Revision b3c0ff0a
Added by Andreas Müller almost 8 years ago
cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/TaxonServiceImplTest.java | ||
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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 static org.junit.Assert.assertNull; |
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import static org.junit.Assert.assertTrue; |
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import java.io.FileNotFoundException; |
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import java.util.ArrayList; |
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import java.util.Iterator; |
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import java.util.List; |
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import java.util.Set; |
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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.dbunit.annotation.DataSet; |
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import org.unitils.spring.annotation.SpringBeanByType; |
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import eu.etaxonomy.cdm.api.service.config.IncludedTaxonConfiguration; |
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import eu.etaxonomy.cdm.api.service.config.NameDeletionConfigurator; |
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import eu.etaxonomy.cdm.api.service.config.NodeDeletionConfigurator.ChildHandling; |
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import eu.etaxonomy.cdm.api.service.config.SynonymDeletionConfigurator; |
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import eu.etaxonomy.cdm.api.service.config.TaxonDeletionConfigurator; |
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import eu.etaxonomy.cdm.api.service.dto.IncludedTaxaDTO; |
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import eu.etaxonomy.cdm.api.service.exception.HomotypicalGroupChangeException; |
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import eu.etaxonomy.cdm.datagenerator.TaxonGenerator; |
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import eu.etaxonomy.cdm.model.common.CdmBase; |
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import eu.etaxonomy.cdm.model.common.IdentifiableSource; |
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import eu.etaxonomy.cdm.model.common.Marker; |
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import eu.etaxonomy.cdm.model.common.MarkerType; |
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import eu.etaxonomy.cdm.model.common.OriginalSourceType; |
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import eu.etaxonomy.cdm.model.common.RelationshipBase; |
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase; |
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import eu.etaxonomy.cdm.model.description.IndividualsAssociation; |
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import eu.etaxonomy.cdm.model.description.TaxonDescription; |
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import eu.etaxonomy.cdm.model.name.BotanicalName; |
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import eu.etaxonomy.cdm.model.name.HomotypicalGroup; |
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import eu.etaxonomy.cdm.model.name.NameRelationship; |
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import eu.etaxonomy.cdm.model.name.NameRelationshipType; |
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import eu.etaxonomy.cdm.model.name.NonViralName; |
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import eu.etaxonomy.cdm.model.name.Rank; |
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import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit; |
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import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent; |
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import eu.etaxonomy.cdm.model.occurrence.FieldUnit; |
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase; |
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType; |
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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.SynonymRelationship; |
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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.model.taxon.TaxonRelationship; |
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType; |
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import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy; |
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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.mueller |
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*/ |
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public class TaxonServiceImplTest extends CdmTransactionalIntegrationTest { |
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private static final Logger logger = Logger.getLogger(TaxonServiceImplTest.class); |
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@SpringBeanByType |
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private ITaxonService service; |
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@SpringBeanByType |
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private INameService nameService; |
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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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@SpringBeanByType |
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private ITaxonNodeService nodeService; |
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@SpringBeanByType |
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private IDescriptionService descriptionService; |
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@SpringBeanByType |
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private IMarkerService markerService; |
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@SpringBeanByType |
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private IEventBaseService eventService; |
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@SpringBeanByType |
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private IOccurrenceService occurenceService; |
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private Synonym synonym; |
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private Synonym synonym2; |
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private Taxon taxWithSyn; |
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private Taxon tax2WithSyn; |
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private Taxon taxWithoutSyn; |
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private UUID uuidSyn; |
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private UUID uuidTaxWithoutSyn; |
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private UUID uuidSyn2; |
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private UUID uuidTaxWithSyn; |
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/****************** TESTS *****************************/ |
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/** |
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* Test method for {@link eu.etaxonomy.cdm.api.service.TaxonServiceImpl#getTaxonByUuid(java.util.UUID)}. |
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*/ |
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@Test |
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public final void testGetTaxonByUuid() { |
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Taxon expectedTaxon = Taxon.NewInstance(null, null); |
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UUID uuid = service.save(expectedTaxon).getUuid(); |
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TaxonBase<?> actualTaxon = service.find(uuid); |
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assertEquals(expectedTaxon, actualTaxon); |
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} |
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/** |
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* Test method for {@link eu.etaxonomy.cdm.api.service.TaxonServiceImpl#saveTaxon(eu.etaxonomy.cdm.model.taxon.TaxonBase)}. |
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*/ |
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@Test |
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public final void testSaveTaxon() { |
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Taxon expectedTaxon = Taxon.NewInstance(null, null); |
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UUID uuid = service.save(expectedTaxon).getUuid(); |
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TaxonBase<?> actualTaxon = service.find(uuid); |
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assertEquals(expectedTaxon, actualTaxon); |
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} |
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@Test |
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public final void testSaveOrUpdateTaxon() { |
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Taxon expectedTaxon = Taxon.NewInstance(null, null); |
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UUID uuid = service.save(expectedTaxon).getUuid(); |
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TaxonBase<?> actualTaxon = service.find(uuid); |
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assertEquals(expectedTaxon, actualTaxon); |
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actualTaxon.setName(BotanicalName.NewInstance(Rank.SPECIES())); |
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try{ |
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service.saveOrUpdate(actualTaxon); |
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}catch(Exception e){ |
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Assert.fail(); |
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} |
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} |
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/** |
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* Test method for {@link eu.etaxonomy.cdm.api.service.TaxonServiceImpl#removeTaxon(eu.etaxonomy.cdm.model.taxon.TaxonBase)}. |
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*/ |
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@Test |
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public final void testRemoveTaxon() { |
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Taxon taxon = Taxon.NewInstance(BotanicalName.NewInstance(Rank.UNKNOWN_RANK()), null); |
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UUID uuid = service.save(taxon).getUuid(); |
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// try { |
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service.deleteTaxon(taxon.getUuid(), null, null); |
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/*} catch (DataChangeNoRollbackException e) { |
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// TODO Auto-generated catch block |
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e.printStackTrace(); |
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}*/ |
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TaxonBase<?> actualTaxon = service.find(uuid); |
