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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.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.FindByIdentifierDTO;
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import eu.etaxonomy.cdm.api.service.dto.FindByMarkerDTO;
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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.DefinedTerm;
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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.common.TermVocabulary;
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import eu.etaxonomy.cdm.model.common.VocabularyEnum;
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import eu.etaxonomy.cdm.model.name.BotanicalName;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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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.SynonymRelationshipType;
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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.persistence.query.MatchMode;
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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 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(TaxonNameBase.class));
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Class clazz = TaxonNameBase.class;
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int stepSize = 2;
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nameService.updateTitleCache(clazz, stepSize, null, null);
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commit();
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// commitAndStartNewTransaction(new String[]{"TaxonNameBase","TaxonNameBase_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<FindByIdentifierDTO<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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FindByIdentifierDTO<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.getCdmUuid());
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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<FindByIdentifierDTO<TaxonNameBase>> names = nameService.findByIdentifier(
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TaxonNameBase.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<FindByIdentifierDTO<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<FindByIdentifierDTO<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<FindByIdentifierDTO<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<FindByIdentifierDTO<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 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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MarkerType markerType = markerType1;
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Pager<FindByMarkerDTO<Taxon>> taxonPager = taxonService.findByMarker(Taxon.class, markerType, markerValue,
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rootNode, true, 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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FindByMarkerDTO<Taxon> dto = taxonPager.getRecords().get(0);
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FindByMarkerDTO<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().getEntityX());
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Assert.assertEquals(5000, dto.getCdmEntity().getEntityX().getId());
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markerValue = false;
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taxonPager = taxonService.findByMarker(Taxon.class, markerType, markerValue, rootNode, false, 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, 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, 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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rootNode = null;
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markerType = markerType1;
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taxonPager = taxonService.findByMarker(Taxon.class, markerType, markerValue, rootNode, false, null, null, null);
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Assert.assertEquals("Result size for no subtree should be 2", Long.valueOf(2), taxonPager.getCount());
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Pager<FindByMarkerDTO<TaxonBase>> taxonBasePager = taxonService.findByMarker(TaxonBase.class, markerType, markerValue, rootNode, false, null, null, null);
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Assert.assertEquals("Result size for taxa and synonyms without subtree filter with flag = true should be 3", Long.valueOf(3), taxonBasePager.getCount());
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markerValue = null;
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taxonBasePager = taxonService.findByMarker(TaxonBase.class, markerType, markerValue, rootNode, false, null, null, null);
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Assert.assertEquals("Result size for taxa and synonyms without subtree filter with any flag value should be 4", Long.valueOf(4), taxonBasePager.getCount());
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markerValue = true;
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Pager<FindByMarkerDTO<TaxonNameBase>> namePager = nameService.findByMarker(TaxonNameBase.class, markerType, markerValue, false, null, null, null);
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Assert.assertEquals("Result size for names with flag = true should be 1", Long.valueOf(1), namePager.getCount());
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}
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// @Test
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@Override
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public void createTestDataSet() throws FileNotFoundException {
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TermVocabulary<DefinedTerm> voc = vocService.find(VocabularyEnum.IdentifierType.getUuid());
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DefinedTerm identifierType1 = DefinedTerm.NewIdentifierTypeInstance(null, "identifierType1", null);
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voc.addTerm(identifierType1);
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termService.save(identifierType1);
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DefinedTerm identifierType2 = DefinedTerm.NewIdentifierTypeInstance(null, "identifierType2", null);
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voc.addTerm(identifierType2);
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termService.save(identifierType2);
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BotanicalName name = BotanicalName.NewInstance(Rank.SPECIES());
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Taxon tb = Taxon.NewInstance(name, null);
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tb.addIdentifier("ext-1234", identifierType1);
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name.addIdentifier("ext-name12", identifierType2);
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taxonService.saveOrUpdate(tb);
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Taxon tb2 = Taxon.NewInstance(null, null);
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tb2.setTitleCache("Cached taxon", true);
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tb2.addIdentifier("ext-cache1", identifierType2);
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taxonService.saveOrUpdate(tb2);
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Classification classification = Classification.NewInstance("My classification");
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classification.addChildTaxon(tb, null, null);
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classificationService.saveOrUpdate(classification);
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tb2.addSynonymName(null, SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF());
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commitAndStartNewTransaction(null);
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// this will write flat xml file to the same package in the test resources
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// the test file is named after the test class like: TestClassName.xml
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writeDbUnitDataSetFile(new String[] {
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294
|
"TAXONBASE", "TAXONNAMEBASE","IDENTIFIER","TAXONBASE_IDENTIFIER",
|
|
295
|
"TAXONNAMEBASE_IDENTIFIER",
|
|
296
|
"REFERENCE",
|
|
297
|
"CLASSIFICATION", "TAXONNODE",
|
|
298
|
"HOMOTYPICALGROUP",
|
|
299
|
"TERMVOCABULARY",
|
|
300
|
"SYNONYMRELATIONSHIP"
|
|
301
|
}, "xxxx");
|
|
302
|
|
|
303
|
}
|
|
304
|
|
|
305
|
|
|
306
|
}
|