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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.assertTrue;
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import java.io.FileNotFoundException;
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import java.lang.reflect.Field;
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import java.util.Arrays;
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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.Ignore;
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import org.junit.Test;
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import org.springframework.security.authentication.AbstractAuthenticationToken;
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import org.springframework.security.authentication.AuthenticationManager;
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import org.springframework.security.authentication.UsernamePasswordAuthenticationToken;
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import org.springframework.security.core.Authentication;
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import org.springframework.security.core.context.SecurityContextHolder;
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import org.springframework.security.core.context.SecurityContextImpl;
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import org.unitils.dbunit.annotation.DataSet;
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import org.unitils.spring.annotation.SpringBeanByName;
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import org.unitils.spring.annotation.SpringBeanByType;
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import eu.etaxonomy.cdm.api.service.config.IdentifiableServiceConfiguratorFactory;
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import eu.etaxonomy.cdm.api.service.config.IdentifiableServiceConfiguratorImpl;
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import eu.etaxonomy.cdm.api.service.config.NameDeletionConfigurator;
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import eu.etaxonomy.cdm.api.service.pager.Pager;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
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import eu.etaxonomy.cdm.model.description.TextData;
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import eu.etaxonomy.cdm.model.name.HybridRelationship;
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import eu.etaxonomy.cdm.model.name.HybridRelationshipType;
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import eu.etaxonomy.cdm.model.name.NameRelationshipType;
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import eu.etaxonomy.cdm.model.name.NameTypeDesignation;
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import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.Registration;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
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import eu.etaxonomy.cdm.model.name.TypeDesignationBase;
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
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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.persistence.dao.common.Restriction;
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import eu.etaxonomy.cdm.persistence.dao.common.Restriction.Operator;
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import eu.etaxonomy.cdm.persistence.query.MatchMode;
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import eu.etaxonomy.cdm.persistence.query.OrderHint;
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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 NameServiceImplTest extends CdmTransactionalIntegrationTest {
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private static final Logger logger = Logger.getLogger(NameServiceImplTest.class);
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private static final UUID NAME1_UUID = UUID.fromString("6dbd41d1-fe13-4d9c-bb58-31f051c2c384");
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private static final int NAME1_ID = 10;
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private static final UUID NAME2_UUID = UUID.fromString("f9e9c13f-5fa5-48d3-88cf-712c921a099e");
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private static final int NAME2_ID = 11;
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private static final UUID NAME3_UUID = UUID.fromString("e1e66264-f16a-4df9-80fd-6ab5028a3c28");
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private static final int NAME3_ID = 12;
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@SpringBeanByType
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private INameService nameService;
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@SpringBeanByType
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private IOccurrenceService occurrenceService;
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@SpringBeanByType
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private IRegistrationService registrationService;
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@SpringBeanByType
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private ITaxonService taxonService;
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@SpringBeanByType
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private ITermService termService;
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@SpringBeanByName
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private AuthenticationManager authenticationManager;
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private void setAuthentication(AbstractAuthenticationToken token) {
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Authentication authentication = authenticationManager.authenticate(token);
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SecurityContextImpl secureContext = new SecurityContextImpl();
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SecurityContextHolder.setContext(secureContext);
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secureContext.setAuthentication(authentication);
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}
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private void unsetAuthentication() {
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SecurityContextImpl secureContext = new SecurityContextImpl();
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SecurityContextHolder.setContext(secureContext);
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secureContext.setAuthentication(null);
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}
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/* ******************** TESTS ********************************************/
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/**
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* Test method for {@link eu.etaxonomy.cdm.api.service.NameServiceImpl#setDao(eu.etaxonomy.cdm.persistence.dao.name.ITaxonNameDao)}.
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*/
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@Test
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public void testSetDao() {
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// Assert.assertNotNull(((NameServiceImpl)nameService).dao);
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}
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/**
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* Test method for {@link eu.etaxonomy.cdm.api.service.NameServiceImpl#setVocabularyDao(eu.etaxonomy.cdm.persistence.dao.common.ITermVocabularyDao)}.
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*/
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@Test
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public void testSetVocabularyDao() {
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// Assert.assertNotNull(( (NameServiceImpl)nameService.vocabularyDao);
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}
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/**
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* Test method for {@link eu.etaxonomy.cdm.api.service.NameServiceImpl#getNamesByName(java.lang.String)}.
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*/
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@Test
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public void testGetNamesByName() {
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logger.warn("Not yet implemented");
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}