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assertNull(actualTaxon); |
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} |
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@Test |
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public final void testMakeTaxonSynonym() { |
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try { |
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createTestDataSet(); |
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} catch (FileNotFoundException e) { |
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// TODO Auto-generated catch block |
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e.printStackTrace(); |
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} |
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service.swapSynonymAndAcceptedTaxon(synonym, taxWithSyn); |
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// find forces flush |
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Taxon tax = (Taxon)service.find(uuidTaxWithSyn); |
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tax.removeSynonym(synonym); |
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tax.addHomotypicSynonym(synonym, null, null); |
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service.saveOrUpdate(tax); |
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TaxonBase<?> syn = service.find(uuidSyn); |
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assertTrue(tax.getName().getTitleCache().equals("Test2")); |
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HomotypicalGroup groupTest = tax.getHomotypicGroup(); |
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HomotypicalGroup groupTest2 = syn.getHomotypicGroup(); |
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assertEquals(groupTest, groupTest2); |
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} |
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@Test |
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public final void testChangeSynonymToAcceptedTaxon(){ |
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try { |
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createTestDataSet(); |
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} catch (FileNotFoundException e1) { |
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// TODO Auto-generated catch block |
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e1.printStackTrace(); |
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} |
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Taxon taxon = null; |
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try { |
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taxon = service.changeSynonymToAcceptedTaxon(synonym, taxWithSyn, true, true, null, null); |
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} catch (HomotypicalGroupChangeException e) { |
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Assert.fail("Invocation of change method should not throw an exception"); |
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} |
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taxWithSyn = null; |
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//test flush (resave deleted object) |
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TaxonBase<?> syn = service.find(uuidSyn); |
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taxWithSyn = (Taxon)service.find(uuidTaxWithSyn); |
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Taxon taxNew = (Taxon)service.find(taxon.getUuid()); |
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assertNull(syn); |
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assertNotNull(taxWithSyn); |
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assertNotNull(taxNew); |
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Assert.assertEquals("New taxon should have 1 synonym relationship (the old homotypic synonym)", 1, taxon.getSynonymRelations().size()); |
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} |
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@Test |
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public final void testChangeSynonymToAcceptedTaxonSynonymForTwoTaxa(){ |
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try { |
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createTestDataSet(); |
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} catch (FileNotFoundException e1) { |
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// TODO Auto-generated catch block |
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e1.printStackTrace(); |
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} |
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Taxon taxon = null; |
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try { |
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taxon = service.changeSynonymToAcceptedTaxon(synonym, taxWithSyn, true, true, null, null); |
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service.save(taxon); |
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} catch (HomotypicalGroupChangeException e) { |
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Assert.fail("Invocation of change method should not throw an exception"); |
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} |
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taxWithSyn = null; |
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tax2WithSyn = null; |
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//test flush (resave deleted object) |
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TaxonBase<?> syn = service.find(uuidSyn); |
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taxWithSyn = (Taxon)service.find(uuidTaxWithSyn); |
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Taxon taxNew = (Taxon)service.find(taxon.getUuid()); |
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assertNull(syn); |
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assertNotNull(taxWithSyn); |
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assertNotNull(taxNew); |
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// Assert.assertEquals("New taxon should have 1 synonym relationship (the old homotypic synonym)", 1, taxon.getSynonymRelations().size()); |
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} |
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/** |
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* Old implementation taken from {@link TaxonServiceImplBusinessTest} for old version of method. |
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* Test method for {@link eu.etaxonomy.cdm.api.service.TaxonServiceImpl#moveSynonymToAnotherTaxon(eu.etaxonomy.cdm.model.taxon.SynonymRelationship, eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType, eu.etaxonomy.cdm.model.reference.Reference, java.lang.String)}. |
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*/ |
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@Test |
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public final void testMoveSynonymToAnotherTaxon_OLD() { |
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SynonymRelationshipType heteroTypicSynonymRelationshipType = SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF(); |
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Reference reference = ReferenceFactory.newGeneric(); |
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String referenceDetail = "test"; |
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NonViralName<?> t1n = NonViralName.NewInstance(null); |
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Taxon t1 = Taxon.NewInstance(t1n, reference); |
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NonViralName<?> t2n = NonViralName.NewInstance(null); |
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Taxon t2 = Taxon.NewInstance(t2n, reference); |
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NonViralName<?> s1n = NonViralName.NewInstance(null); |
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Synonym s1 = Synonym.NewInstance(s1n, reference); |
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t1.addSynonym(s1, heteroTypicSynonymRelationshipType); |
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service.saveOrUpdate(t1); |
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SynonymRelationship synonymRelation = t1.getSynonymRelations().iterator().next(); |
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boolean keepReference = false; |
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boolean moveHomotypicGroup = false; |
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try { |
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service.moveSynonymToAnotherTaxon(synonymRelation, t2, moveHomotypicGroup, heteroTypicSynonymRelationshipType, reference, referenceDetail, keepReference); |
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} catch (HomotypicalGroupChangeException e) { |
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Assert.fail("Method call should not throw exception"); |
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} |
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Assert.assertTrue("t1 should have no synonym relationships", t1.getSynonymRelations().isEmpty()); |
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Set<SynonymRelationship> synonymRelations = t2.getSynonymRelations(); |
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Assert.assertTrue("t2 should have exactly one synonym relationship", synonymRelations.size() == 1); |
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synonymRelation = synonymRelations.iterator().next(); |
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Assert.assertEquals(t2, synonymRelation.getAcceptedTaxon()); |
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Assert.assertEquals(heteroTypicSynonymRelationshipType, synonymRelation.getType()); |
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Assert.assertEquals(reference, synonymRelation.getCitation()); |
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Assert.assertEquals(referenceDetail, synonymRelation.getCitationMicroReference()); |
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} |
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@Test |
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@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="TaxonServiceImplTest.testMoveSynonymToAnotherTaxon.xml") |
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public final void testMoveSynonymToAnotherTaxon() throws Exception { |
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final String[] tableNames = new String[]{"SynonymRelationship"}; |
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// printDataSet(System.err, new String[]{"AgentBase", "TaxonBase"}); |
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// printDataSet(System.err, new String[]{"TaxonNode"}); |
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UUID uuidNewTaxon = UUID.fromString("2d9a642d-5a82-442d-8fec-95efa978e8f8"); |
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UUID uuidOldTaxon = UUID.fromString("c47fdb72-f32c-452e-8305-4b44f01179d0"); |
