarkerType markerType = markerType1;
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Pager<MarkedEntityDTO<Taxon>> taxonPager = taxonService.findByMarker(Taxon.class, markerType, markerValue,
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rootNode, true, titleType, null, null, null);
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Assert.assertEquals("Result size for 'marker1=true' should be 1", Long.valueOf(1), taxonPager.getCount());
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Assert.assertEquals("Result size for 'marker1=true' should be 1", 1, taxonPager.getRecords().size());
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MarkedEntityDTO<Taxon> dto = taxonPager.getRecords().get(0);
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MarkedEntityDTO<Taxon>.Marker marker = dto.getMarker();
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Assert.assertTrue("Flag must be true", marker.getFlag());
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Assert.assertEquals("Flag must be true", uuidMarkerTypeCompleted, marker.getTypeUuid());
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Assert.assertNotNull("the CDM entity in the dto must not be empty if includeEntity=true", dto.getCdmEntity().getEntity());
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Assert.assertEquals(5000, dto.getCdmEntity().getEntity().getId());
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markerValue = false;
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taxonPager = taxonService.findByMarker(Taxon.class, markerType, markerValue, rootNode, false, titleType, null, null, null);
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Assert.assertEquals("Result size for 'marker1=false' should be 0", Long.valueOf(0), taxonPager.getCount());
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markerValue = true;
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markerType = noMarkerType;
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taxonPager = taxonService.findByMarker(Taxon.class, markerType, markerValue, rootNode, false, titleType, null, null, null);
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Assert.assertEquals("Result size for not existing marker type should be 0", Long.valueOf(0), taxonPager.getCount());
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markerType = markerType2;
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taxonPager = taxonService.findByMarker(Taxon.class, markerType, markerValue, rootNode, false, titleType, null, null, null);
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Assert.assertEquals("Result size for markerType2 should be 0", Long.valueOf(0), taxonPager.getCount());
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|
283
|
rootNode = null;
|
|
284
|
markerType = markerType1;
|
|
285
|
taxonPager = taxonService.findByMarker(Taxon.class, markerType, markerValue, rootNode, false, titleType, null, null, null);
|
|
286
|
Assert.assertEquals("Result size for no subtree should be 2", Long.valueOf(2), taxonPager.getCount());
|
|
287
|
|
|
288
|
Pager<MarkedEntityDTO<TaxonBase>> taxonBasePager = taxonService.findByMarker(TaxonBase.class, markerType, markerValue, rootNode, false, titleType, null, null, null);
|
|
289
|
Assert.assertEquals("Result size for taxa and synonyms without subtree filter with flag = true should be 3", Long.valueOf(3), taxonBasePager.getCount());
|
|
290
|
|
|
291
|
markerValue = null;
|
|
292
|
taxonBasePager = taxonService.findByMarker(TaxonBase.class, markerType, markerValue, rootNode, false, titleType, null, null, null);
|
|
293
|
Assert.assertEquals("Result size for taxa and synonyms without subtree filter with any flag value should be 4", Long.valueOf(4), taxonBasePager.getCount());
|
|
294
|
|
|
295
|
markerValue = true;
|
|
296
|
Pager<MarkedEntityDTO<TaxonName>> namePager = nameService.findByMarker(TaxonName.class, markerType, markerValue, false, null, null, null);
|
|
297
|
Assert.assertEquals("Result size for names with flag = true should be 1", Long.valueOf(1), namePager.getCount());
|
|
298
|
|
|
299
|
}
|
|
300
|
|
|
301
|
|
|
302
|
|
|
303
|
// @Test
|
|
304
|
@Override
|
|
305
|
public void createTestDataSet() throws FileNotFoundException {
|
|
306
|
TermVocabulary<DefinedTerm> voc = vocService.find(VocabularyEnum.IdentifierType.getUuid());
|
|
307
|
|
|
308
|
DefinedTerm identifierType1 = DefinedTerm.NewIdentifierTypeInstance(null, "identifierType1", null);
|
|
309
|
voc.addTerm(identifierType1);
|
|
310
|
termService.save(identifierType1);
|
|
311
|
DefinedTerm identifierType2 = DefinedTerm.NewIdentifierTypeInstance(null, "identifierType2", null);
|
|
312
|
voc.addTerm(identifierType2);
|
|
313
|
termService.save(identifierType2);
|
|
314
|
|
|
315
|
|
|
316
|
IBotanicalName name = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
317
|
Taxon tb = Taxon.NewInstance(name, null);
|
|
318
|
tb.addIdentifier("ext-1234", identifierType1);
|
|
319
|
name.addIdentifier("ext-name12", identifierType2);
|
|
320
|
taxonService.saveOrUpdate(tb);
|
|
321
|
|
|
322
|
Taxon tb2 = Taxon.NewInstance(null, null);
|
|
323
|
tb2.setTitleCache("Cached taxon", true);
|
|
324
|
tb2.addIdentifier("ext-cache1", identifierType2);
|
|
325
|
taxonService.saveOrUpdate(tb2);
|
|
326
|
|
|
327
|
Classification classification = Classification.NewInstance("My classification");
|
|
328
|
classification.addChildTaxon(tb, null, null);
|
|
329
|
classificationService.saveOrUpdate(classification);
|
|
330
|
|
|
331
|
tb2.addSynonymName(null, SynonymType.HOMOTYPIC_SYNONYM_OF());
|
|
332
|
|
|
333
|
commitAndStartNewTransaction(null);
|
|
334
|
|
|
335
|
// this will write flat xml file to the same package in the test resources
|
|
336
|
// the test file is named after the test class like: TestClassName.xml
|
|
337
|
writeDbUnitDataSetFile(new String[] {
|
|
338
|
"TAXONBASE", "TAXONNAME","IDENTIFIER","TAXONBASE_IDENTIFIER",
|
|
339
|
"TAXONNAME_IDENTIFIER",
|
|
340
|
"REFERENCE",
|
|
341
|
"CLASSIFICATION", "TAXONNODE",
|
|
342
|
"HOMOTYPICALGROUP",
|
|
343
|
"TERMVOCABULARY"
|
|
344
|
}, "xxxx", true);
|
|
345
|
|
|
346
|
}
|
|
347
|
|
|
348
|
|
|
349
|
}
|