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@Test
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@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class)
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public void testDeleteTaxonNameWithNameRelations() {
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final String[] tableNames = new String[]{"USERACCOUNT", "TaxonName","NameRelationship","HybridRelationship","DescriptionBase","NomenclaturalStatus","TaxonBase","SpecimenOrObservationBase","OriginalSourceBase","DescriptionElementBase"};
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// printDataSet(System.err, true, null);
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TaxonName name1 = TaxonNameFactory.NewBotanicalInstance(getSpeciesRank());
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name1.setTitleCache("Name1", true);
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TaxonName nameWithBasionym = TaxonNameFactory.NewBotanicalInstance(getSpeciesRank());
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nameWithBasionym.setTitleCache("nameWithBasionym", true);
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NameRelationshipType nameRelType = (NameRelationshipType)termService.find(NameRelationshipType.BASIONYM().getUuid());
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name1.addRelationshipToName(nameWithBasionym,nameRelType , null, null, null, null);
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// nameWithBasionym.addBasionym(name1);
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nameService.save(name1);
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nameService.save(nameWithBasionym);
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commitAndStartNewTransaction(tableNames);
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name1 = nameService.find(name1.getUuid());
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DeleteResult result = nameService.delete(name1);
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if (!result.isOk()){
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Exception e = result.getExceptions().iterator().next();
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Assert.assertEquals("The Ecxeption should be a ReferencedObjectException because it is a basionym", "Name can't be deleted as it is a basionym.", e.getMessage());
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} else{
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Assert.fail();
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}
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name1 = nameService.find(name1.getUuid());
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Assert.assertNotNull("Name should still be in database",name1);
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nameWithBasionym = name1.getNameRelations().iterator().next().getToName();
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nameWithBasionym.removeBasionyms();
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result = nameService.delete(name1); //should throw now exception
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commitAndStartNewTransaction(tableNames);
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name1 = nameService.find(name1.getUuid());
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Assert.assertNull("Name should not be in database anymore",name1);
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}
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@Test
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@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class)
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public void testDeleteTaxonNameConfiguratorWithNameRelations() {
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final String[] tableNames = new String[]{"TaxonName","NameRelationship","HybridRelationship"};
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// printDataSet(System.err, new String[]{"TaxonName","NameRelationship","HybridRelationship","DescriptionBase","NomenclaturalStatus","TaxonBase","SpecimenOrObservationBase","OriginalSourceBase",
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// "DescriptionElementBase",
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// "AGENTBASE", "USERACCOUNT", "PERMISSIONGROUP", "USERACCOUNT_PERMISSIONGROUP", "USERACCOUNT_GRANTEDAUTHORITYIMPL", "GRANTEDAUTHORITYIMPL"});
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TaxonName name1 = TaxonNameFactory.NewBotanicalInstance(getSpeciesRank());
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name1.setTitleCache("Name1", true);
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TaxonName nameWithBasionym = TaxonNameFactory.NewBotanicalInstance(getSpeciesRank());
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nameWithBasionym.setTitleCache("nameWithBasionym", true);
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NameRelationshipType nameRelType = (NameRelationshipType)termService.find(NameRelationshipType.BASIONYM().getUuid());
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name1.addRelationshipToName(nameWithBasionym,nameRelType , null, null, null, null);
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nameService.save(name1);
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nameService.save(nameWithBasionym);
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commitAndStartNewTransaction(tableNames);
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NameDeletionConfigurator config = new NameDeletionConfigurator();
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name1 = nameService.find(name1.getUuid());
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DeleteResult result = nameService.delete(name1.getUuid(), config);
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if (result.isOk()){
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Assert.fail("This should throw an error as long as name relationships exist.");
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}
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name1 = nameService.find(name1.getUuid());
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Assert.assertNotNull("Name should still be in database",name1);
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//ignore is basionym for
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config.setIgnoreIsBasionymFor(true);
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name1 = nameService.find(name1.getUuid());
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nameService.delete(name1.getUuid(), config);
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commitAndStartNewTransaction(tableNames);
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name1 = nameService.find(name1.getUuid());
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Assert.assertNull("Name should not be in database anymore",name1);
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}
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@Test
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public void testDeleteTaxonNameConfiguratorWithNameRelationsAll() {
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final String[] tableNames = new String[]{"TaxonName","NameRelationship","HybridRelationship"};
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TaxonName name1 = TaxonNameFactory.NewBotanicalInstance(getSpeciesRank());
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name1.setTitleCache("Name1", true);
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TaxonName nameWithBasionym = TaxonNameFactory.NewBotanicalInstance(getSpeciesRank());
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nameWithBasionym.setTitleCache("nameWithBasionym", true);
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NameRelationshipType nameRelType = (NameRelationshipType)termService.find(NameRelationshipType.BASIONYM().getUuid());
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name1.addRelationshipToName(nameWithBasionym,nameRelType , null, null, null, null);
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nameService.save(name1);
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nameService.save(nameWithBasionym);
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commitAndStartNewTransaction(tableNames);
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NameDeletionConfigurator config = new NameDeletionConfigurator();
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name1 = nameService.find(name1.getUuid());