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UUID uuidSyn1 = UUID.fromString("7da85381-ad9d-4886-9d4d-0eeef40e3d88"); |
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UUID uuidSyn3 = UUID.fromString("3fba2b22-22ae-4291-af67-faab748a5232"); |
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UUID uuidSyn4 = UUID.fromString("f9b589c7-50cf-4df2-a52e-1b85eb7e4805"); |
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UUID uuidSyn5 = UUID.fromString("fcc0bcf8-8bac-43bd-9508-1e97821587dd"); |
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UUID uuidSyn6 = UUID.fromString("0ccd4e7c-6fbd-4b7c-bd47-29e45b92f34b"); |
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UUID uuidRef1 = UUID.fromString("336f9b38-698c-45d7-be7b-993ed3355bdc"); |
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UUID uuidRef2 = UUID.fromString("c8f49d1a-69e1-48a3-98bb-45d61f3da3e7"); |
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boolean moveHomotypicGroup = true; |
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SynonymRelationshipType newSynonymRelationshipType = null; |
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boolean keepReference = true; |
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Reference newReference = null; |
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String newReferenceDetail = null; |
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Taxon newTaxon = (Taxon)service.load(uuidNewTaxon); |
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Synonym homotypicSynonym = (Synonym)service.load(uuidSyn1); |
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Assert.assertNotNull("Synonym should exist", homotypicSynonym); |
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Assert.assertEquals("Synonym should have 1 relation", 1, homotypicSynonym.getSynonymRelations().size()); |
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SynonymRelationship rel = homotypicSynonym.getSynonymRelations().iterator().next(); |
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Assert.assertEquals("Accepted taxon of single relation should be the old taxon", uuidOldTaxon, rel.getAcceptedTaxon().getUuid()); |
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Taxon oldTaxon = rel.getAcceptedTaxon(); |
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try { |
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service.moveSynonymToAnotherTaxon(rel, newTaxon, moveHomotypicGroup, newSynonymRelationshipType, newReference, newReferenceDetail, keepReference); |
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Assert.fail("Homotypic synonym move to other taxon should throw an exception"); |
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} catch (HomotypicalGroupChangeException e) { |
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if (e.getMessage().contains("Synonym is in homotypic group with accepted taxon and other synonym(s). First remove synonym from homotypic group of accepted taxon before moving to other taxon")){ |
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//OK |
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commitAndStartNewTransaction(tableNames); |
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}else{ |
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Assert.fail("Unexpected exception occurred: " + e.getMessage()); |
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} |
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} |
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//Asserts |
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homotypicSynonym = (Synonym)service.load(uuidSyn1); |
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Assert.assertNotNull("Synonym should still exist", homotypicSynonym); |
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Assert.assertEquals("Synonym should still have 1 relation", 1, homotypicSynonym.getSynonymRelations().size()); |
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rel = homotypicSynonym.getSynonymRelations().iterator().next(); |
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Assert.assertEquals("Accepted taxon of single relation should be the old taxon", oldTaxon, rel.getAcceptedTaxon()); |
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//test heterotypic synonym with other synonym in homotypic group |
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newTaxon = (Taxon)service.load(uuidNewTaxon); |
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Synonym heterotypicSynonym = (Synonym)service.load(uuidSyn3); |
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Assert.assertNotNull("Synonym should exist", heterotypicSynonym); |
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Assert.assertEquals("Synonym should have 1 relation", 1, heterotypicSynonym.getSynonymRelations().size()); |
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rel = heterotypicSynonym.getSynonymRelations().iterator().next(); |
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Assert.assertEquals("Accepted taxon of single relation should be the old taxon", uuidOldTaxon, rel.getAcceptedTaxon().getUuid()); |
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oldTaxon = rel.getAcceptedTaxon(); |
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moveHomotypicGroup = false; |
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try { |
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service.moveSynonymToAnotherTaxon(rel, newTaxon, moveHomotypicGroup, newSynonymRelationshipType, newReference, newReferenceDetail, keepReference); |
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Assert.fail("Heterotypic synonym move to other taxon should throw an exception"); |
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} catch (HomotypicalGroupChangeException e) { |
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if (e.getMessage().contains("Synonym is in homotypic group with other synonym(s). Either move complete homotypic group or remove synonym from homotypic group prior to moving to other taxon")){ |
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//OK |
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commitAndStartNewTransaction(tableNames); |
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}else{ |
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Assert.fail("Unexpected exception occurred: " + e.getMessage()); |
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} |
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} |
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//Asserts |
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heterotypicSynonym = (Synonym)service.load(uuidSyn3); |
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Assert.assertNotNull("Synonym should still exist", heterotypicSynonym); |
|
381 |
Assert.assertEquals("Synonym should still have 1 relation", 1, heterotypicSynonym.getSynonymRelations().size()); |
|
382 |
rel = heterotypicSynonym.getSynonymRelations().iterator().next(); |
|
383 |
Assert.assertEquals("Accepted taxon of single relation should still be the old taxon", oldTaxon, rel.getAcceptedTaxon()); |
|
384 |
|
|
385 |
|
|
386 |
//test heterotypic synonym with no other synonym in homotypic group |
|
387 |
//+ keep reference |
|
388 |
|
|
389 |
// printDataSet(System.err, new String[]{"TaxonBase"}); |
|
390 |
|
|
391 |
newTaxon = (Taxon)service.load(uuidNewTaxon); |
|
392 |
heterotypicSynonym = (Synonym)service.load(uuidSyn5); |
|
393 |
Assert.assertNotNull("Synonym should exist", heterotypicSynonym); |
|
394 |
Assert.assertEquals("Synonym should have 1 relation", 1, heterotypicSynonym.getSynonymRelations().size()); |
|
395 |
rel = heterotypicSynonym.getSynonymRelations().iterator().next(); |
|
396 |
Assert.assertEquals("Accepted taxon of single relation should be the old taxon", uuidOldTaxon, rel.getAcceptedTaxon().getUuid()); |
|
397 |
oldTaxon = rel.getAcceptedTaxon(); |
|
398 |
moveHomotypicGroup = false; |
|
399 |
|
|
400 |
|
|
401 |
try { |
|
402 |
service.moveSynonymToAnotherTaxon(rel, newTaxon, moveHomotypicGroup, newSynonymRelationshipType, newReference, newReferenceDetail, keepReference); |
|
403 |
} catch (HomotypicalGroupChangeException e) { |
|
404 |
Assert.fail("Move of single heterotypic synonym should not throw exception: " + e.getMessage()); |
|
405 |
} |
|
406 |
//Asserts |
|
407 |
//FIXME throws exception |
|
408 |
commitAndStartNewTransaction(tableNames); |
|
409 |
|
|
410 |
// printDataSet(System.err, new String[]{"AgentBase", "TaxonBase"}); |
|
411 |
// |
|
412 |
// printDataSet(System.err, new String[]{"TaxonBase"}); |
|
413 |
|
|
414 |
heterotypicSynonym = (Synonym)service.load(uuidSyn5); |
|
415 |
|
|
416 |
// printDataSet(System.err, new String[]{"TaxonBase"}); |
|
417 |
// System.exit(0); |
|
418 |
|
|
419 |
Assert.assertNotNull("Synonym should still exist", heterotypicSynonym); |
|
420 |
Assert.assertEquals("Synonym should still have 1 relation", 1, heterotypicSynonym.getSynonymRelations().size()); |
|
421 |
rel = heterotypicSynonym.getSynonymRelations().iterator().next(); |
|
422 |
Assert.assertEquals("Accepted taxon of single relation should be new taxon", newTaxon, rel.getAcceptedTaxon()); |
|
423 |
Assert.assertEquals("Old detail should be kept", "rel5", rel.getCitationMicroReference()); |
|
424 |
|
|
425 |
|
|
426 |
//test heterotypic synonym with other synonym in homotypic group and moveHomotypicGroup="true" |
|
427 |
//+ new detail |
|
428 |
newTaxon = (Taxon)service.load(uuidNewTaxon); |
|
429 |
heterotypicSynonym = (Synonym)service.load(uuidSyn3); |
|
430 |
Reference ref1 = referenceService.load(uuidRef1); |
|
431 |
Assert.assertNotNull("Synonym should exist", heterotypicSynonym); |
|
432 |
Assert.assertEquals("Synonym should have 1 relation", 1, heterotypicSynonym.getSynonymRelations().size()); |
|
433 |
rel = heterotypicSynonym.getSynonymRelations().iterator().next(); |
|
434 |
Assert.assertEquals("Accepted taxon of single relation should be the old taxon", uuidOldTaxon, rel.getAcceptedTaxon().getUuid()); |
|
435 |
oldTaxon = rel.getAcceptedTaxon(); |
|
436 |
Assert.assertEquals("Detail should be ref1", ref1, rel.getCitation()); |
|
437 |
Assert.assertEquals("Detail should be 'rel3'", "rel3", rel.getCitationMicroReference()); |
|
438 |
TaxonNameBase<?,?> oldSynName3 = heterotypicSynonym.getName(); |
|
439 |
|
|
440 |
Synonym heterotypicSynonym4 = (Synonym)service.load(uuidSyn4); |
|
441 |
Assert.assertNotNull("Synonym should exist", heterotypicSynonym4); |
|
442 |
Assert.assertEquals("Synonym should have 1 relation", 1, heterotypicSynonym4.getSynonymRelations().size()); |
|
443 |
SynonymRelationship rel4 = heterotypicSynonym4.getSynonymRelations().iterator().next(); |
|
444 |
Assert.assertEquals("Accepted taxon of other synonym in group should be the old taxon", uuidOldTaxon, rel4.getAcceptedTaxon().getUuid()); |
|
445 |
Assert.assertSame("Homotypic group of both synonyms should be same", oldSynName3.getHomotypicalGroup() , heterotypicSynonym4.getName().getHomotypicalGroup() ); |
|
446 |
|
|
447 |
moveHomotypicGroup = true; |
|
448 |
keepReference = false; |
|
449 |
|
|
450 |
try { |
|
451 |