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DeleteResult result = nameService.delete(name1.getUuid(), config);
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if (result.isOk()){
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Assert.fail("Delete should throw an error as long as name relationships exist.");
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}
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name1 = nameService.find(name1.getUuid());
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Assert.assertNotNull("Name should still be in database",name1);
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//ignore all name relationships
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config.setRemoveAllNameRelationships(true);
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name1 = nameService.find(name1.getUuid());
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result = nameService.delete(name1.getUuid(), config);
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logger.debug(result);
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commitAndStartNewTransaction(tableNames);
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name1 = nameService.find(name1.getUuid());
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Assert.assertNull("Name should not be in database anymore",name1);
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}
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@Test
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public void testDeleteTaxonNameConfiguratorWithHasBasionym() {
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final String[] tableNames = new String[]{"TaxonName","NameRelationship","HybridRelationship"};
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TaxonName name1 = TaxonNameFactory.NewBotanicalInstance(getSpeciesRank());
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name1.setTitleCache("Name1", true);
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TaxonName basionym = TaxonNameFactory.NewBotanicalInstance(getSpeciesRank());
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basionym.setTitleCache("basionym", true);
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NameRelationshipType nameRelType = (NameRelationshipType)termService.find(NameRelationshipType.BASIONYM().getUuid());
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basionym.addRelationshipToName(name1,nameRelType , null, null, null, null);
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nameService.save(name1);
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nameService.save(basionym);
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commitAndStartNewTransaction(tableNames);
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NameDeletionConfigurator config = new NameDeletionConfigurator();
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config.setIgnoreHasBasionym(false);
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name1 = nameService.find(name1.getUuid());
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DeleteResult result = nameService.delete(name1.getUuid(), config);
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if (result.isOk()){
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Assert.fail("Delete should throw an error as long as name relationships exist.");
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}
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name1 = nameService.find(name1.getUuid());
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Assert.assertNotNull("Name should still be in database",name1);
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//ignore has basionym
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config.setIgnoreHasBasionym(true);
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try {
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name1 = nameService.find(name1.getUuid());
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result = nameService.delete(name1.getUuid(), config);
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logger.debug(result);
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commitAndStartNewTransaction(tableNames);
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name1 = nameService.find(name1.getUuid());
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Assert.assertNull("Name should not be in database anymore",name1);
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} catch (Exception e) {
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Assert.fail("Delete should not throw an error for .");
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}
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}
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@Test
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public void testDeleteTaxonNameWithHybridRelations() {
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final String[] tableNames = new String[]{"TaxonName","NameRelationship","HybridRelationship"};
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TaxonName name1 = TaxonNameFactory.NewBotanicalInstance(getSpeciesRank());
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name1.setTitleCache("Name1", true);
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TaxonName parent = TaxonNameFactory.NewBotanicalInstance(getSpeciesRank());
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parent.setTitleCache("parent", true);
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TaxonName child = TaxonNameFactory.NewBotanicalInstance(getSpeciesRank());
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child.setTitleCache("child", true);
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TaxonName hybrid = TaxonNameFactory.PARSED_BOTANICAL("Abies alba x Pinus beta");
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Set<HybridRelationship> childRelations = hybrid.getHybridChildRelations();
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for (HybridRelationship rel : childRelations){
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nameService.save(rel.getHybridName());
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nameService.save(rel.getParentName());
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}
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commitAndStartNewTransaction(tableNames); //otherwise first save is rolled back with following failing delete
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328
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HybridRelationshipType relType = (HybridRelationshipType)termService.find(HybridRelationshipType.FIRST_PARENT().getUuid());
|
|
329
|
name1.addHybridParent(parent, relType, null);
|
|
330
|
nameService.save(name1);
|
|
331
|
nameService.save(parent);
|
|
332
|
commitAndStartNewTransaction(tableNames); //otherwise first save is rolled back with following failing delete
|
|
333
|
Assert.assertEquals("'Parent' should be a parent in a hybrid relation.", 1,parent.getHybridParentRelations().size());
|
|
334
|
|
|
335
|
//parent
|
|
336
|
|
|
337
|
name1 = nameService.find(name1.getUuid());
|
|
338
|
DeleteResult result = nameService.delete(name1);
|
|
339
|
if (result.isError()){
|
|
340
|
Assert.fail("Delete should throw NO exception when deleting a hybrid child: " + result.getExceptions().iterator().next().getMessage());
|
|
341
|
}
|
|
342
|
commitAndStartNewTransaction(tableNames);
|
|
343
|
name1 = nameService.find(name1.getUuid());
|
|
344
|
Assert.assertNull("Name should not be in database anymore",name1);
|
|
345
|
parent = nameService.find(parent.getUuid());
|
|
346
|
Assert.assertEquals("'Parent' should not be a parent anymore.", 0,parent.getHybridParentRelations().size());
|
|
347
|
|
|
348
|
//child
|
|
349
|
name1 = TaxonNameFactory.NewBotanicalInstance(getSpeciesRank());
|
|
350
|
name1.addHybridChild(child, relType, null);
|
|
351
|
nameService.save(name1);
|
|
352
|
nameService.save(child);
|
|
353
|
commitAndStartNewTransaction(tableNames);
|
|
354
|
|
|
355
|
|
|
356
|
result = nameService.delete(name1);
|
|
357
|
if (result.isOk()){
|
|
358
|
Assert.fail("Delete should throw an error as long as hybrid child exist.");
|
|
359
|
}
|
|
360
|
name1 = nameService.find(name1.getUuid());
|
|
361
|
Assert.assertNotNull("Name should still be in database",name1);
|
|
362
|
name1.removeHybridChild(child);
|
|
363
|
|
|
364
|
result = nameService.delete(name1); //should throw now exception
|
|
365
|
if (result.isError()){
|
|
366
|
Assert.fail("Delete should throw NO exception when deleting a hybrid child: " +result.getExceptions().iterator().next().getMessage());
|
|
367
|
}
|
|
368
|
|
|
369
|
commitAndStartNewTransaction(tableNames);
|
|
370
|
name1 = nameService.find(name1.getUuid());
|
|
371
|
Assert.assertNull("Name should not be in database anymore",name1);
|
|
372
|
}
|
|
373
|
|
|
374
|
@Test
|
|
375
|
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class)
|
|
376
|
public void testDeleteTaxonNameInConcept() {
|
|
377
|
final String[] tableNames = new String[]{"TaxonName","TaxonBase"};
|
|
378
|
|
|
379
|
TaxonName name1 = TaxonNameFactory.NewBotanicalInstance(getSpeciesRank());
|
|
380
|
name1.setTitleCache("Name1", true);
|
|
381
|
TaxonName basionym = TaxonNameFactory.NewBotanicalInstance(getSpeciesRank());
|
|
382
|
basionym.setTitleCache("basionym", true);
|
|
383
|
|
|
384
|
Taxon taxon = Taxon.NewInstance(name1, null);
|
|
385
|
nameService.save(name1);
|
|
386
|
taxonService.save(taxon);
|
|
387
|
commitAndStartNewTransaction(tableNames);
|
|
388
|
|
|
389
|
DeleteResult result = nameService.delete(name1);
|
|
390
|
|
|
391
|
if (result.isOk()){
|
|
392
|
Assert.fail("Delete should throw an error as long as name is used in a concept.");
|
|
393
|
}
|
|
394
|
TaxonName nameBase =nameService.find(name1.getUuid());
|
|
395
|
Assert.assertNotNull("Name should still be in database",nameBase);
|
|
396
|
TaxonBase<?> taxonBase = taxonService.find(taxon.getUuid());
|
|
397
|
Assert.assertNotNull("Taxon should still be in database",taxonBase);
|
|
398
|
taxon = (Taxon)taxonBase;
|
|
399
|
taxon.setName(basionym);
|
|
400
|
taxonService.save(taxon);
|
|
401
|
nameBase =nameService.find(name1.getUuid());
|
|
402
|
|
|
403
|
|
|
404
|
result = nameService.delete(nameBase); //should throw no exception
|
|
405
|
if (result.isError()){
|
|
406
|
Assert.fail("Delete should throw NO error ");
|
|
407
|
}
|
|
408
|
commitAndStartNewTransaction(tableNames);
|
|
409
|
name1 = nameService.find(name1.getUuid());
|
|
410
|
Assert.assertNull("Name should still be in database",name1);
|
|
411
|
taxon = (Taxon)taxonService.find(taxon.getUuid());
|
|
412
|
Assert.assertNotNull("Taxon should still be in database",taxon);
|
|
413
|
}
|
|
414
|
|
|
415
|
@Test
|
|
416
|
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class)
|
|
417
|
public void testDeleteTaxonNameAsStoredUnder() {
|
|
418
|
final String[] tableNames = new String[]{"TaxonName","SpecimenOrObservationBase"};
|
|
419
|
|
|
420
|
TaxonName name1 = TaxonNameFactory.NewBotanicalInstance(getSpeciesRank());
|
|
421
|
name1.setTitleCache("Name1", true);
|
|
422
|
DerivedUnit specimen = DerivedUnit.NewPreservedSpecimenInstance();
|
|
423
|
specimen.setStoredUnder(name1);
|
|
424
|
|
|
425
|
occurrenceService.save(specimen);
|
|
426
|
UUID uuidName1 = nameService.save(name1).getUuid();
|
|
427
|
|
|
428
|
commitAndStartNewTransaction(tableNames);
|
|
429
|
DeleteResult result = nameService.delete(name1);
|
|
430
|
if (result.isOk()){
|
|
431
|
Assert.fail("This should throw an error because name is used for specimen#storedUnder.");
|
|
432
|
}
|
|
433
|
commitAndStartNewTransaction(tableNames);
|
|
434
|
|
|
435
|
name1 = nameService.find(uuidName1);
|
|
436
|
Assert.assertNotNull("Name should still be in database",name1);
|
|
437
|
specimen = (DerivedUnit)occurrenceService.find(specimen.getUuid());
|
|
438
|
Assert.assertNotNull("Specimen should still be in database",name1);
|
|
439
|
specimen.setStoredUnder(null);
|
|
440
|
occurrenceService.saveOrUpdate(specimen);
|
|
441
|
|
|
442
|
nameService.delete(name1); //should throw no exception
|
|
443
|
commitAndStartNewTransaction(tableNames);
|
|
444
|
|
|
445
|
name1 = nameService.find(uuidName1);
|
|
446
|
Assert.assertNull("Name should not be in database anymore",name1);
|
|
447
|
specimen = (DerivedUnit)occurrenceService.find(specimen.getUuid());
|
|
448
|
Assert.assertNotNull("Specimen should still be in database",specimen);
|
|
449
|
|
|
450
|
occurrenceService.delete(specimen); //this is to better run this test in the test suit
|
|
451
|
|
|
452
|
}
|
|
453
|
|
|
454
|
@Test
|
|
455
|
@Ignore //currently does not run in suite
|
|
456
|
public void testDeleteTaxonNameInSource() {
|
|
457
|
final String[] tableNames = new String[]{"TaxonName","DescriptionBase","TaxonBase","OriginalSourceBase","DescriptionElementBase"};
|
|
458
|
|
|
459
|
TaxonName name1 = TaxonNameFactory.NewBotanicalInstance(getSpeciesRank());
|
|
460
|
name1.setTitleCache("Name1", true);
|
|
461
|
TaxonName taxonName = TaxonNameFactory.NewBotanicalInstance(getSpeciesRank());
|
|
462
|
taxonName.setTitleCache("taxonName", true);
|
|
463
|
Taxon taxon = Taxon.NewInstance(taxonName, null);
|
|
464
|
|
|
465
|
TaxonDescription taxonDescription = TaxonDescription.NewInstance(taxon);
|
|
466
|
Feature feature = (Feature)termService.find(Feature.DESCRIPTION().getUuid());
|
|
467
|
Language lang = (Language)termService.find(Language.DEFAULT().getUuid());
|
|
468
|
TextData textData = TextData.NewInstance("Any text", lang, null);
|
|
469
|
textData.setFeature(feature);
|
|
470
|
taxonDescription.addElement(textData);
|
|
471
|
DescriptionElementSource source = DescriptionElementSource.NewPrimarySourceInstance(null, null, name1, "");
|
|
472
|
textData.addSource(source);
|
|
473
|
taxonService.saveOrUpdate(taxon);
|
|
474
|
nameService.save(name1);
|
|
475
|
try {
|
|
476
|
commitAndStartNewTransaction(tableNames);
|
|
477
|
name1 = nameService.find(name1.getUuid());
|
|
478
|
nameService.delete(name1);
|
|
479
|
Assert.fail("Delete should throw an error as long as name is used in a source.");
|
|
480
|
} catch (Exception e) {
|
|
481
|
if (e.getMessage().contains("Name can't be deleted as it is used as descriptionElementSource#nameUsedInSource")){
|
|
482
|
//ok
|
|
483
|
endTransaction(); //exception rolls back transaction!
|
|
484
|
startNewTransaction();
|
|
485
|
}else{
|
|
486
|
Assert.fail("Unexpected error occurred when trying to delete taxon name: " + e.getMessage());
|
|
487
|
}
|
|
488
|
}
|
|
489
|
name1 = nameService.find(name1.getUuid());
|
|
490
|
Assert.assertNotNull("Name should still be in database",name1);
|
|
491
|
taxon = (Taxon)taxonService.find(taxon.getUuid());
|
|
492
|
Assert.assertNotNull("Taxon should still be in database",name1);
|
|
493
|
source = taxon.getDescriptions().iterator().next().getElements().iterator().next().getSources().iterator().next();
|
|
494
|
source.setNameUsedInSource(null);
|
|
495
|
taxonService.saveOrUpdate(taxon);
|
|
496
|
|
|
497
|
nameService.delete(name1); //should throw now exception
|
|
498
|
|
|
499
|
commitAndStartNewTransaction(tableNames);
|
|
500
|
name1 = nameService.find(name1.getUuid());
|
|
501
|
Assert.assertNull("Name should not be in database anymore",name1);
|
|
502
|
taxon = (Taxon)taxonService.find(taxon.getUuid());
|
|
503
|
Assert.assertNotNull("Taxon should still be in database",taxon);
|
|
504
|
source = taxon.getDescriptions().iterator().next().getElements().iterator().next().getSources().iterator().next();
|
|
505
|
Assert.assertNull("Source should not have a nameUsedInSource anymore",source.getNameUsedInSource());
|
|
506
|
}
|
|
507
|
|
|
508
|
|
|
509
|
@Test
|
|
510
|
public void testDeleteTaxonNameAsType() {
|
|
511
|
final String[] tableNames = new String[]{"TaxonName","TypeDesignationBase","TaxonName_TypeDesignationBase"};
|
|
512
|
|
|
513
|
TaxonName name1 = TaxonNameFactory.NewBotanicalInstance(getSpeciesRank());
|
|
514
|
name1.setTitleCache("Name used as type", true);
|
|
515
|
|
|
516
|
TaxonName higherName = TaxonNameFactory.NewBotanicalInstance(getGenusRank());
|
|
517
|
higherName.setTitleCache("genus name", true);
|
|
518
|
NameTypeDesignationStatus typeStatus = (NameTypeDesignationStatus)termService.find(NameTypeDesignationStatus.AUTOMATIC().getUuid());
|
|
519
|
boolean addToAllHomotypicNames = true;
|
|
520
|
higherName.addNameTypeDesignation(name1, null, null, null, typeStatus, addToAllHomotypicNames);
|
|
521
|
nameService.save(higherName);
|
|
522
|
|
|
523
|
commitAndStartNewTransaction(tableNames);
|
|
524
|
name1 = nameService.find(name1.getUuid());
|
|
525
|
DeleteResult result = nameService.delete(name1);
|
|
526
|
if (result.isOk()){
|
|
527
|
Assert.fail("This should throw an error because name is used in a type designation.");
|
|
528
|
}
|
|
529
|
|
|
530
|
commitAndStartNewTransaction(tableNames);
|
|
531
|
name1 = nameService.find(name1.getUuid());
|
|
532
|
Assert.assertNotNull("Name should still be in database",name1);
|
|
533
|
higherName = nameService.find(higherName.getUuid());
|
|
534
|