service.moveSynonymToAnotherTaxon(rel, newTaxon, moveHomotypicGroup, newSynonymRelationshipType, newReference, newReferenceDetail, keepReference); |
|
452 |
} catch (HomotypicalGroupChangeException e) { |
|
453 |
Assert.fail("Move with 'moveHomotypicGroup = true' should not throw exception: " + e.getMessage()); |
|
454 |
} |
|
455 |
//Asserts |
|
456 |
commitAndStartNewTransaction(tableNames); |
|
457 |
heterotypicSynonym = (Synonym)service.load(uuidSyn3); |
|
458 |
Assert.assertNotNull("Synonym should still exist", heterotypicSynonym); |
|
459 |
Assert.assertEquals("Synonym should still have 1 relation", 1, heterotypicSynonym.getSynonymRelations().size()); |
|
460 |
rel = heterotypicSynonym.getSynonymRelations().iterator().next(); |
|
461 |
Assert.assertEquals("Accepted taxon of relation should be new taxon now", newTaxon, rel.getAcceptedTaxon()); |
|
462 |
TaxonNameBase<?,?> synName3 = rel.getSynonym().getName(); |
|
463 |
|
|
464 |
heterotypicSynonym = (Synonym)service.load(uuidSyn4); |
|
465 |
Assert.assertNotNull("Synonym should still exist", heterotypicSynonym); |
|
466 |
Assert.assertEquals("Synonym should still have 1 relation", 1, heterotypicSynonym.getSynonymRelations().size()); |
|
467 |
rel = heterotypicSynonym.getSynonymRelations().iterator().next(); |
|
468 |
Assert.assertEquals("Accepted taxon of relation should be new taxon now", newTaxon, rel.getAcceptedTaxon()); |
|
469 |
Assert.assertNull("Old citation should be removed", rel.getCitation()); |
|
470 |
Assert.assertNull("Old detail should be removed", rel.getCitationMicroReference()); |
|
471 |
TaxonNameBase<?,?> synName4 = rel.getSynonym().getName(); |
|
472 |
Assert.assertEquals("Homotypic group of both synonyms should be equal", synName3.getHomotypicalGroup() , synName4.getHomotypicalGroup() ); |
|
473 |
Assert.assertSame("Homotypic group of both synonyms should be same", synName3.getHomotypicalGroup() , synName4.getHomotypicalGroup() ); |
|
474 |
Assert.assertEquals("Homotypic group of both synonyms should be equal to old homotypic group", oldSynName3.getHomotypicalGroup() , synName3.getHomotypicalGroup() ); |
|
475 |
|
|
476 |
|
|
477 |
//test single heterotypic synonym to homotypic synonym of new taxon |
|
478 |
//+ new reference |
|
479 |
newTaxon = (Taxon)service.load(uuidNewTaxon); |
|
480 |
Reference ref2 = referenceService.load(uuidRef2); |
|
481 |
heterotypicSynonym = (Synonym)service.load(uuidSyn6); |
|
482 |
Assert.assertNotNull("Synonym should exist", heterotypicSynonym); |
|
483 |
Assert.assertEquals("Synonym should have 1 relation", 1, heterotypicSynonym.getSynonymRelations().size()); |
|
484 |
rel = heterotypicSynonym.getSynonymRelations().iterator().next(); |
|
485 |
Assert.assertEquals("Accepted taxon of single relation should be the old taxon", uuidOldTaxon, rel.getAcceptedTaxon().getUuid()); |
|
486 |
oldTaxon = rel.getAcceptedTaxon(); |
|
487 |
moveHomotypicGroup = false; |
|
488 |
keepReference = false; |
|
489 |
newReference = ref2; |
|
490 |
newReferenceDetail = "newRefDetail"; |
|
491 |
newSynonymRelationshipType = SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF(); |
|
492 |
|
|
493 |
try { |
|
494 |
service.moveSynonymToAnotherTaxon(rel, newTaxon, moveHomotypicGroup, newSynonymRelationshipType, newReference, newReferenceDetail, keepReference); |
|
495 |
} catch (HomotypicalGroupChangeException e) { |
|
496 |
Assert.fail("Move of single heterotypic synonym should not throw exception: " + e.getMessage()); |
|
497 |
} |
|
498 |
//Asserts |
|
499 |
commitAndStartNewTransaction(tableNames); |
|
500 |
heterotypicSynonym = (Synonym)service.load(uuidSyn6); |
|
501 |
Assert.assertNotNull("Synonym should still exist", heterotypicSynonym); |
|
502 |
Assert.assertEquals("Synonym should still have 1 relation", 1, heterotypicSynonym.getSynonymRelations().size()); |
|
503 |
rel = heterotypicSynonym.getSynonymRelations().iterator().next(); |
|
504 |
Assert.assertEquals("Relationship type should be 'homotypic synonym'", newSynonymRelationshipType, rel.getType()); |
|
505 |
Assert.assertEquals("Accepted taxon of single relation should be new taxon", newTaxon, rel.getAcceptedTaxon()); |
|
506 |
Assert.assertEquals("New citation should be ref2", ref2 ,rel.getCitation()); |
|
507 |
Assert.assertEquals("New detail should be kept", "newRefDetail", rel.getCitationMicroReference()); |
|
508 |
|
|
509 |
Assert.assertEquals("New taxon and new synonym should have equal homotypical group", rel.getSynonym().getHomotypicGroup(), rel.getAcceptedTaxon().getHomotypicGroup()); |
|
510 |
Assert.assertSame("New taxon and new synonym should have same homotypical group", rel.getSynonym().getHomotypicGroup(), rel.getAcceptedTaxon().getHomotypicGroup()); |
|
511 |
} |
|
512 |
|
|
513 |
|
|
514 |
|
|
515 |
@Test |
|
516 |
public final void testGetHeterotypicSynonymyGroups(){ |
|
517 |
Rank rank = Rank.SPECIES(); |
|
518 |
Reference ref1 = ReferenceFactory.newGeneric(); |
|
519 |
//HomotypicalGroup group = HomotypicalGroup.NewInstance(); |
|
520 |
Taxon taxon1 = Taxon.NewInstance(BotanicalName.NewInstance(rank, "Test3", null, null, null, null, null, null, null), null); |
|
521 |
Synonym synonym0 = Synonym.NewInstance(BotanicalName.NewInstance(rank, "Test2", null, null, null, null, null, null, null), null); |
|
522 |
Synonym synonym1 = Synonym.NewInstance(BotanicalName.NewInstance(rank, "Test2", null, null, null, null, null, null, null), null); |
|
523 |
Synonym synonym2 = Synonym.NewInstance(BotanicalName.NewInstance(rank, "Test4", null, null, null, null, null, null, null), null); |
|
524 |
synonym0.getName().setHomotypicalGroup(taxon1.getHomotypicGroup()); |
|
525 |
synonym2.getName().setHomotypicalGroup(synonym1.getHomotypicGroup()); |
|
526 |
//tax2.addHeterotypicSynonymName(synonym.getName()); |
|
527 |
taxon1.addSynonym(synonym1, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF()); |
|
528 |
taxon1.addSynonym(synonym2, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF()); |
|
529 |
|
|
530 |
service.save(synonym1); |
|
531 |
service.save(synonym2); |
|
532 |
service.save(taxon1); |
|
533 |
|
|
534 |
List<List<Synonym>> heteroSyns = service.getHeterotypicSynonymyGroups(taxon1, null); |
|
535 |
Assert.assertEquals("There should be 1 heterotypic group", 1, heteroSyns.size()); |
|
536 |
List<Synonym> synList = heteroSyns.get(0); |
|
537 |
Assert.assertEquals("There should be 2 heterotypic syns in group 1", 2, synList.size()); |
|
538 |
|
|
539 |
//test sec |
|
540 |
synonym2.setSec(ref1); |
|
541 |
heteroSyns = service.getHeterotypicSynonymyGroups(taxon1, null); |
|
542 |
Assert.assertEquals("There should be 1 heterotypic group", 1, heteroSyns.size()); |
|
543 |
synList = heteroSyns.get(0); |
|
544 |
Assert.assertEquals("getHeterotypicSynonymyGroups should be independent of sec reference", 2, synList.size()); |
|
545 |
|
|
546 |
} |
|
547 |
|
|
548 |
|
|
549 |
@Test |
|
550 |
public final void testGetHomotypicSynonymsByHomotypicGroup(){ |
|
551 |
Rank rank = Rank.SPECIES(); |
|
552 |
Reference ref1 = ReferenceFactory.newGeneric(); |
|
553 |
//HomotypicalGroup group = HomotypicalGroup.NewInstance(); |
|
554 |
Taxon taxon1 = Taxon.NewInstance(BotanicalName.NewInstance(rank, "Test3", null, null, null, null, null, null, null), null); |
|
555 |
Synonym synonym0 = Synonym.NewInstance(BotanicalName.NewInstance(rank, "Test2", null, null, null, null, null, null, null), null); |
|
556 |
Synonym synonym1 = Synonym.NewInstance(BotanicalName.NewInstance(rank, "Test2", null, null, null, null, null, null, null), null); |
|
557 |
Synonym synonym2 = Synonym.NewInstance(BotanicalName.NewInstance(rank, "Test4", null, null, null, null, null, null, null), null); |
|
558 |
synonym0.getName().setHomotypicalGroup(taxon1.getHomotypicGroup()); |
|
559 |
synonym2.getName().setHomotypicalGroup(synonym1.getHomotypicGroup()); |
|
560 |
//tax2.addHeterotypicSynonymName(synonym.getName()); |
|
561 |
taxon1.addSynonym(synonym0, SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF()); |
|
562 |
taxon1.addSynonym(synonym1, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF()); |
|
563 |
taxon1.addSynonym(synonym2, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF()); |
|
564 |
|
|
565 |
service.save(synonym1); |
|
566 |
service.save(synonym2); |
|
567 |
service.save(taxon1); |
|
568 |
|
|
569 |
List<Synonym> homoSyns = service.getHomotypicSynonymsByHomotypicGroup(taxon1, null); |
|
570 |
Assert.assertEquals("There should be 1 heterotypic group", 1, homoSyns.size()); |
|
571 |
Assert.assertSame("The homotypic synonym should be synonym0", synonym0, homoSyns.get(0)); |
|
572 |
|
|
573 |
//test sec |
|
574 |
synonym0.setSec(ref1); |
|
575 |
homoSyns = service.getHomotypicSynonymsByHomotypicGroup(taxon1, null); |
|
576 |
Assert.assertEquals("getHeterotypicSynonymyGroups should be independent of sec reference", 1, homoSyns.size()); |
|
577 |
|
|
578 |
} |
|
579 |
|
|
580 |
@Test |
|
581 |
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="TaxonServiceImplTest.testDeleteSynonym.xml") |
|
582 |
//test delete synonym, but the name will not be deleted |
|
583 |
public final void testDeleteSynonymSynonymTaxonDontDeleteName(){ |
|
584 |
final String[]tableNames = {"TaxonBase","TaxonBase_AUD", "TaxonNameBase","TaxonNameBase_AUD", |
|
585 |
"SynonymRelationship","SynonymRelationship_AUD", |
|
586 |
"HomotypicalGroup","HomotypicalGroup_AUD"}; |
|
587 |
|
|
588 |
int nSynonyms = service.count(Synonym.class); |
|
589 |
Assert.assertEquals("There should be 2 synonyms in the database", 2, nSynonyms); |
|
590 |
int nNames = nameService.count(TaxonNameBase.class); |
|
591 |
Assert.assertEquals("There should be 4 names in the database", 4, nNames); |
|
592 |
int nRelations = service.countAllRelationships(); |
|
593 |
Assert.assertEquals("There should be two relationship left in the database", 2, nRelations); |
|
594 |
|
|
595 |
UUID uuidSynonym1=UUID.fromString("7da85381-ad9d-4886-9d4d-0eeef40e3d88"); |
|
596 |
|
|
597 |
|
|
598 |
Synonym synonym1 = (Synonym)service.load(uuidSynonym1); |
|
599 |
SynonymDeletionConfigurator config = new SynonymDeletionConfigurator(); |
|
600 |
config.setDeleteNameIfPossible(false); |
|
601 |
config.setNewHomotypicGroupIfNeeded(true); |
|
602 |
service.deleteSynonym(synonym1, config); |
|
603 |
|
|
604 |
this.commitAndStartNewTransaction(tableNames); |
|
605 |
|
|
606 |
nSynonyms = service.count(Synonym.class); |
|
607 |
Assert.assertEquals("There should be 1 synonym left in the database", 1, nSynonyms); |
|
608 |
nNames = nameService.count(TaxonNameBase.class); |
|
609 |
Assert.assertEquals("There should be 4 names left in the database", 4, nNames); |
|
610 |
nRelations = service.countAllRelationships(); |
|
611 |
Assert.assertEquals("There should be no relationship left in the database", 1, nRelations); |
|
612 |
} |
|
613 |
|
|
614 |
@Test |
|
615 |
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="TaxonServiceImplTest.testDeleteSynonym.xml") |
|
616 |
//test delete synonym and his name |
|
617 |
public final void testDeleteSynonymSynonymTaxonDeleteName(){ |
|
618 |
final String[]tableNames = {"TaxonBase","TaxonBase_AUD", "TaxonNameBase","TaxonNameBase_AUD", |
|
619 |
"SynonymRelationship","SynonymRelationship_AUD", |
|
620 |
"HomotypicalGroup","HomotypicalGroup_AUD"}; |
|
621 |
|
|
622 |
int nSynonyms = service.count(Synonym.class); |