higherName.getNameTypeDesignations().iterator().next().removeType(); //keeps the designation but removes the name from it
|
|
535
|
// nameService.deleteTypeDesignation(higherName,commitAndStartNewTransaction(tableNames) ); //deletes the complete designation //both options can be used
|
|
536
|
|
|
537
|
nameService.delete(name1); //should throw now exception
|
|
538
|
|
|
539
|
commitAndStartNewTransaction(tableNames);
|
|
540
|
name1 = nameService.find(name1.getUuid());
|
|
541
|
Assert.assertNull("Name should not be in database anymore",name1);
|
|
542
|
higherName = nameService.find(higherName.getUuid());
|
|
543
|
Assert.assertNotNull("Higher name should still exist in database",higherName);
|
|
544
|
Assert.assertEquals("Higher name should not have type designations anymore",1, higherName.getTypeDesignations().size());
|
|
545
|
}
|
|
546
|
|
|
547
|
|
|
548
|
@Test
|
|
549
|
public void testDeleteTaxonName() {
|
|
550
|
final String[] tableNames = new String[]{"TaxonName","NameRelationship","HybridRelationship","DescriptionBase","NomenclaturalStatus","TaxonBase","SpecimenOrObservationBase","OriginalSourceBase","DescriptionElementBase","TypeDesignationBase","TaxonName_TypeDesignationBase"};
|
|
551
|
|
|
552
|
TaxonName name1 = TaxonNameFactory.NewBotanicalInstance(getSpeciesRank());
|
|
553
|
name1.setTitleCache("Name1", true);
|
|
554
|
|
|
555
|
//TaxonNameDescription
|
|
556
|
name1 = TaxonNameFactory.NewBotanicalInstance(getSpeciesRank());
|
|
557
|
TaxonNameDescription.NewInstance(name1);
|
|
558
|
nameService.saveOrUpdate(name1);
|
|
559
|
commitAndStartNewTransaction(tableNames);
|
|
560
|
|
|
561
|
name1 = nameService.find(name1.getUuid());
|
|
562
|
DeleteResult result = nameService.delete(name1);//should throw now exception
|
|
563
|
|
|
564
|
setComplete();
|
|
565
|
endTransaction();
|
|
566
|
name1 = nameService.find(name1.getUuid());
|
|
567
|
Assert.assertNull("Name should not be in database anymore",name1);
|
|
568
|
|
|
569
|
// printDataSet(System.out, tableNames);
|
|
570
|
|
|
571
|
|
|
572
|
//NomenclaturalStatus
|
|
573
|
name1 = TaxonNameFactory.NewBotanicalInstance(getSpeciesRank());
|
|
574
|
NomenclaturalStatusType nomStatusType = (NomenclaturalStatusType)termService.find(NomenclaturalStatusType.ILLEGITIMATE().getUuid());
|
|
575
|
NomenclaturalStatus status = NomenclaturalStatus.NewInstance(nomStatusType);
|
|
576
|
name1.addStatus(status);
|
|
577
|
nameService.saveOrUpdate(name1);
|
|
578
|
commitAndStartNewTransaction(tableNames);
|
|
579
|
|
|
580
|
name1 = nameService.find(name1.getUuid());
|
|
581
|
|
|
582
|
nameService.delete(name1); //should throw now exception
|
|
583
|
if (!result.isOk()){
|
|
584
|
Assert.fail();
|
|
585
|
}
|
|
586
|
setComplete();
|
|
587
|
endTransaction();
|
|
588
|
// printDataSet(System.out, tableNames);
|
|
589
|
|
|
590
|
|
|
591
|
//Type Designations
|
|
592
|
name1 = TaxonNameFactory.NewBotanicalInstance(getSpeciesRank());
|
|
593
|
name1.setTitleCache("Name with type designation", true);
|
|
594
|
SpecimenTypeDesignation typeDesignation = SpecimenTypeDesignation.NewInstance();
|
|
595
|
SpecimenTypeDesignationStatus typeStatus = (SpecimenTypeDesignationStatus)termService.find(SpecimenTypeDesignationStatus.HOLOTYPE().getUuid());
|
|
596
|
typeDesignation.setTypeStatus(typeStatus);
|
|
597
|
DerivedUnit specimen = DerivedUnit.NewPreservedSpecimenInstance();
|
|
598
|
specimen.setTitleCache("Type specimen", true);
|
|
599
|
occurrenceService.save(specimen);
|
|
600
|
typeDesignation.setTypeSpecimen(specimen);
|
|
601
|
|
|
602
|
name1.addTypeDesignation(typeDesignation, true);
|
|
603
|
nameService.save(name1);
|
|
604
|
commitAndStartNewTransaction(tableNames);
|
|
605
|
// printDataSet(System.out, tableNames);
|
|
606
|
|
|
607
|
name1 = nameService.find(name1.getUuid());
|
|
608
|
|
|
609
|
result = nameService.delete(name1); //should throw now exception
|
|
610
|
if (!result.isOk()){
|
|
611
|
Assert.fail();
|
|
612
|
}
|
|
613
|
setComplete();
|
|
614
|
endTransaction();
|
|
615
|
// printDataSet(System.out, tableNames);
|
|
616
|
|
|
617
|
}
|
|
618
|
|
|
619
|
@Test
|
|
620
|
public void testDeleteTaxonNameWithTypeInHomotypicalGroup() {
|
|
621
|
final String[] tableNames = new String[]{"TaxonName","NameRelationship","HybridRelationship","DescriptionBase","NomenclaturalStatus","TaxonBase","SpecimenOrObservationBase","OriginalSourceBase","DescriptionElementBase","TypeDesignationBase","TaxonName_TypeDesignationBase"};
|
|
622
|
|
|
623
|
//Type Designations for homotypical group with > 1 names
|
|
624
|
TaxonName name1 = TaxonNameFactory.NewBotanicalInstance(getSpeciesRank());
|
|
625
|
name1.setTitleCache("Name1 with type designation", true);
|
|
626
|
TaxonName name2 = TaxonNameFactory.NewBotanicalInstance(getSpeciesRank());
|
|
627
|
name2.setTitleCache("Name2 with type designation", true);
|
|
628
|
name2.setHomotypicalGroup(name1.getHomotypicalGroup());
|
|
629
|
|
|
630
|
DerivedUnit specimen = DerivedUnit.NewPreservedSpecimenInstance();
|
|
631
|
specimen.setTitleCache("Type specimen 2", true);
|
|
632
|
occurrenceService.save(specimen);
|
|
633
|
SpecimenTypeDesignationStatus typeStatus = (SpecimenTypeDesignationStatus)termService.find(SpecimenTypeDesignationStatus.HOLOTYPE().getUuid());
|
|
634
|
|
|
635
|
SpecimenTypeDesignation typeDesignation = SpecimenTypeDesignation.NewInstance();
|
|
636
|
typeDesignation.setTypeStatus(typeStatus);
|
|
637
|
typeDesignation.setTypeSpecimen(specimen);
|
|
638
|
|
|
639
|
boolean addToAllNames = true;
|
|
640
|
name1.addTypeDesignation(typeDesignation, addToAllNames);
|
|
641
|
nameService.saveOrUpdate(name1);
|
|
642
|
commitAndStartNewTransaction(tableNames);
|
|
643
|
|
|
644
|
name1 = nameService.find(name1.getUuid());
|
|
645
|
|
|
646
|
nameService.delete(name1); //should throw now exception
|
|
647
|
|
|
648
|
setComplete();
|
|
649
|
endTransaction();
|
|
650
|
}
|
|
651
|
|
|
652
|
@Test
|
|
653
|
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class)
|
|
654
|
public void testDeleteTypeDesignation() {
|
|
655
|
|
|
656
|
// final String[] tableNames = new String[]{
|
|
657
|
// "TaxonName","TypeDesignationBase","TaxonName_TypeDesignationBase",
|
|
658
|
// "SpecimenOrObservationBase"};
|
|
659
|
|
|
660
|
TaxonName name1 = this.nameService.load(UUID.fromString("6dbd41d1-fe13-4d9c-bb58-31f051c2c384"));
|
|
661
|
TaxonName name2 = this.nameService.load(UUID.fromString("f9e9c13f-5fa5-48d3-88cf-712c921a099e"));
|
|
662
|
TaxonName name3 = this.nameService.load(UUID.fromString("e1e66264-f16a-4df9-80fd-6ab5028a3c28"));
|
|
663
|
DerivedUnit specimen1 = CdmBase.deproxy(this.occurrenceService.load(UUID.fromString("0d19a9ca-21a7-4adb-8640-8d6719e15eea")), DerivedUnit.class);
|
|
664
|
DerivedUnit fossil = CdmBase.deproxy(this.occurrenceService.load(UUID.fromString("4c48b7c8-4c8d-4e48-b083-0837fe51a0a9")), DerivedUnit.class);
|
|
665
|
|
|
666
|
@SuppressWarnings("rawtypes")
|
|
667
|
Set<TypeDesignationBase> desigs1 = name1.getTypeDesignations();
|
|
668
|
@SuppressWarnings("rawtypes")
|
|
669
|
Set<TypeDesignationBase> desigs2 = name2.getTypeDesignations();
|
|
670
|
@SuppressWarnings("rawtypes")
|
|
671
|
Set<TypeDesignationBase> desigs3 = name3.getTypeDesignations();
|
|
672
|
|
|
673
|
Assert.assertEquals("name1 should have 2 type designations", 2, desigs1.size());
|
|
674
|
Assert.assertEquals("name2 should have 1 type designations", 1, desigs2.size());
|
|
675
|
Assert.assertEquals("name3 should have 1 type designations", 1, desigs3.size());
|
|
676
|
Assert.assertEquals("Specimen1 should be used in 1 type designation", 1, specimen1.getSpecimenTypeDesignations().size());
|
|
677
|
Assert.assertEquals("Fossil should be used in 1 type designation", 1, fossil.getSpecimenTypeDesignations().size());
|
|
678
|
|
|
679
|
nameService.deleteTypeDesignation((TaxonName)null, null);
|
|
680
|
|
|
681
|
commitAndStartNewTransaction(/*tableNames*/);
|
|
682
|
|
|
683
|
name1 = this.nameService.load(UUID.fromString("6dbd41d1-fe13-4d9c-bb58-31f051c2c384"));
|
|
684
|
name2 = this.nameService.load(UUID.fromString("f9e9c13f-5fa5-48d3-88cf-712c921a099e"));
|
|
685
|
name3 = this.nameService.load(UUID.fromString("e1e66264-f16a-4df9-80fd-6ab5028a3c28"));
|
|
686
|
specimen1 = CdmBase.deproxy(this.occurrenceService.load(UUID.fromString("0d19a9ca-21a7-4adb-8640-8d6719e15eea")), DerivedUnit.class);
|
|
687
|
fossil = CdmBase.deproxy(this.occurrenceService.load(UUID.fromString("4c48b7c8-4c8d-4e48-b083-0837fe51a0a9")), DerivedUnit.class);
|
|
688
|
|
|
689
|
desigs1 = name1.getTypeDesignations();
|
|
690
|
desigs2 = name2.getTypeDesignations();
|
|
691
|
desigs3 = name3.getTypeDesignations();
|
|
692
|
//nothing should be deleted
|
|
693
|
Assert.assertEquals("name1 should have 2 type designations", 2, desigs1.size());
|
|
694
|
Assert.assertEquals("name2 should have 1 type designations", 1, desigs2.size());
|
|
695
|
Assert.assertEquals("name3 should have 1 type designations", 1, desigs3.size());
|
|
696
|
Assert.assertEquals("Specimen1 should be used in 1 type designation", 1, specimen1.getSpecimenTypeDesignations().size());
|
|
697
|
Assert.assertEquals("Fossil should be used in 1 type designation", 1, fossil.getSpecimenTypeDesignations().size());
|
|
698
|
|
|
699
|
nameService.deleteTypeDesignation(name1, null);
|
|
700
|
|
|
701
|
commitAndStartNewTransaction(/*tableNames*/);
|
|
702
|
|
|
703
|
name1 = this.nameService.load(UUID.fromString("6dbd41d1-fe13-4d9c-bb58-31f051c2c384"));
|
|
704
|
name2 = this.nameService.load(UUID.fromString("f9e9c13f-5fa5-48d3-88cf-712c921a099e"));
|
|
705
|
name3 = this.nameService.load(UUID.fromString("e1e66264-f16a-4df9-80fd-6ab5028a3c28"));
|
|
706
|
specimen1 = CdmBase.deproxy(this.occurrenceService.load(UUID.fromString("0d19a9ca-21a7-4adb-8640-8d6719e15eea")), DerivedUnit.class);
|
|
707
|
fossil = CdmBase.deproxy(this.occurrenceService.load(UUID.fromString("4c48b7c8-4c8d-4e48-b083-0837fe51a0a9")), DerivedUnit.class);
|
|
708
|
|
|
709
|
desigs1 = name1.getTypeDesignations();
|
|
710
|
desigs2 = name2.getTypeDesignations();
|
|
711
|
desigs3 = name3.getTypeDesignations();
|
|
712
|
//only the types of name1 should be deleted
|
|
713
|
Assert.assertEquals("name1 should have 0 type designations", 0, desigs1.size());
|
|
714
|
Assert.assertEquals("name2 should have 1 type designations", 1, desigs2.size());
|
|
715
|
Assert.assertEquals("name3 should have 1 type designations", 1, desigs3.size());
|
|
716
|
Assert.assertEquals("Specimen1 should be used in 1 type designation", 1, specimen1.getSpecimenTypeDesignations().size());
|
|
717
|
Assert.assertEquals("Fossil should be used in 0 type designation", 0, fossil.getSpecimenTypeDesignations().size());
|
|
718
|
|
|
719
|
SpecimenTypeDesignation desig2 = (SpecimenTypeDesignation)name2.getTypeDesignations().iterator().next();
|
|
720
|
nameService.deleteTypeDesignation(name2, desig2);
|
|
721
|
|
|
722
|
commitAndStartNewTransaction(/*tableNames*/);
|
|
723
|
|
|
724
|
name1 = this.nameService.load(UUID.fromString("6dbd41d1-fe13-4d9c-bb58-31f051c2c384"));
|
|
725
|
name2 = this.nameService.load(UUID.fromString("f9e9c13f-5fa5-48d3-88cf-712c921a099e"));
|
|
726
|
name3 = this.nameService.load(UUID.fromString("e1e66264-f16a-4df9-80fd-6ab5028a3c28"));
|
|
727
|
specimen1 = CdmBase.deproxy(this.occurrenceService.load(UUID.fromString("0d19a9ca-21a7-4adb-8640-8d6719e15eea")), DerivedUnit.class);
|
|
728
|
fossil = CdmBase.deproxy(this.occurrenceService.load(UUID.fromString("4c48b7c8-4c8d-4e48-b083-0837fe51a0a9")), DerivedUnit.class);
|
|
729
|
|
|
730
|
desigs1 = name1.getTypeDesignations();
|
|
731
|
desigs2 = name2.getTypeDesignations();
|
|
732
|
desigs3 = name3.getTypeDesignations();
|
|
733
|
|
|
734
|
Assert.assertEquals("name1 should have 0 type designations", 0, desigs1.size());
|
|
735
|
Assert.assertEquals("name2 should have 0 type designations", 0, desigs2.size());
|
|
736
|
Assert.assertEquals("name3 should have 1 type designations", 1, desigs3.size());
|
|
737
|
Assert.assertEquals("Specimen1 should be used in 0 type designation", 0, specimen1.getSpecimenTypeDesignations().size());
|
|
738
|
Assert.assertEquals("Fossil should be used in 0 type designation", 0, fossil.getSpecimenTypeDesignations().size());
|
|
739
|
|
|
740
|
NameTypeDesignation desig3 = (NameTypeDesignation)name3.getTypeDesignations().iterator().next();
|
|
741
|
name3.addTypeDesignation(SpecimenTypeDesignation.NewInstance(), false);
|
|
742
|
this.nameService.update(name3);
|
|
743
|
|
|
744
|
this.nameService.load(UUID.fromString("e1e66264-f16a-4df9-80fd-6ab5028a3c28"));
|
|
745
|
desigs3 = name3.getTypeDesignations();
|
|
746
|
|
|
747
|
commitAndStartNewTransaction(/*tableNames*/);
|
|
748
|
name3 = nameService.load(name3.getUuid());
|
|
749
|
|
|
750
|
Assert.assertEquals("name3 should have 2 type designations", 2, desigs3.size());
|
|
751
|
|
|
752
|
nameService.deleteTypeDesignation(name3, desig3);
|
|
753
|
commitAndStartNewTransaction(/*tableNames*/);
|
|
754
|
|
|
755
|
name1 = this.nameService.load(UUID.fromString("6dbd41d1-fe13-4d9c-bb58-31f051c2c384"));
|
|
756
|
name2 = this.nameService.load(UUID.fromString("f9e9c13f-5fa5-48d3-88cf-712c921a099e"));
|
|
757
|
name3 = this.nameService.load(UUID.fromString("e1e66264-f16a-4df9-80fd-6ab5028a3c28"));
|
|
758
|
specimen1 = CdmBase.deproxy(this.occurrenceService.load(UUID.fromString("0d19a9ca-21a7-4adb-8640-8d6719e15eea")), DerivedUnit.class);
|
|
759
|
fossil = CdmBase.deproxy(this.occurrenceService.load(UUID.fromString("4c48b7c8-4c8d-4e48-b083-0837fe51a0a9")), DerivedUnit.class);
|
|
760
|
|
|
761
|
desigs1 = name1.getTypeDesignations();
|
|
762
|
desigs2 = name2.getTypeDesignations();
|
|
763
|
desigs3 = name3.getTypeDesignations();
|
|
764
|
|
|
765
|
Assert.assertEquals("name1 should have 0 type designations", 0, desigs1.size());
|
|
766
|
Assert.assertEquals("name2 should have 0 type designations", 0, desigs2.size());
|
|
767
|
Assert.assertEquals("name3 should have 0 type designations", 1, desigs3.size());
|
|
768
|
Assert.assertEquals("Specimen1 should be used in 0 type designation", 0, specimen1.getSpecimenTypeDesignations().size());
|
|
769
|
Assert.assertEquals("Fossil should be used in 0 type designation", 0, fossil.getSpecimenTypeDesignations().size());
|
|
770
|
}
|
|
771
|
|
|
772
|
@Test
|
|
773
|
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class)
|
|
774
|
public void testDeleteTypeDesignationWithRegistration() {
|
|
775
|
// final String[] tableNames = new String[]{
|
|
776
|
// "TaxonName","TypeDesignationBase","TaxonName_TypeDesignationBase",
|
|
777
|
// "SpecimenOrObservationBase"};
|
|
778
|
|
|
779
|
TaxonName name3 = this.nameService.load(UUID.fromString("e1e66264-f16a-4df9-80fd-6ab5028a3c28"));
|
|
780
|
|
|
781
|
@SuppressWarnings("rawtypes")
|
|
782
|
Set<TypeDesignationBase> desigs3 = name3.getTypeDesignations();
|
|
783
|
|
|
784
|
NameTypeDesignation desig3 = (NameTypeDesignation)name3.getTypeDesignations().iterator().next();
|
|
785
|
name3.addTypeDesignation(SpecimenTypeDesignation.NewInstance(), false);
|
|
786
|
this.nameService.update(name3);
|
|
787
|
|
|
788
|
name3 = this.nameService.load(UUID.fromString("e1e66264-f16a-4df9-80fd-6ab5028a3c28"));
|
|
789
|
desigs3 = name3.getTypeDesignations();
|
|
790
|
|
|
791
|
NameTypeDesignation desigNew = NameTypeDesignation.NewInstance();
|
|
792
|
|
|
793
|
UsernamePasswordAuthenticationToken submiterToken = new UsernamePasswordAuthenticationToken("admin","sPePhAz6");
|
|
794
|
setAuthentication(submiterToken);
|
|
795
|
Registration registration = Registration.NewInstance("abc", "abc", name3, null);
|
|
796
|
registration.addTypeDesignation(desigNew);
|
|
797
|
registrationService.saveOrUpdate(registration);
|
|
798
|
unsetAuthentication();
|
|
799
|
|
|
800
|
commitAndStartNewTransaction(/*tableNames*/);
|
|
801
|
|
|
802
|
name3 = nameService.load(name3.getUuid());
|
|
803
|
|
|
804
|
Set<Registration> regs = name3.getRegistrations();
|
|
805
|
desigs3 = name3.getTypeDesignations();
|
|
806
|
Assert.assertEquals("name3 should have 2 type designations", 2, desigs3.size());
|
|
807
|
Assert.assertEquals("name should have 1 registrations", 1, regs.size());
|
|
808
|
Assert.assertEquals("registration should have 1 type designations",1, regs.iterator().next().getTypeDesignations().size());
|
|
809
|
|
|
810
|
nameService.deleteTypeDesignation(name3, desig3);
|
|
811
|
commitAndStartNewTransaction(/*tableNames*/);
|
|
812
|
|
|
813
|
name3 = this.nameService.load(UUID.fromString("e1e66264-f16a-4df9-80fd-6ab5028a3c28"));
|
|
814
|
|
|
815
|
regs = name3.getRegistrations();
|
|
816
|
Assert.assertEquals("name3 should have 1 registration", 1, regs.size());
|
|
817
|
Assert.assertEquals("registration should have 1 type designations",1, regs.iterator().next().getTypeDesignations().size());
|
|
818
|
|
|
819
|
desigs3 = name3.getTypeDesignations();
|
|
820
|
|
|
821
|
nameService.deleteTypeDesignation(name3, desigNew);
|
|
822
|
commitAndStartNewTransaction(/*tableNames*/);
|
|
823
|
name3 = this.nameService.load(UUID.fromString("e1e66264-f16a-4df9-80fd-6ab5028a3c28"));
|
|
824
|
regs = name3.getRegistrations();
|
|
825
|
desigs3 = name3.getTypeDesignations();
|
|
826
|
|
|
827
|