|
623 |
Assert.assertEquals("There should be 2 synonyms in the database", 2, nSynonyms); |
|
624 |
int nNames = nameService.count(TaxonNameBase.class); |
|
625 |
Assert.assertEquals("There should be 4 names in the database", 4, nNames); |
|
626 |
int nRelations = service.countAllRelationships(); |
|
627 |
Assert.assertEquals("There should be 2 relationship left in the database", 2, nRelations); |
|
628 |
|
|
629 |
UUID uuidSynonym1=UUID.fromString("7da85381-ad9d-4886-9d4d-0eeef40e3d88"); |
|
630 |
|
|
631 |
|
|
632 |
Synonym synonym1 = (Synonym)service.load(uuidSynonym1); |
|
633 |
service.deleteSynonym(synonym1, new SynonymDeletionConfigurator()); |
|
634 |
|
|
635 |
this.commitAndStartNewTransaction(tableNames); |
|
636 |
|
|
637 |
nSynonyms = service.count(Synonym.class); |
|
638 |
Assert.assertEquals("There should be 1 synonym left in the database", 1, nSynonyms); |
|
639 |
nNames = nameService.count(TaxonNameBase.class); |
|
640 |
Assert.assertEquals("There should be 3 names left in the database", 3, nNames); |
|
641 |
nRelations = service.countAllRelationships(); |
|
642 |
Assert.assertEquals("There should be 1 relationship left in the database", 1, nRelations); |
|
643 |
|
|
644 |
} |
|
645 |
|
|
646 |
@Test |
|
647 |
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="TaxonServiceImplTest.testDeleteSynonym.xml") |
|
648 |
//test remove synonym from taxon -> synonym and name still in the db and the synonymrelationship to the other taxon |
|
649 |
//test delete synonym -> all relationships are deleted, the name is deleted and the synonym itself |
|
650 |
public final void testDeleteSynonymSynonymTaxonBooleanRelToOneTaxon(){ |
|
651 |
final String[]tableNames = {"TaxonBase","TaxonBase_AUD", "TaxonNameBase","TaxonNameBase_AUD", |
|
652 |
"SynonymRelationship","SynonymRelationship_AUD", |
|
653 |
"HomotypicalGroup","HomotypicalGroup_AUD"}; |
|
654 |
|
|
655 |
int nSynonyms = service.count(Synonym.class); |
|
656 |
Assert.assertEquals("There should be 2 synonyms in the database", 2, nSynonyms); |
|
657 |
int nNames = nameService.count(TaxonNameBase.class); |
|
658 |
Assert.assertEquals("There should be 4 names in the database", 4, nNames); |
|
659 |
|
|
660 |
UUID uuidTaxon1=UUID.fromString("c47fdb72-f32c-452e-8305-4b44f01179d0"); |
|
661 |
UUID uuidTaxon2=UUID.fromString("2d9a642d-5a82-442d-8fec-95efa978e8f8"); |
|
662 |
UUID uuidSynonym1=UUID.fromString("7da85381-ad9d-4886-9d4d-0eeef40e3d88"); |
|
663 |
|
|
664 |
|
|
665 |
Taxon taxon2 = (Taxon)service.load(uuidTaxon1); |
|
666 |
|
|
667 |
List<String> initStrat = new ArrayList<String>(); |
|
668 |
initStrat.add("markers"); |
|
669 |
Synonym synonym1 = (Synonym)service.load(uuidSynonym1, initStrat); |
|
670 |
int nRelations = service.countAllRelationships(); |
|
671 |
Assert.assertEquals("There should be 2 relationship left in the database", 2, nRelations); |
|
672 |
|
|
673 |
taxon2.removeSynonym(synonym1, false); |
|
674 |
service.saveOrUpdate(taxon2); |
|
675 |
|
|
676 |
commitAndStartNewTransaction(null); |
|
677 |
|
|
678 |
nSynonyms = service.count(Synonym.class); |
|
679 |
Assert.assertEquals("There should be 2 synonyms in the database", 2, nSynonyms); |
|
680 |
nNames = nameService.count(TaxonNameBase.class); |
|
681 |
Assert.assertEquals("There should be 4 names in the database", 4, nNames); |
|
682 |
nRelations = service.countAllRelationships(); |
|
683 |
Assert.assertEquals("There should be 1 relationship left in the database", 1, nRelations); |
|
684 |
Marker marker1 = Marker.NewInstance(MarkerType.IMPORTED(), true); |
|
685 |
Marker marker2 = Marker.NewInstance(MarkerType.COMPUTED(), true); |
|
686 |
synonym1.addMarker(marker1); |
|
687 |
synonym1.addMarker(marker2); |
|
688 |
service.update(synonym1); |
|
689 |
synonym1 =(Synonym) service.load(uuidSynonym1); |
|
690 |
|
|
691 |
|
|
692 |
Set<Marker> markers = synonym1.getMarkers(); |
|
693 |
Marker marker = markers.iterator().next(); |
|
694 |
UUID markerUUID = marker.getUuid(); |
|
695 |
// taxon2 = (Taxon)service.load(uuidTaxon2); |
|
696 |
synonym1 = (Synonym)service.load(uuidSynonym1); |
|
697 |
//the marker should not prevent the deletion |
|
698 |
DeleteResult result = service.deleteSynonym(synonym1, new SynonymDeletionConfigurator()); |
|
699 |
if (!result.isOk()){ |
|
700 |
Assert.fail(); |
|
701 |
} |
|
702 |
|
|
703 |
|
|
704 |
|
|
705 |
|
|
706 |
commitAndStartNewTransaction(tableNames); |
|
707 |
nSynonyms = service.count(Synonym.class); |
|
708 |
Assert.assertEquals("There should be 1 synonym left in the database", 1, nSynonyms); |
|
709 |
nNames = nameService.count(TaxonNameBase.class); |
|
710 |
Assert.assertEquals("There should be 3 names left in the database", 3, nNames); |
|
711 |
nRelations = service.countAllRelationships(); |
|
712 |
Assert.assertEquals("There should be no relationship left in the database", 1, nRelations); |
|
713 |
marker = markerService.load(markerUUID); |
|
714 |
assertNull(marker); |
|
715 |
|
|
716 |
} |
|
717 |
|
|
718 |
@Test |
|
719 |
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="TaxonServiceImplTest.testDeleteSynonym.xml") |
|
720 |
//test delete synonym, only for a special taxon, but because of other relationships it will not be deleted at all |
|
721 |
public final void testDeleteSynonymSynonymTaxonBooleanDeleteOneTaxon(){ |
|
722 |
final String[]tableNames = {"TaxonBase","TaxonBase_AUD", "TaxonNameBase","TaxonNameBase_AUD", |
|
723 |
"SynonymRelationship","SynonymRelationship_AUD", |
|
724 |
"HomotypicalGroup","HomotypicalGroup_AUD"}; |
|
725 |
|
|
726 |
|
|
727 |
int nSynonyms = service.count(Synonym.class); |
|
728 |
Assert.assertEquals("There should be 2 synonyms in the database", 2, nSynonyms); |
|
729 |
int nNames = nameService.count(TaxonNameBase.class); |
|
730 |
Assert.assertEquals("There should be 4 names in the database", 4, nNames); |
|
731 |
|
|
732 |
UUID uuidTaxon1=UUID.fromString("c47fdb72-f32c-452e-8305-4b44f01179d0"); |
|
733 |
UUID uuidTaxon2=UUID.fromString("2d9a642d-5a82-442d-8fec-95efa978e8f8"); |
|
734 |
UUID uuidSynonym1=UUID.fromString("7da85381-ad9d-4886-9d4d-0eeef40e3d88"); |
|
735 |
UUID uuidSynonym2=UUID.fromString("f8d86dc9-5f18-4877-be46-fbb9412465e4"); |
|
736 |
|
|
737 |
Taxon taxon1 = (Taxon)service.load(uuidTaxon1); |
|
738 |
Taxon taxon2 = (Taxon)service.load(uuidTaxon2); |
|
739 |
Synonym synonym1 = (Synonym)service.load(uuidSynonym1); |
|
740 |
taxon2.addSynonym(synonym1, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF()); |
|
741 |
service.saveOrUpdate(synonym1); |
|
742 |
int nRelations = service.countAllRelationships(); |
|
743 |
Assert.assertEquals("There should be 3 relationship left in the database", 3, nRelations); |
|
744 |
service.deleteSynonym(synonym1, taxon1, new SynonymDeletionConfigurator()); |
|
745 |
|
|
746 |
this.commitAndStartNewTransaction(tableNames); |
|
747 |
|
|
748 |
nSynonyms = service.count(Synonym.class); |
|
749 |
Assert.assertEquals("There should still be 2 synonyms left in the database (synonym is related to taxon2)", 2, nSynonyms); |
|
750 |
nNames = nameService.count(TaxonNameBase.class); |
|
751 |
Assert.assertEquals("There should be 4 names left in the database (name not deleted as synonym was not deleted)", 4, nNames); |
|
752 |
nRelations = service.countAllRelationships(); |
|
753 |
Assert.assertEquals("There should be 2 relationship left in the database", 2, nRelations); |
|
754 |
|
|
755 |
|
|
756 |
} |
|
757 |
|
|
758 |
@Test |
|
759 |
@DataSet("TaxonServiceImplTest.testDeleteSynonym.xml") |
|
760 |
|
|
761 |
public final void testDeleteSynonymSynonymTaxonBooleanWithRelatedName(){ |
|
762 |
final String[]tableNames = {"TaxonBase","TaxonBase_AUD", "TaxonNameBase","TaxonNameBase_AUD", |
|
763 |
"SynonymRelationship","SynonymRelationship_AUD", |
|
764 |
"HomotypicalGroup","HomotypicalGroup_AUD"}; |
|
765 |
|
|
766 |
int nSynonyms = service.count(Synonym.class); |
|
767 |
Assert.assertEquals("There should be 2 synonyms in the database", 2, nSynonyms); |
|
768 |
int nNames = nameService.count(TaxonNameBase.class); |
|
769 |
Assert.assertEquals("There should be 4 names in the database", 4, nNames); |
|
770 |
|
|
771 |
UUID uuidTaxon1=UUID.fromString("c47fdb72-f32c-452e-8305-4b44f01179d0"); |
|
772 |
UUID uuidTaxon2=UUID.fromString("2d9a642d-5a82-442d-8fec-95efa978e8f8"); |
|
773 |
UUID uuidSynonym1=UUID.fromString("7da85381-ad9d-4886-9d4d-0eeef40e3d88"); |
|
774 |
UUID uuidSynonym2=UUID.fromString("f8d86dc9-5f18-4877-be46-fbb9412465e4"); |
|
775 |
UUID uuidSynonymName2=UUID.fromString("613f3c93-013e-4ffc-aadc-1c98d71c335e"); |
|
776 |
|
|
777 |
Synonym synonym1 = (Synonym)service.load(uuidSynonym1); |
|
778 |
TaxonNameBase name2 = nameService.load(uuidSynonymName2); |
|
779 |
UUID name3Uuid = synonym1.getName().getUuid(); |
|
780 |
TaxonNameBase name3 = nameService.load(name3Uuid); |
|
781 |
name3.addRelationshipFromName(name2, NameRelationshipType.LATER_HOMONYM(), null); |
|
782 |
|
|
783 |
service.saveOrUpdate(synonym1); |
|
784 |
|
|
785 |
int nRelations = nameService.getAllRelationships(1000, 0).size(); |
|
786 |
logger.info("number of name relations: " + nRelations); |
|
787 |
Assert.assertEquals("There should be 1 name relationship left in the database", 1, nRelations); |
|
788 |
SynonymDeletionConfigurator config = new SynonymDeletionConfigurator(); |
|
789 |
|
|
790 |
service.deleteSynonym(synonym1, config); |
|
791 |
|
|
792 |
this.commitAndStartNewTransaction(tableNames); |
|
793 |
//synonym is deleted, but the name can not be deleted because of a name relationship |
|
794 |
nSynonyms = service.count(Synonym.class); |
|
795 |
Assert.assertEquals("There should still be 1 synonyms left in the database", 1, nSynonyms); |
|
796 |
nNames = nameService.count(TaxonNameBase.class); |
|
797 |
Assert.assertEquals("There should be 4 names left in the database (name is related to synonymName2)", 4, nNames); |
|
798 |
nRelations = service.countAllRelationships(); |
|
799 |
//may change with better implementation of countAllRelationships (see #2653) |
|
800 |
nRelations = nameService.getAllRelationships(1000, 0).size(); |
|
801 |
logger.info("number of name relations: " + nRelations); |
|
802 |
Assert.assertEquals("There should be 1 name relationship left in the database", 1, nRelations); |
|
803 |
|
|
804 |
|
|
805 |
//clean up database |
|
806 |
name2 = nameService.load(uuidSynonymName2); |
|
807 |
NameRelationship rel = CdmBase.deproxy(name2.getNameRelations().iterator().next(), NameRelationship.class); |
|
808 |
name2.removeNameRelationship(rel); |
|
809 |
nameService.save(name2); |
|
810 |
this.setComplete(); |
|
811 |
this.endTransaction(); |
|
812 |
|
|
813 |
} |
|
814 |
@Test |
|
815 |
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="TaxonServiceImplTest.testDeleteSynonym.xml") |
|
816 |
public final void testDeleteSynonymSynonymTaxonBooleanWithRelatedNameDeleteAllNameRelations(){ |
|
817 |
final String[]tableNames = {"TaxonBase","TaxonBase_AUD", "TaxonNameBase","TaxonNameBase_AUD", |
|
818 |
"SynonymRelationship","SynonymRelationship_AUD", |
|
819 |
"HomotypicalGroup","HomotypicalGroup_AUD"}; |
|
820 |
|
|
821 |
int nSynonyms = service.count(Synonym.class); |
|
822 |
Assert.assertEquals("There should be 2 synonyms in the database", 2, nSynonyms); |
|
823 |
int nNames = nameService.count(TaxonNameBase.class); |
|
824 |
Assert.assertEquals("There should be 4 names in the database", 4, nNames); |
|
825 |
|
|
826 |
UUID uuidTaxon1=UUID.fromString("c47fdb72-f32c-452e-8305-4b44f01179d0"); |
|
827 |
UUID uuidTaxon2=UUID.fromString("2d9a642d-5a82-442d-8fec-95efa978e8f8"); |
|
828 |
UUID uuidSynonym1=UUID.fromString("7da85381-ad9d-4886-9d4d-0eeef40e3d88"); |
|
829 |
UUID uuidSynonym2=UUID.fromString("f8d86dc9-5f18-4877-be46-fbb9412465e4"); |
|
830 |
UUID uuidSynonymName2=UUID.fromString("613f3c93-013e-4ffc-aadc-1c98d71c335e"); |
|
831 |
|
|
832 |
Synonym synonym1 = (Synonym)service.load(uuidSynonym1); |
|
833 |
TaxonNameBase name2 = nameService.load(uuidSynonymName2); |
|
834 |
UUID name3Uuid = synonym1.getName().getUuid(); |
|
835 |
TaxonNameBase name3 = nameService.load(name3Uuid); |
|
836 |
name3.addRelationshipFromName(name2, NameRelationshipType.LATER_HOMONYM(), null); |
|
837 |
|
|
838 |
service.saveOrUpdate(synonym1); |
|
839 |
|
|
840 |
int nRelations = nameService.getAllRelationships(1000, 0).size(); |
|
841 |
logger.info("number of name relations: " + nRelations); |
|
842 |
Assert.assertEquals("There should be 1 name relationship left in the database", 1, nRelations); |
|
843 |
SynonymDeletionConfigurator config = new SynonymDeletionConfigurator(); |
|
844 |
NameDeletionConfigurator nameDeletionConfig = new NameDeletionConfigurator(); |
|
845 |
nameDeletionConfig.setRemoveAllNameRelationships(true); |
|
846 |
config.setNameDeletionConfig(nameDeletionConfig); |
|
847 |
|
|
848 |
service.deleteSynonym(synonym1, config); |
|
849 |
|
|
850 |
this.commitAndStartNewTransaction(tableNames); |
|
851 |
|
|
852 |
nSynonyms = service.count(Synonym.class); |
|
853 |
Assert.assertEquals("There should still be 1 synonyms left in the database", 1, nSynonyms); |
|
854 |
nNames = nameService.count(TaxonNameBase.class); |
|
855 |
Assert.assertEquals("There should be 3 names left in the database ", 3, nNames); |
|
856 |
nRelations = service.countAllRelationships(); |
|
857 |
//may change with better implementation of countAllRelationships (see #2653) |
|
858 |
nRelations = nameService.getAllRelationships(1000, 0).size(); |
|
859 |
logger.info("number of name relations: " + nRelations); |
|
860 |
Assert.assertEquals("There should be no name relationship left in the database", 0, nRelations); |
|
861 |
} |
|
862 |
|
|
863 |
@Test |
|
864 |
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="TaxonServiceImplTest.testDeleteSynonym.xml") |
|
865 |
public final void testDeleteSynonymSynonymTaxonBooleanWithRelatedNameIgnoreIsBasionym(){ |
|
866 |
final String[]tableNames = {"TaxonBase","TaxonBase_AUD", "TaxonNameBase","TaxonNameBase_AUD", |
|
867 |
"SynonymRelationship","SynonymRelationship_AUD", |
|
868 |
"HomotypicalGroup","HomotypicalGroup_AUD"}; |
|
869 |
|
|
870 |
int nSynonyms = service.count(Synonym.class); |
|
871 |
Assert.assertEquals("There should be 2 synonyms in the database", 2, nSynonyms); |
|
872 |
int nNames = nameService.count(TaxonNameBase.class); |
|
873 |
Assert.assertEquals("There should be 4 names in the database", 4, nNames); |
|
874 |
|
|
875 |
UUID uuidTaxon1=UUID.fromString("c47fdb72-f32c-452e-8305-4b44f01179d0"); |
|
876 |
UUID uuidTaxon2=UUID.fromString("2d9a642d-5a82-442d-8fec-95efa978e8f8"); |
|
877 |
UUID uuidSynonym1=UUID.fromString("7da85381-ad9d-4886-9d4d-0eeef40e3d88"); |
|
878 |
UUID uuidSynonym2=UUID.fromString("f8d86dc9-5f18-4877-be46-fbb9412465e4"); |
|
879 |
UUID uuidSynonymName2=UUID.fromString("613f3c93-013e-4ffc-aadc-1c98d71c335e"); |
|
880 |
|
|
881 |
Synonym synonym1 = (Synonym)service.load(uuidSynonym1); |
|
882 |
TaxonNameBase synName2 = nameService.load(uuidSynonymName2); |
|
883 |
UUID name3Uuid = synonym1.getName().getUuid(); |
|
884 |
TaxonNameBase synName1 = nameService.load(name3Uuid); |
|
885 |
synName1.addRelationshipFromName(synName2, NameRelationshipType.BASIONYM(), null); |
|
886 |
|
|
887 |
service.saveOrUpdate(synonym1); |
|
888 |
|
|
889 |
int nRelations = nameService.getAllRelationships(1000, 0).size(); |
|
890 |
logger.info("number of name relations: " + nRelations); |
|
891 |
Assert.assertEquals("There should be 1 name relationship left in the database", 1, nRelations); |
|
892 |
SynonymDeletionConfigurator config = new SynonymDeletionConfigurator(); |
|
893 |
NameDeletionConfigurator nameDeletionConfig = new NameDeletionConfigurator(); |
|
894 |
nameDeletionConfig.setIgnoreIsBasionymFor(true); |
|
895 |
config.setNameDeletionConfig(nameDeletionConfig); |
|
896 |
|
|
897 |
DeleteResult result =service.deleteSynonym(synonym1, config); |
|
898 |
if (!result.isOk()){ |
|
899 |
Assert.fail(); |
|
900 |
} |
|
901 |
|
|
902 |
|
|
903 |
logger.debug(result); |
|
904 |
this.commitAndStartNewTransaction(tableNames); |
|
905 |
|
|
906 |
nSynonyms = service.count(Synonym.class); |
|
907 |
Assert.assertEquals("There should still be 1 synonyms left in the database", 1, nSynonyms); |
|
908 |
nNames = nameService.count(TaxonNameBase.class); |
|
909 |
Assert.assertEquals("There should be 3 names left in the database ", 3, nNames); |
|
910 |
nRelations = service.countAllRelationships(); |
|
911 |
//may change with better implementation of countAllRelationships (see #2653) |
|
912 |
nRelations = nameService.getAllRelationships(1000, 0).size(); |
|
913 |
logger.info("number of name relations: " + nRelations); |
|
914 |
Assert.assertEquals("There should be no name relationship left in the database", 0, nRelations); |
|
915 |
} |
|
916 |
|
|
917 |
|
|
918 |
@Test |
|
919 |
@DataSet("TaxonServiceImplTest.testDeleteSynonym.xml") |
|
920 |
public final void testDeleteSynonymSynonymTaxonBooleanWithRollback(){ |
|
921 |
final String[]tableNames = {"TaxonBase","TaxonBase_AUD", "TaxonNameBase","TaxonNameBase_AUD", |
|
922 |
"SynonymRelationship","SynonymRelationship_AUD", |
|
923 |
"HomotypicalGroup","HomotypicalGroup_AUD"}; |
|
924 |
|
|
925 |
int nSynonyms = service.count(Synonym.class); |
|
926 |
Assert.assertEquals("There should be 2 synonyms in the database", 2, nSynonyms); |
|
927 |
int nNames = nameService.count(TaxonNameBase.class); |
|
928 |
Assert.assertEquals("There should be 4 names in the database", 4, nNames); |
|
929 |
int nRelations = service.countAllRelationships(); |
|
930 |
|
|
931 |
|
|
932 |
//may change with better implementation of countAllRelationships (see #2653) |
|
933 |
|
|
934 |
logger.debug(""); |
|
935 |
Assert.assertEquals("There should be 2 relationships in the database (the 2 synonym relationship) but no name relationship", 2, nRelations); |
|
936 |
|
|
937 |
UUID uuidSynonym1=UUID.fromString("7da85381-ad9d-4886-9d4d-0eeef40e3d88"); |
|
938 |
UUID uuidSynonymName2=UUID.fromString("613f3c93-013e-4ffc-aadc-1c98d71c335e"); |
|
939 |
|
|
940 |
Synonym synonym1 = (Synonym)service.load(uuidSynonym1); |
|
941 |
TaxonNameBase name2 = nameService.load(uuidSynonymName2); |
|
942 |
synonym1.getName().addRelationshipFromName(name2, NameRelationshipType.LATER_HOMONYM(), null); |
|
943 |
|
|
944 |
service.deleteSynonym(synonym1, new SynonymDeletionConfigurator()); |
|
945 |
|
|
946 |
this.rollback(); |
|
947 |
// printDataSet(System.out, tableNames); |
|
948 |
this.startNewTransaction(); |
|
949 |
|
|
950 |
nSynonyms = service.count(Synonym.class); |
|
951 |
Assert.assertEquals("There should still be 2 synonyms left in the database", 2, nSynonyms); |
|
952 |
nNames = nameService.count(TaxonNameBase.class); |
|
953 |
Assert.assertEquals("There should be 4 names left in the database", 4, nNames); |
|
954 |
nRelations = service.countAllRelationships(); |
|
955 |
//may change with better implementation of countAllRelationships (see #2653) |
|
956 |
Assert.assertEquals("There should be 2 relationship in the database (the 2 synonym relationship) but no name relationship", 2, nRelations); |
|
957 |
|
|
958 |
} |
|
959 |
|
|
960 |
@Test |
|
961 |
@DataSet("TaxonServiceImplTest.testDeleteSynonym.xml") |
|
962 |
public final void testDeleteSynonymSynonymTaxonBooleanWithoutTransaction(){ |
|
963 |
final String[]tableNames = {"TaxonBase","TaxonBase_AUD", "TaxonNameBase","TaxonNameBase_AUD", |
|
964 |
"SynonymRelationship","SynonymRelationship_AUD", |
|
965 |
"HomotypicalGroup","HomotypicalGroup_AUD"}; |
|
966 |
|
|
967 |
int nSynonyms = service.count(Synonym.class); |
|
968 |
Assert.assertEquals("There should be 2 synonyms in the database", 2, nSynonyms); |
|
969 |
int nNames = nameService.count(TaxonNameBase.class); |
|
970 |
Assert.assertEquals("There should be 4 names in the database", 4, nNames); |
|
971 |
int nRelations = service.countAllRelationships(); |
|
972 |
//may change with better implementation of countAllRelationships (see #2653) |
|
973 |
Assert.assertEquals("There should be 2 relationship in the database (the 2 synonym relationships) but no name relationship", 2, nRelations); |
|
974 |
|
|
975 |
UUID uuidSynonym1=UUID.fromString("7da85381-ad9d-4886-9d4d-0eeef40e3d88"); |
|
976 |
UUID uuidSynonymName2=UUID.fromString("613f3c93-013e-4ffc-aadc-1c98d71c335e"); |
|
977 |
|
|
978 |
Synonym synonym1 = (Synonym)service.load(uuidSynonym1); |
|
979 |
TaxonNameBase name2 = nameService.load(uuidSynonymName2); |
|
980 |
synonym1.getName().addRelationshipFromName(name2, NameRelationshipType.LATER_HOMONYM(), null); |
|
981 |
|
|
982 |
service.saveOrUpdate(synonym1); |
|
983 |
nRelations = service.countAllRelationships(); |
|
984 |
Assert.assertEquals("There should be two relationships in the database", 2, nRelations); |
|
985 |
this.setComplete(); |
|
986 |
this.endTransaction(); |
|
987 |
|
|
988 |
// printDataSet(System.out, tableNames); |
|
989 |
|
|
990 |
//out of wrapping transaction |
|
991 |
service.deleteSynonym(synonym1, new SynonymDeletionConfigurator()); |
|
992 |
|
|
993 |
this.startNewTransaction(); |
|
994 |
|
|
995 |
nSynonyms = service.count(Synonym.class); |
|
996 |
Assert.assertEquals("There should still be 1 synonyms left in the database. The rollback on name delete should not lead to rollback in synonym delete.", 1, nSynonyms); |
|
997 |
nNames = nameService.count(TaxonNameBase.class); |
|
998 |
Assert.assertEquals("There should be 4 names left in the database", 4, nNames); |
|
999 |
nRelations = service.countAllRelationships(); |
|
1000 |
Assert.assertEquals("There should be no taxon or synonym relationship in the database", 1, nRelations); |
|
1001 |
nRelations = nameService.getAllRelationships(1000,0).size(); |
|
1002 |
Assert.assertEquals("There should be one name relationship in the database", 1, nRelations); |
|
1003 |
|
|
1004 |
} |
|
1005 |
|
|
1006 |
@Test |
|
1007 |
@DataSet("TaxonServiceImplTest.testInferredSynonyms.xml") |
|
1008 |
public void testCreateInferredSynonymy(){ |
|
1009 |
|
|
1010 |
UUID classificationUuid = UUID.fromString("aeee7448-5298-4991-b724-8d5b75a0a7a9"); |
|
1011 |
Classification tree = classificationService.find(classificationUuid); |
|
1012 |
UUID taxonUuid = UUID.fromString("bc09aca6-06fd-4905-b1e7-cbf7cc65d783"); |
|
1013 |
TaxonBase<?> taxonBase = service.find(taxonUuid); |
|
1014 |
List <Synonym> synonyms = service.list(Synonym.class, null, null, null, null); |
|
1015 |
assertEquals("Number of synonyms should be 2",2,synonyms.size()); |
|
1016 |
Taxon taxon = (Taxon)taxonBase; |
|
1017 |
|
|
1018 |
//synonyms = taxonDao.getAllSynonyms(null, null); |