Assert.assertEquals("name3 should have 1 type designations", 1, desigs3.size());
|
|
828
|
Assert.assertEquals("registration should have 0 type designations",0, regs.iterator().next().getTypeDesignations().size());
|
|
829
|
}
|
|
830
|
|
|
831
|
@Test
|
|
832
|
@DataSet
|
|
833
|
public void testDeleteTypeDesignationAllNames() {
|
|
834
|
// final String[] tableNames = new String[]{
|
|
835
|
// "TaxonName","TypeDesignationBase",
|
|
836
|
// "TaxonName_TypeDesignationBase","SpecimenOrObservationBase"};
|
|
837
|
|
|
838
|
TaxonName name1 = this.nameService.load(UUID.fromString("6dbd41d1-fe13-4d9c-bb58-31f051c2c384"));
|
|
839
|
TaxonName name2 = this.nameService.load(UUID.fromString("f9e9c13f-5fa5-48d3-88cf-712c921a099e"));
|
|
840
|
TaxonName name3 = this.nameService.load(UUID.fromString("e1e66264-f16a-4df9-80fd-6ab5028a3c28"));
|
|
841
|
DerivedUnit specimen1 = CdmBase.deproxy(this.occurrenceService.load(UUID.fromString("0d19a9ca-21a7-4adb-8640-8d6719e15eea")), DerivedUnit.class);
|
|
842
|
DerivedUnit fossil = CdmBase.deproxy(this.occurrenceService.load(UUID.fromString("4c48b7c8-4c8d-4e48-b083-0837fe51a0a9")), DerivedUnit.class);
|
|
843
|
|
|
844
|
@SuppressWarnings("rawtypes")
|
|
845
|
Set<TypeDesignationBase> desigs1 = name1.getTypeDesignations();
|
|
846
|
@SuppressWarnings("rawtypes")
|
|
847
|
Set<TypeDesignationBase> desigs2 = name2.getTypeDesignations();
|
|
848
|
@SuppressWarnings("rawtypes")
|
|
849
|
Set<TypeDesignationBase> desigs3 = name3.getTypeDesignations();
|
|
850
|
|
|
851
|
Assert.assertEquals("name1 should have 2 type designations", 2, desigs1.size());
|
|
852
|
Assert.assertEquals("name2 should have 1 type designations", 1, desigs2.size());
|
|
853
|
Assert.assertEquals("name3 should have 1 type designations", 1, desigs3.size());
|
|
854
|
Assert.assertEquals("Specimen1 should be used in 1 type designation", 1, specimen1.getSpecimenTypeDesignations().size());
|
|
855
|
Assert.assertEquals("Fossil should be used in 1 type designation", 1, fossil.getSpecimenTypeDesignations().size());
|
|
856
|
|
|
857
|
SpecimenTypeDesignation desig2 = (SpecimenTypeDesignation)name2.getTypeDesignations().iterator().next();
|
|
858
|
|
|
859
|
nameService.deleteTypeDesignation(null, desig2);
|
|
860
|
|
|
861
|
commitAndStartNewTransaction(/*tableNames*/);
|
|
862
|
|
|
863
|
name1 = this.nameService.load(UUID.fromString("6dbd41d1-fe13-4d9c-bb58-31f051c2c384"));
|
|
864
|
name2 = this.nameService.load(UUID.fromString("f9e9c13f-5fa5-48d3-88cf-712c921a099e"));
|
|
865
|
name3 = this.nameService.load(UUID.fromString("e1e66264-f16a-4df9-80fd-6ab5028a3c28"));
|
|
866
|
specimen1 = CdmBase.deproxy(this.occurrenceService.load(UUID.fromString("0d19a9ca-21a7-4adb-8640-8d6719e15eea")), DerivedUnit.class);
|
|
867
|
fossil = CdmBase.deproxy(this.occurrenceService.load(UUID.fromString("4c48b7c8-4c8d-4e48-b083-0837fe51a0a9")), DerivedUnit.class);
|
|
868
|
|
|
869
|
desigs1 = name1.getTypeDesignations();
|
|
870
|
desigs2 = name2.getTypeDesignations();
|
|
871
|
desigs3 = name3.getTypeDesignations();
|
|
872
|
|
|
873
|
Assert.assertEquals("name1 should have 1 type designations", 1, desigs1.size());
|
|
874
|
Assert.assertEquals("name2 should have 0 type designations", 0, desigs2.size());
|
|
875
|
Assert.assertEquals("name3 should have 1 type designations", 1, desigs3.size());
|
|
876
|
Assert.assertEquals("Specimen1 should be used in 0 type designation", 0, specimen1.getSpecimenTypeDesignations().size());
|
|
877
|
Assert.assertEquals("Fossil should be used in 1 type designation", 1, fossil.getSpecimenTypeDesignations().size());
|
|
878
|
}
|
|
879
|
|
|
880
|
@Test
|
|
881
|
@DataSet
|
|
882
|
public void findByTitleWithRestrictions(){
|
|
883
|
|
|
884
|
// The following typeDesignations per name are assumed:
|
|
885
|
// Name1 -> SpecimenTypeDesignation -> Specimen1
|
|
886
|
// -> SpecimenTypeDesignation -> Specimen2
|
|
887
|
// Name2 -> SpecimenTypeDesignation -> Specimen2
|
|
888
|
|
|
889
|
// Logger.getLogger("org.hibernate.SQL").setLevel(Level.TRACE);
|
|
890
|
|
|
891
|
List<Restriction<?>> restrictions;
|
|
892
|
Pager<TaxonName> result;
|
|
893
|
|
|
894
|
result = nameService.findByTitleWithRestrictions(null, "Name1", MatchMode.EXACT, null, null, null, null, null);
|
|
895
|
assertEquals(1l, result.getCount().longValue());
|
|
896
|
assertEquals("Name1", result.getRecords().iterator().next().getTitleCache());
|
|
897
|
|
|
898
|
result = nameService.findByTitleWithRestrictions(null, "Name", MatchMode.BEGINNING, null, null, null, null, null);
|
|
899
|
assertEquals(3l, result.getCount().longValue());
|
|
900
|
|
|
901
|
restrictions = Arrays.asList(new Restriction<UUID>("typeDesignations.uuid", null, UUID.fromString("9bbda70b-7272-4e65-a807-852a3f2eba63")));
|
|
902
|
result = nameService.findByTitleWithRestrictions(null, "Name", MatchMode.BEGINNING, restrictions, null, null, null, null);
|
|
903
|
assertEquals(1l, result.getCount().longValue());
|
|
904
|
assertEquals("Name1", result.getRecords().iterator().next().getTitleCache());
|
|
905
|
|
|
906
|
result = nameService.findByTitleWithRestrictions(null, "me1", MatchMode.END, restrictions, null, null, null, null);
|
|
907
|
assertEquals(1l, result.getCount().longValue());
|
|
908
|
assertEquals("Name1", result.getRecords().iterator().next().getTitleCache());
|
|
909
|
|
|
910
|
result = nameService.findByTitleWithRestrictions(null, "Name2", MatchMode.EXACT, restrictions, null, null, null, null);
|
|
911
|
assertEquals(0l, result.getCount().longValue());
|
|
912
|
|
|
913
|
// Logger.getLogger("eu.etaxonomy.cdm.persistence.dao.hibernate.common").setLevel(Level.DEBUG);
|
|
914
|
|
|
915
|
restrictions = Arrays.asList(new Restriction<String>("typeDesignations.typeSpecimen.titleCache", MatchMode.EXACT, "Specimen2"));
|
|
916
|
result = nameService.findByTitleWithRestrictions(null, "Name2", MatchMode.EXACT, restrictions, null, null, null, null);
|
|
917
|
assertEquals(1l, result.getCount().longValue());
|
|
918
|
assertEquals("Name2", result.getRecords().iterator().next().getTitleCache());
|
|
919
|
|
|
920
|
restrictions = Arrays.asList(new Restriction<String>("typeDesignations.typeSpecimen.titleCache", MatchMode.EXACT, "Specimen1"));
|
|
921
|
result = nameService.findByTitleWithRestrictions(null, "Name2", MatchMode.EXACT, restrictions, null, null, null, null);
|
|
922
|
assertEquals(0l, result.getCount().longValue());
|
|
923
|
|
|
924
|
restrictions = Arrays.asList(new Restriction<String>("typeDesignations.typeSpecimen.titleCache", Restriction.Operator.OR, MatchMode.EXACT, "Specimen1"));
|
|
925
|
result = nameService.findByTitleWithRestrictions(null, "Name2", MatchMode.EXACT, restrictions, null, null, null, null);
|
|
926
|
assertEquals(2l, result.getCount().longValue());
|
|
927
|
|
|
928
|
restrictions = Arrays.asList(new Restriction<String>("typeDesignations.typeSpecimen.titleCache", MatchMode.BEGINNING, "Specimen"));
|
|
929
|
result = nameService.findByTitleWithRestrictions(null, "Name1", MatchMode.EXACT, restrictions, null, null, null, null);
|
|
930
|
assertEquals("names with multiple matching typeSpecimens must be deduplicated", 1l, result.getCount().longValue());
|
|
931
|
assertEquals("Name1", result.getRecords().iterator().next().getTitleCache());
|
|
932
|
|
|
933
|
restrictions = Arrays.asList(new Restriction<String>("typeDesignations.typeSpecimen.titleCache", MatchMode.BEGINNING, "Specimen"));
|
|
934
|
result = nameService.findByTitleWithRestrictions(null, "Name", MatchMode.BEGINNING, restrictions, null, null, null, null);
|
|
935
|
assertEquals(2l, result.getCount().longValue());
|
|
936
|
}
|
|
937
|
|
|
938
|
@Test
|
|
939
|
@DataSet
|
|
940
|
public void testFindByTitleTitleWithRestrictionsMultiValue(){
|
|
941
|
|
|
942
|
// The following typedesigbnations per name are assumed:
|
|
943
|
// Name1 -> SpecimenTypeDesignation -> Specimen1
|
|
944
|
// -> SpecimenTypeDesignation -> Specimen2
|
|
945
|
// Name2 -> SpecimenTypeDesignation -> Specimen2
|
|
946
|
// Name3 -> NameTypeDesignaton-> typeName = Name1
|
|
947
|
|
|
948
|
List<Restriction<?>> restrictions;
|
|
949
|
Pager<TaxonName> result;
|
|
950
|
|
|
951
|
restrictions = Arrays.asList(new Restriction<UUID>("typeDesignations.uuid", null, UUID.fromString("9bbda70b-7272-4e65-a807-852a3f2eba63"), UUID.fromString("1357c307-00c3-499c-8e20-0849d4706125")));
|
|
952
|
result = nameService.findByTitleWithRestrictions(null, "Name", MatchMode.BEGINNING, restrictions, null, null, null, null);
|
|
953
|
assertEquals(2l, result.getCount().longValue());
|
|
954
|
|
|
955
|
restrictions = Arrays.asList(new Restriction<String>("typeDesignations.typeSpecimen.titleCache", null, "Specimen1", "Specimen2"));