|
1019 |
//assertEquals("Number of synonyms should be 2",2,synonyms.size()); |
|
1020 |
List<Synonym> inferredSynonyms = service.createInferredSynonyms(taxon, tree, SynonymRelationshipType.INFERRED_EPITHET_OF(), true); |
|
1021 |
assertNotNull("there should be a new synonym ", inferredSynonyms); |
|
1022 |
assertEquals ("the name of inferred epithet should be SynGenus lachesis", "SynGenus lachesis sec. Sp. Pl.", inferredSynonyms.get(0).getTitleCache()); |
|
1023 |
|
|
1024 |
inferredSynonyms = service.createInferredSynonyms(taxon, tree, SynonymRelationshipType.INFERRED_GENUS_OF(), true); |
|
1025 |
assertNotNull("there should be a new synonym ", inferredSynonyms); |
|
1026 |
assertEquals ("the name of inferred epithet should be SynGenus lachesis", "Acherontia ciprosus sec. Sp. Pl.", inferredSynonyms.get(0).getTitleCache()); |
|
1027 |
|
|
1028 |
inferredSynonyms = service.createInferredSynonyms(taxon, tree, SynonymRelationshipType.POTENTIAL_COMBINATION_OF(), true); |
|
1029 |
assertNotNull("there should be a new synonym ", inferredSynonyms); |
|
1030 |
assertEquals ("the name of inferred epithet should be SynGenus lachesis", "SynGenus ciprosus sec. Sp. Pl.", inferredSynonyms.get(0).getTitleCache()); |
|
1031 |
//assertTrue("set of synonyms should contain an inferred Synonym ", synonyms.contains(arg0)) |
|
1032 |
} |
|
1033 |
|
|
1034 |
@Test |
|
1035 |
@DataSet("BlankDataSet.xml") |
|
1036 |
public final void testTaxonDeletionConfig(){ |
|
1037 |
final String[]tableNames = { |
|
1038 |
"Classification", "Classification_AUD", |
|
1039 |
"TaxonBase","TaxonBase_AUD", |
|
1040 |
"TaxonNode","TaxonNode_AUD", |
|
1041 |
"TaxonNameBase","TaxonNameBase_AUD", |
|
1042 |
"SynonymRelationship","SynonymRelationship_AUD", |
|
1043 |
"TaxonRelationship", "TaxonRelationship_AUD", |
|
1044 |
"TaxonDescription", "TaxonDescription_AUD", |
|
1045 |
"HomotypicalGroup","HomotypicalGroup_AUD", |
|
1046 |
"PolytomousKey","PolytomousKey_AUD", |
|
1047 |
"PolytomousKeyNode","PolytomousKeyNode_AUD", |
|
1048 |
"Media","Media_AUD", |
|
1049 |
"WorkingSet","WorkingSet_AUD", |
|
1050 |
"DescriptionElementBase","DescriptionElementBase_AUD", |
|
1051 |
"DeterminationEvent","DeterminationEvent_AUD", |
|
1052 |
"SpecimenOrObservationBase","SpecimenOrObservationBase_AUD"}; |
|
1053 |
|
|
1054 |
UUID uuidParent=UUID.fromString("b5271d4f-e203-4577-941f-00d76fa9f4ca"); |
|
1055 |
UUID uuidChild1=UUID.fromString("326167f9-0b97-4e7d-b1bf-4ca47b82e21e"); |
|
1056 |
UUID uuidSameAs=UUID.fromString("c2bb0f01-f2dd-43fb-ba12-2a85727ccb8d"); |
|
1057 |
commitAndStartNewTransaction(tableNames); |
|
1058 |
Taxon testTaxon = TaxonGenerator.getTestTaxon(); |
|
1059 |
service.save(testTaxon); |
|
1060 |
commitAndStartNewTransaction(tableNames); |
|
1061 |
int nTaxa = service.count(Taxon.class); |
|
1062 |
|
|
1063 |
Assert.assertEquals("There should be 4 taxa in the database", 4, nTaxa); |
|
1064 |
Taxon parent = (Taxon)service.find(TaxonGenerator.GENUS_UUID); |
|
1065 |
Assert.assertNotNull("Parent taxon should exist", parent); |
|
1066 |
Taxon child1 = (Taxon)service.find(TaxonGenerator.SPECIES1_UUID); |
|
1067 |
Assert.assertNotNull("Child taxon should exist", child1); |
|
1068 |
TaxonDeletionConfigurator config = new TaxonDeletionConfigurator(); |
|
1069 |
config.setDeleteTaxonNodes(false); |
|
1070 |
config.setDeleteMisappliedNamesAndInvalidDesignations(false); |
|
1071 |
//try { |
|
1072 |
//commitAndStartNewTransaction(tableNames); |
|
1073 |
|
|
1074 |
DeleteResult result = service.deleteTaxon(child1.getUuid(), config, null); |
|
1075 |
if (result.isOk()){ |
|
1076 |
Assert.fail("Delete should throw an error as long as name is used in classification."); |
|
1077 |
} |
|
1078 |
|
|
1079 |
nTaxa = service.count(Taxon.class); |
|
1080 |
Assert.assertEquals("There should be 4 taxa in the database", 4, nTaxa); |
|
1081 |
child1 = (Taxon)service.find(TaxonGenerator.SPECIES1_UUID); |
|
1082 |
Assert.assertNotNull("Child taxon should exist", child1); |
|
1083 |
Assert.assertEquals("Child should belong to 1 node", 1, child1.getTaxonNodes().size()); |
|
1084 |
|
|
1085 |
TaxonNode node = child1.getTaxonNodes().iterator().next(); |
|
1086 |
child1.addSource(IdentifiableSource.NewInstance(OriginalSourceType.Import)); |
|
1087 |
|
|
1088 |
SpecimenOrObservationBase<IIdentifiableEntityCacheStrategy> identifiedUnit = DerivedUnit.NewInstance(SpecimenOrObservationType.DerivedUnit); |
|
1089 |
DeterminationEvent determinationEvent = DeterminationEvent.NewInstance(child1, identifiedUnit); |
|
1090 |
//UUID eventUUID = eventService.save(determinationEvent); |
|
1091 |
UUID identifiedUnitUUID = occurenceService.save(identifiedUnit).getUuid(); |
|
1092 |
|
|
1093 |
|
|
1094 |
TaxonNode parentNode = node.getParent(); |
|
1095 |
parentNode =CdmBase.deproxy(parentNode, TaxonNode.class); |
|
1096 |
parentNode.deleteChildNode(node); |
|
1097 |
nodeService.save(parentNode); |
|
1098 |
//commitAndStartNewTransaction(tableNames); |
|
1099 |
|
|
1100 |
// try { |
|
1101 |
|
|
1102 |
result = service.deleteTaxon(child1 |
|
1103 |
.getUuid(), config, null); |
|
1104 |
if (result.isOk()){ |
|
1105 |
Assert.fail("Delete should throw an exception because of the determination event"); |
|
1106 |
} |
|
1107 |
|
|
1108 |
|
|
1109 |
|
|
1110 |
//determinationEvent = (DeterminationEvent)eventService.load(eventUUID); |
|
1111 |
commitAndStartNewTransaction(tableNames); |
|
1112 |
identifiedUnit = occurenceService.load(identifiedUnitUUID); |
|
1113 |
|
|
1114 |
occurenceService.delete(identifiedUnit); |
|
1115 |
|
|
1116 |
commitAndStartNewTransaction(tableNames); |
|
1117 |
child1 = (Taxon)service.find(TaxonGenerator.SPECIES1_UUID); |
|
1118 |
|
|
1119 |
assertEquals(0, child1.getTaxonNodes().size()); |
|
1120 |
// try { |
|
1121 |
|
|
1122 |
result = service.deleteTaxon(child1.getUuid(), config, null); |
|
1123 |
|
|
1124 |
if (!result.isOk()){ |
|
1125 |
Assert.fail("Delete should not throw an exception anymore"); |
|
1126 |
} |
|
1127 |
|
|
1128 |
nTaxa = service.count(Taxon.class); |
|
1129 |
Assert.assertEquals("There should be 3 taxa in the database", 3, nTaxa); |
|
1130 |
|
|
1131 |
config.setDeleteTaxonNodes(true); |
|
1132 |
Taxon child2 =(Taxon) service.find(TaxonGenerator.SPECIES2_UUID); |
|
1133 |
|
|
1134 |
// try { |
|
1135 |
result = service.deleteTaxon(child2.getUuid(), config, child2.getTaxonNodes().iterator().next().getClassification().getUuid()); |
|
1136 |
if (!result.isOk()){ |
|
1137 |
Assert.fail("Delete should not throw an exception"); |
|
1138 |
} |
|
1139 |
|
|
1140 |
|
|
1141 |
//service.find(uuid); |
|
1142 |
|
|
1143 |
nTaxa = service.count(Taxon.class); |
|
1144 |
Assert.assertEquals("There should be 2 taxa in the database",2, nTaxa); |
|
1145 |
// nNames = nameService.count(TaxonNameBase.class); |
|
1146 |
// Assert.assertEquals("There should be 3 names left in the database", 3, nNames); |
|
1147 |
// int nRelations = service.countAllRelationships(); |
|
1148 |
// Assert.assertEquals("There should be no relationship left in the database", 0, nRelations); |
|
1149 |
} |
|
1150 |
|
|
1151 |
|
|
1152 |
@Test |
|
1153 |
@DataSet(value="BlankDataSet.xml") |
|
1154 |
public final void testDeleteTaxon(){ |
|
1155 |
|
|
1156 |
//create a small classification |
|
1157 |
Taxon testTaxon = TaxonGenerator.getTestTaxon(); |
|
1158 |
|
|
1159 |
UUID uuid = service.save(testTaxon).getUuid(); |
|
1160 |
|
|
1161 |
Taxon speciesTaxon = (Taxon)service.find(TaxonGenerator.SPECIES1_UUID); |
|
1162 |
Iterator<TaxonDescription> descriptionIterator = speciesTaxon.getDescriptions().iterator(); |
|
1163 |
UUID descrUUID = null; |
|
1164 |
UUID descrElementUUID = null; |
|
1165 |
if (descriptionIterator.hasNext()){ |
|
1166 |
TaxonDescription descr = descriptionIterator.next(); |
|
1167 |
descrUUID = descr.getUuid(); |
|
1168 |
descrElementUUID = descr.getElements().iterator().next().getUuid(); |
|
1169 |
} |
|
1170 |
BotanicalName taxonName = (BotanicalName) nameService.find(TaxonGenerator.SPECIES1_NAME_UUID); |
|
1171 |
assertNotNull(taxonName); |
|
1172 |
|
|
1173 |
TaxonDeletionConfigurator config = new TaxonDeletionConfigurator(); |
|
1174 |
config.setDeleteNameIfPossible(false); |
|
1175 |
|
|
1176 |
|
|
1177 |
|
|
1178 |
// try { |
|
1179 |
|
|
1180 |
DeleteResult result = service.deleteTaxon(speciesTaxon.getUuid(), config, speciesTaxon.getTaxonNodes().iterator().next().getClassification().getUuid()); |
|
1181 |
if (!result.isOk()){ |
|
1182 |
Assert.fail(); |
|
1183 |
} |
|
1184 |
commitAndStartNewTransaction(null); |
|
1185 |
|
|
1186 |
taxonName = (BotanicalName) nameService.find(TaxonGenerator.SPECIES1_NAME_UUID); |
|
1187 |
Taxon taxon = (Taxon)service.find(TaxonGenerator.SPECIES1_UUID); |
|
1188 |
|
|
1189 |
//descriptionService.find(descrUUID); |
|
1190 |
assertNull(descriptionService.find(descrUUID)); |
|
1191 |
assertNull(descriptionService.getDescriptionElementByUuid(descrElementUUID)); |
|
1192 |
//assertNull(synName); |
|
1193 |
assertNotNull(taxonName); |
|
1194 |
assertNull(taxon); |
|
1195 |
config.setDeleteNameIfPossible(true); |
|
1196 |
Taxon newTaxon = Taxon.NewInstance(BotanicalName.NewInstance(Rank.SPECIES()), null); |
|
1197 |
service.save(newTaxon); |
|
1198 |
result = service.deleteTaxon(newTaxon.getUuid() |
|
1199 |
, config, null); |
|
1200 |
if (!result.isOk()){ |
|
1201 |
Assert.fail(); |
|
1202 |
} |
|
1203 |
|
|
1204 |
|
|
1205 |
} |
|
1206 |
|
|
1207 |
@Test |
|
1208 |
@DataSet(value="BlankDataSet.xml") |
|
1209 |
public final void testDeleteTaxonUsedInTaxonRelation(){ |
|
1210 |
|
|
1211 |
//create a small classification |
|
1212 |
Taxon testTaxon = TaxonGenerator.getTestTaxon(); |
|
1213 |
|
|
1214 |
UUID uuid = service.save(testTaxon).getUuid(); |
|
1215 |
|
|
1216 |
Taxon speciesTaxon = (Taxon)service.find(TaxonGenerator.SPECIES1_UUID); |
|
1217 |
Taxon speciesTaxon2 = (Taxon)service.find(TaxonGenerator.SPECIES2_UUID); |
|
1218 |
speciesTaxon.addTaxonRelation(speciesTaxon2, TaxonRelationshipType.MISAPPLIED_NAME_FOR(), null, null); |
|
1219 |
|
|
1220 |
BotanicalName taxonName = (BotanicalName) nameService.find(TaxonGenerator.SPECIES1_NAME_UUID); |
|
1221 |
assertNotNull(taxonName); |
|
1222 |
|
|
1223 |
TaxonDeletionConfigurator config = new TaxonDeletionConfigurator(); |
|
1224 |
config.setDeleteNameIfPossible(false); |
|
1225 |
config.setDeleteTaxonRelationships(false); |
|
1226 |
|
|
1227 |
|
|
1228 |
// try { |
|
1229 |
|
|
1230 |
DeleteResult result = service.deleteTaxon(speciesTaxon.getUuid(), config, speciesTaxon.getTaxonNodes().iterator().next().getClassification().getUuid()); |
|
1231 |
if (result.isOk()){ |
|
1232 |
Assert.fail(); |
|
1233 |
} |
|
1234 |
commitAndStartNewTransaction(null); |
|
1235 |
|
|
1236 |
taxonName = (BotanicalName) nameService.find(TaxonGenerator.SPECIES1_NAME_UUID); |
|
1237 |
Taxon taxon = (Taxon)service.find(TaxonGenerator.SPECIES1_UUID); |
|
1238 |
|
|
1239 |
|
|
1240 |
assertNotNull(taxonName); |
|
1241 |
assertNotNull(taxon); |
|
1242 |
|
|
1243 |
|
|
1244 |
config.setDeleteNameIfPossible(false); |
|
1245 |
config.setDeleteTaxonRelationships(true); |
|
1246 |
|
|
1247 |
|
|
1248 |
// try { |
|
1249 |
|
|
1250 |
result = service.deleteTaxon(speciesTaxon.getUuid(), config, speciesTaxon.getTaxonNodes().iterator().next().getClassification().getUuid()); |
|
1251 |
if (!result.isOk()){ |
|
1252 |
Assert.fail(); |
|
1253 |
} |
|
1254 |
commitAndStartNewTransaction(null); |
|
1255 |
|
|
1256 |
|
|
1257 |
config.setDeleteNameIfPossible(true); |
|
1258 |
Taxon newTaxon = Taxon.NewInstance(BotanicalName.NewInstance(Rank.SPECIES()), null); |
|
1259 |
service.save(newTaxon); |
|
1260 |
result = service.deleteTaxon(newTaxon.getUuid() |
|
1261 |
, config, null); |
|
1262 |
if (!result.isOk()){ |
|
1263 |
Assert.fail(); |
|
1264 |
} |
|
1265 |
|
|
1266 |
|
|
1267 |
} |
|
1268 |
|
|
1269 |
@Test |
|
1270 |
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="BlankDataSet.xml") |
|
1271 |
public final void testDeleteTaxonDeleteSynonymRelations(){ |
|
1272 |
|
|
1273 |
final String[]tableNames = { |
|
1274 |
"Classification", "Classification_AUD", |
|
1275 |
"TaxonBase","TaxonBase_AUD", |
|
1276 |
"TaxonNode","TaxonNode_AUD", |
|
1277 |
"TaxonNameBase","TaxonNameBase_AUD"}; |
|
1278 |
commitAndStartNewTransaction(tableNames); |
|
1279 |
//create a small classification |
|
1280 |
Taxon testTaxon = TaxonGenerator.getTestTaxon(); |
|
1281 |
|
|
1282 |
UUID uuid = service.save(testTaxon).getUuid(); |
|
1283 |
|
|
1284 |
Taxon speciesTaxon = (Taxon)service.find(TaxonGenerator.SPECIES2_UUID); |
|
1285 |
|
|
1286 |
SynonymRelationship synRel = speciesTaxon.getSynonymRelations().iterator().next(); |
|
1287 |
UUID synonymRelationUuid = synRel.getUuid(); |
|
1288 |
UUID synonymUuid = synRel.getSynonym().getUuid(); |
|
1289 |
int i = service.getAllRelationships(1000, 0).size(); |
|
1290 |
|
|
1291 |
TaxonDeletionConfigurator config = new TaxonDeletionConfigurator(); |
|
1292 |
config.setDeleteSynonymsIfPossible(false); |
|
1293 |
|
|
1294 |
|
|
1295 |
DeleteResult result = service.deleteTaxon(speciesTaxon.getUuid(), config, speciesTaxon.getTaxonNodes().iterator().next().getClassification().getUuid()); |
|
1296 |
if (!result.isOk()){ |
|
1297 |
Assert.fail(); |
|
1298 |
} |
|
1299 |
commitAndStartNewTransaction(null); |
|
1300 |
|
|
1301 |
Taxon taxon = (Taxon)service.find(TaxonGenerator.SPECIES2_UUID); |
|
1302 |
assertNull("The deleted taxon should no longer exist", taxon); |
|
1303 |
|
|
1304 |
assertNotNull("The synonym should still exist since DeleteSynonymsIfPossible was false", service.find(synonymUuid)); |
|
1305 |
|
|
1306 |
for(RelationshipBase rel : service.getAllRelationships(1000, 0)){ |
|
1307 |
if(rel instanceof SynonymRelationship && rel.getUuid().equals(synonymRelationUuid)){ |
|
1308 |
Assert.fail("The SynonymRelationship should no longer exist"); |
|
1309 |
} |
|
1310 |
} |
|
1311 |
} |
|
1312 |
|
|
1313 |
|
|
1314 |
@Test |
|
1315 |
@DataSet(value="BlankDataSet.xml") |
|
1316 |
public final void testDeleteTaxonNameUsedInOtherContext(){ |
|
1317 |
|
|
1318 |
//create a small classification |
|
1319 |
Taxon testTaxon = TaxonGenerator.getTestTaxon(); |
|
1320 |
|
|
1321 |
UUID uuid = service.save(testTaxon).getUuid(); |
|
1322 |
|
|
1323 |
Taxon speciesTaxon = (Taxon)service.find(TaxonGenerator.SPECIES1_UUID); |
|
1324 |
|
|
1325 |
BotanicalName taxonName = (BotanicalName) nameService.find(TaxonGenerator.SPECIES1_NAME_UUID); |
|
1326 |
assertNotNull(taxonName); |
|
1327 |
BotanicalName fromName = BotanicalName.NewInstance(Rank.SPECIES()); |
|
1328 |
taxonName.addRelationshipFromName(fromName, NameRelationshipType.VALIDATED_BY_NAME(), null); |
|
1329 |
|
|
1330 |
TaxonDeletionConfigurator config = new TaxonDeletionConfigurator(); |
|
1331 |
config.setDeleteNameIfPossible(true); |
|
1332 |
DeleteResult result = service.deleteTaxon(speciesTaxon.getUuid(), config, speciesTaxon.getTaxonNodes().iterator().next().getClassification().getUuid()); |
|
1333 |
if (!result.isOk()){ |
|
1334 |
Assert.fail(); |
|
1335 |
} |
|
1336 |
commitAndStartNewTransaction(null); |
|
1337 |
|
|
1338 |
taxonName = (BotanicalName) nameService.find(TaxonGenerator.SPECIES1_NAME_UUID); |
|
1339 |
Taxon taxon = (Taxon)service.find(TaxonGenerator.SPECIES1_UUID); |
|
1340 |
//because of the namerelationship the name cannot be deleted |
|
1341 |
assertNotNull(taxonName); |
|
1342 |
assertNull(taxon); |
|
1343 |
|
|
1344 |
} |
|
1345 |
|
|
1346 |
@Test |
|
1347 |
@DataSet(value="BlankDataSet.xml") |
|
1348 |
public final void testDeleteTaxonNameUsedInTwoClassificationsDeleteAllNodes(){ |
|
1349 |
commitAndStartNewTransaction(null); |
|
1350 |
TaxonDeletionConfigurator config = new TaxonDeletionConfigurator(); |
|
1351 |
//create a small classification |
|
1352 |
Taxon testTaxon = TaxonGenerator.getTestTaxon(); |
|
1353 |
|
|
1354 |
UUID uuid = service.save(testTaxon).getUuid(); |
|
1355 |
//BotanicalName name = nameService.find(uuid); |
|
1356 |
Set<TaxonNode> nodes = testTaxon.getTaxonNodes(); |
|
1357 |
TaxonNode node = nodes.iterator().next(); |
|
1358 |
List<TaxonNode> childNodes = node.getChildNodes(); |
|
1359 |
TaxonNode childNode = childNodes.iterator().next(); |
|
1360 |
UUID childUUID = childNode.getTaxon().getUuid(); |
|
1361 |
Classification secondClassification = TaxonGenerator.getTestClassification("secondClassification"); |
|
1362 |
|
|
1363 |
secondClassification.addChildTaxon(testTaxon, null, null); |
|
1364 |
//delete the taxon in all classifications |
|
1365 |
config.setDeleteInAllClassifications(true); |
|
1366 |
DeleteResult result = service.deleteTaxon(testTaxon.getUuid(), config, null); |
|
1367 |
if (!result.isOk()){ |
|
1368 |
Assert.fail(); |
|
1369 |
} |
|
1370 |
commitAndStartNewTransaction(null); |
|
1371 |
Taxon tax = (Taxon)service.find(uuid); |
|
1372 |
assertNull(tax); |
|
1373 |
Taxon childTaxon = (Taxon)service.find(childUUID); |
|
1374 |
assertNull(tax); |
|
1375 |
commitAndStartNewTransaction(null); |
|
1376 |
|
|
1377 |
|
|
1378 |
|
|
1379 |
|
|
1380 |
|
|
1381 |
} |
|
1382 |
|
|
1383 |
@Test |
|
1384 |
@DataSet(value="BlankDataSet.xml") |
|
1385 |
public final void testDeleteTaxonNameUsedInTwoClassificationsDoNotDeleteAllNodes(){ |
|
1386 |
// delete the taxon only in second classification, this should delete only the nodes, not the taxa |
|
1387 |
Taxon testTaxon = TaxonGenerator.getTestTaxon(); |
|
1388 |
UUID uuid = service.save(testTaxon).getUuid(); |
|
1389 |
Classification secondClassification = TaxonGenerator.getTestClassification("secondClassification"); |
|
1390 |
Set<TaxonNode> nodes = testTaxon.getTaxonNodes(); |
|
1391 |
TaxonNode node = nodes.iterator().next(); |
|
1392 |
List<TaxonNode> childNodes = node.getChildNodes(); |
|
1393 |
TaxonNode childNode = childNodes.iterator().next(); |
|
1394 |
UUID childUUID = childNode.getTaxon().getUuid(); |
|
1395 |
childNode = secondClassification.addChildTaxon(testTaxon, null, null); |
|
1396 |
UUID childNodeUUID = childNode.getUuid(); |
|
1397 |
|
|
1398 |
TaxonDeletionConfigurator config = new TaxonDeletionConfigurator() ; |
|
1399 |
config.setDeleteInAllClassifications(false); |
|
1400 |
// try { |
|
1401 |
DeleteResult result = service.deleteTaxon(testTaxon.getUuid(), config, secondClassification.getUuid()); |
|
1402 |
/* Assert.fail("The taxon should not be deletable because it is used in a second classification and the configuration is set to deleteInAllClassifications = false"); |
|
1403 |
} catch (DataChangeNoRollbackException e) { |
|
1404 |
logger.debug(e.getMessage()); |
|
1405 |
} |
|
1406 |
*/ |
|
1407 |
|
|
1408 |
if (result.isOk()){ |
|
1409 |
Assert.fail("The taxon should not be deletable because it is used in a second classification and the configuration is set to deleteInAllClassifications = false"); |
|
1410 |
} |
|
1411 |
|
|
1412 |
//commitAndStartNewTransaction(null); |
|
1413 |
Taxon tax = (Taxon)service.find(uuid); |
|
1414 |
assertNotNull(tax); |
|
1415 |
Taxon childTaxon = (Taxon)service.find(childUUID); |
|
1416 |
assertNotNull(tax); |
|
1417 |
node = nodeService.find(childNodeUUID); |
|
1418 |
assertNull(node); |
|
1419 |
} |
|
1420 |
|
|
1421 |
@Test |
|
1422 |
@DataSet(value="BlankDataSet.xml") |
|
1423 |
public final void testTaxonNodeDeletionConfiguratorMoveToParent(){ |
|
1424 |
//test childHandling MOVE_TO_PARENT: |
|
1425 |
Taxon testTaxon = TaxonGenerator.getTestTaxon(); |
|
1426 |
UUID uuid = service.save(testTaxon).getUuid(); |
|
1427 |
|
|
1428 |
Taxon topMost = Taxon.NewInstance(BotanicalName.NewInstance(Rank.FAMILY()), null); |
|
1429 |
|
|
1430 |
Iterator<TaxonNode> nodes = testTaxon.getTaxonNodes().iterator(); |
|
1431 |
TaxonNode node =nodes.next(); |
|
1432 |
Classification classification = node.getClassification(); |
|
1433 |
classification.addParentChild(topMost, testTaxon, null, null); |
|
1434 |
UUID topMostUUID = service.save(topMost).getUuid(); |
|
1435 |
|
|
1436 |
TaxonDeletionConfigurator config = new TaxonDeletionConfigurator() ; |
|
1437 |
config.getTaxonNodeConfig().setChildHandling(ChildHandling.MOVE_TO_PARENT); |
|
1438 |
|
|
1439 |
|
|
1440 |
DeleteResult result = service.deleteTaxon(testTaxon.getUuid(), config, classification.getUuid()); |
|
1441 |
if(!result.isOk()){ |
|
1442 |
Assert.fail(); |
|
1443 |
} |
|
1444 |
|
|
1445 |
commitAndStartNewTransaction(null); |
|
1446 |
Taxon tax = (Taxon)service.find(uuid); |
|
1447 |
assertNull(tax); |
|
1448 |
tax = (Taxon)service.find(topMostUUID); |
|
1449 |
Set<TaxonNode> topMostNodes = tax.getTaxonNodes(); |
|
1450 |
assertNotNull(topMostNodes); |
|
1451 |
assertEquals("there should be one taxon node", 1, topMostNodes.size()); |
|
1452 |
nodes = topMostNodes.iterator(); |
|
1453 |
TaxonNode topMostNode = nodes.next(); |
|
1454 |
int size = topMostNode.getChildNodes().size(); |
|
1455 |
|
|
1456 |
assertEquals(2, size); |
|
1457 |
} |
|
1458 |
|
|
1459 |
@Test |
|
1460 |
@DataSet(value="BlankDataSet.xml") |
|
1461 |
public final void testTaxonNodeDeletionConfiguratorDeleteChildren(){ |
|
1462 |
//test childHandling DELETE: |
|
1463 |
Taxon testTaxon = TaxonGenerator.getTestTaxon(); |
|
1464 |
UUID uuid = service.save(testTaxon).getUuid(); |
|
1465 |
|
|
1466 |
Taxon topMost = Taxon.NewInstance(BotanicalName.NewInstance(Rank.FAMILY()), null); |
|
1467 |
|
|
1468 |
Iterator<TaxonNode> nodes = testTaxon.getTaxonNodes().iterator(); |
|
1469 |
TaxonNode node =nodes.next(); |
|
1470 |
UUID taxonNodeUUID = node.getUuid(); |
|
1471 |
Classification classification = node.getClassification(); |
|
1472 |
classification.addParentChild(topMost, testTaxon, null, null); |
|
1473 |
UUID topMostUUID = service.save(topMost).getUuid(); |
|
1474 |
|
|
1475 |
TaxonDeletionConfigurator config = new TaxonDeletionConfigurator() ; |
|
1476 |
config.getTaxonNodeConfig().setChildHandling(ChildHandling.DELETE); |
|
1477 |
|
|
1478 |
// try { |
|
1479 |
DeleteResult result = service.deleteTaxon(testTaxon.getUuid(), config, testTaxon.getTaxonNodes().iterator().next().getClassification().getUuid()); |
|
1480 |
if(!result.isOk()){ |
|
1481 |
Assert.fail(); |
|
1482 |
} |
|
1483 |
commitAndStartNewTransaction(null); |
|
1484 |
Taxon tax = (Taxon)service.find(uuid); |
|
1485 |
assertNull(tax); |
|
1486 |
tax = (Taxon)service.find(topMostUUID); |
|
1487 |
Set<TaxonNode> topMostNodes = tax.getTaxonNodes(); |
|
1488 |
assertNotNull(topMostNodes); |
|
1489 |
assertEquals("there should be one taxon node", 1, topMostNodes.size()); |
|
1490 |
nodes = topMostNodes.iterator(); |
Also available in: Unified diff
Fix failing test for syn. sec. (#5902) and clean up a bit