|
|
956
|
result = nameService.findByTitleWithRestrictions(null, "Name1", MatchMode.EXACT, restrictions, null, null, null, null);
|
|
957
|
assertEquals("names with multiple matching typeSpecimens must be distinct", 1l, result.getCount().longValue());
|
|
958
|
assertEquals("Name1", result.getRecords().iterator().next().getTitleCache());
|
|
959
|
}
|
|
960
|
|
|
961
|
@Test
|
|
962
|
@DataSet
|
|
963
|
public void testFindByTitleTitleWithRestrictionsLogicalOperators(){
|
|
964
|
|
|
965
|
// The following typedesigbnations per name are assumed:
|
|
966
|
// Name1 -> SpecimenTypeDesignation -> Specimen1
|
|
967
|
// -> SpecimenTypeDesignation -> Specimen2
|
|
968
|
// Name2 -> SpecimenTypeDesignation -> Specimen2
|
|
969
|
// Name3 -> NameTypeDesignaton-> typeName = Name1
|
|
970
|
|
|
971
|
List<Restriction<?>> restrictions;
|
|
972
|
Pager<TaxonName> result;
|
|
973
|
|
|
974
|
//Logger.getLogger("org.hibernate.SQL").setLevel(Level.TRACE);
|
|
975
|
|
|
976
|
restrictions = Arrays.asList(new Restriction<String>("typeDesignations.typeName.titleCache", Operator.AND, null, "Name1"));
|
|
977
|
result = nameService.findByTitleWithRestrictions(null, "Name3", MatchMode.EXACT, restrictions, null, null, null, null);
|
|
978
|
assertEquals(1l, result.getCount().longValue());
|
|
979
|
|
|
980
|
restrictions = Arrays.asList(new Restriction<String>("typeDesignations.typeName.titleCache", Operator.AND_NOT, null, "Name1"));
|
|
981
|
result = nameService.findByTitleWithRestrictions(null, "Name", MatchMode.BEGINNING, restrictions, null, null, null, null);
|
|
982
|
assertEquals(2l, result.getCount().longValue());
|
|
983
|
|
|
984
|
restrictions = Arrays.asList(new Restriction<String>("titleCache", Operator.AND_NOT, null, "Name1", "Name2"));
|
|
985
|
result = nameService.findByTitleWithRestrictions(null, "Name", MatchMode.BEGINNING, restrictions, null, null, null, null);
|
|
986
|
assertEquals(1l, result.getCount().longValue());
|
|
987
|
assertEquals("Name3", result.getRecords().get(0).getTitleCache());
|
|
988
|
|
|
989
|
restrictions = Arrays.asList(new Restriction<String>("typeDesignations.typeName.titleCache", Operator.OR, null, "Name1"));
|
|
990
|
result = nameService.findByTitleWithRestrictions(null, "Name1", MatchMode.EXACT, restrictions, null, null, null, null);
|
|
991
|
assertEquals(2l, result.getCount().longValue());
|
|
992
|
|
|
993
|
restrictions = Arrays.asList(new Restriction<String>("typeDesignations.typeName.titleCache", Operator.OR_NOT, null, "Name1"));
|
|
994
|
result = nameService.findByTitleWithRestrictions(null, "Name1", MatchMode.EXACT, restrictions, null, null, null, null);
|
|
995
|
assertEquals(2l, result.getCount().longValue());
|
|
996
|
}
|
|
997
|
|
|
998
|
@Test
|
|
999
|
@DataSet
|
|
1000
|
public void testFindByTitleTitle_using_Configurator(){
|
|
1001
|
|
|
1002
|
String searchString = "*";
|
|
1003
|
IdentifiableServiceConfiguratorImpl<TaxonName> searchConfigurator = new IdentifiableServiceConfiguratorImpl<TaxonName>();
|
|
1004
|
|
|
1005
|
searchConfigurator = IdentifiableServiceConfiguratorFactory.getConfigurator(TaxonName.class);
|
|
1006
|
searchConfigurator.setTitleSearchString(searchString);
|
|
1007
|
searchConfigurator.setMatchMode(null);
|
|
1008
|
searchConfigurator.setOrderHints(OrderHint.ORDER_BY_TITLE_CACHE.asList());
|
|
1009
|
|
|
1010
|
Pager<TaxonName> results = nameService.findByTitle(searchConfigurator);
|
|
1011
|
assertTrue(results.getRecords().size() > 0);
|
|
1012
|
}
|
|
1013
|
|
|
1014
|
@Test //7874 //8030
|
|
1015
|
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="NameServiceImplTest.testUpdateCaches.xml")
|
|
1016
|
public void testUpdateCaches() throws NoSuchFieldException, SecurityException, IllegalArgumentException, IllegalAccessException{
|
|
1017
|
|
|
1018
|
Field titleCacheField = IdentifiableEntity.class.getDeclaredField("titleCache");
|
|
1019
|
titleCacheField.setAccessible(true);
|
|
1020
|
Field nameCacheField = TaxonName.class.getDeclaredField("nameCache");
|
|
1021
|
nameCacheField.setAccessible(true);
|
|
1022
|
Field authorCacheField = TaxonName.class.getDeclaredField("authorshipCache");
|
|
1023
|
authorCacheField.setAccessible(true);
|
|
1024
|
Field fullTitleCacheField = TaxonName.class.getDeclaredField("fullTitleCache");
|
|
1025
|
fullTitleCacheField.setAccessible(true);
|
|
1026
|
|
|
1027
|
TaxonName name1 = nameService.loadWithoutInitializing(NAME1_ID);
|
|
1028
|
TaxonName name2 = nameService.loadWithoutInitializing(NAME2_ID);
|
|
1029
|
TaxonName name3 = nameService.loadWithoutInitializing(NAME3_ID);
|
|
1030
|
|
|
1031
|
name1 = CdmBase.deproxy(name1);
|
|
1032
|
assertEquals("TitleCache should be the persisted one", "Name1", titleCacheField.get(name1));
|
|
1033
|
assertEquals("NameCache should be the persisted one", "", nameCacheField.get(name1));
|
|
1034
|
assertEquals("AuthorCache should be the persisted one", "", authorCacheField.get(name1));
|
|
1035
|
assertEquals("FullTitleCache should be the persisted one", "", fullTitleCacheField.get(name1));
|
|
1036
|
|
|
1037
|
name2 = CdmBase.deproxy(name2);
|
|
1038
|
assertEquals("TitleCache should be the persisted one", "Name2", titleCacheField.get(name2));
|
|
1039
|
assertEquals("NameCache should be the persisted one", "Protected name", nameCacheField.get(name2));
|
|
1040
|
assertEquals("AuthorCache should be the persisted one", null, authorCacheField.get(name2));
|
|
1041
|
assertEquals("FullTitleCache should be the persisted one", "", fullTitleCacheField.get(name2));
|
|
1042
|
|
|
1043
|
name3 = CdmBase.deproxy(name3);
|
|
1044
|
assertEquals("TitleCache should be the persisted one", "Name3", titleCacheField.get(name3));
|
|
1045
|
assertEquals("NameCache should be the persisted one", "", nameCacheField.get(name3));
|
|
1046
|
assertEquals("AuthorCache should be the persisted one", "No-author", authorCacheField.get(name3));
|
|
1047
|
assertEquals("FullTitleCache should be the persisted one", "", fullTitleCacheField.get(name3));
|
|
1048
|
|
|
1049
|
nameService.updateCaches();
|
|
1050
|
|
|
1051
|
assertEquals("Expecting titleCache to be updated", "First name Turl.", titleCacheField.get(name1));
|
|
1052
|
assertEquals("Expecting nameCache to be updated", "First name", nameCacheField.get(name1));
|
|
1053
|
assertEquals("Expecting authorshipCache to be updated", "Turl.", authorCacheField.get(name1));
|
|
1054
|
assertEquals("Expecting fullTitleCache to be updated", "First name Turl.", fullTitleCacheField.get(name1));
|
|
1055
|
|
|
1056
|
assertEquals("Expecting titleCache to be updated", "Protected name", titleCacheField.get(name2));
|
|
1057
|
assertEquals("Expecting nameCache to not be updated", "Protected name", nameCacheField.get(name2));
|
|
1058
|
assertEquals("Expecting authorshipCache to be updated", "", authorCacheField.get(name2));
|
|
1059
|
assertEquals("Expecting fullTitleCache to be updated", "Protected name", fullTitleCacheField.get(name2));
|
|
1060
|
|
|
1061
|
assertEquals("Expecting titleCache to be updated", "Name3", titleCacheField.get(name3));
|
|
1062
|
assertEquals("Expecting nameCache to be updated", "Third", nameCacheField.get(name3));
|
|
1063
|
assertEquals("Expecting authorshipCache to be updated", "No-author", authorCacheField.get(name3));
|
|
1064
|
assertEquals("Expecting fullTitleCache to be updated", "Name3", fullTitleCacheField.get(name3));
|
|
1065
|
}
|
|
1066
|
|
|
1067
|
@Test //#3666 and others
|
|
1068
|
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="NameServiceImplTest.xml")
|
|
1069
|
public void testParseName() {
|
|
1070
|
Assert.assertEquals(3, nameService.count(TaxonName.class));
|
|
1071
|
String nameToParseStr = "Abies alba Mill, Sp. Pl. 2: 333. 1751 [as \"alpa\"]";
|
|
1072
|
TaxonName parsedName = (TaxonName)nameService.parseName(nameToParseStr, NomenclaturalCode.ICNAFP, Rank.SPECIES(), true).getCdmEntity();
|
|
1073
|
UUID parsedNameUuid = parsedName.getUuid();
|
|
1074
|
UUID originalSpellingUuid = parsedName.getOriginalSpelling().getUuid();
|
|
1075
|
nameService.save(parsedName);
|
|
1076
|
|
|
1077
|
TaxonName parsedName2 = (TaxonName)nameService.parseName(nameToParseStr, NomenclaturalCode.ICNAFP, Rank.SPECIES(), true).getCdmEntity();
|
|
1078
|
UUID parsedNameUuid2 = parsedName2.getUuid();
|
|
1079
|
UUID originalSpelling2Uuid = parsedName2.getOriginalSpelling().getUuid();
|
|
1080
|
Assert.assertEquals(originalSpellingUuid, originalSpelling2Uuid);
|
|
1081
|
Assert.assertNotEquals(parsedNameUuid, parsedNameUuid2); //currently we do not deduplicate the main name yet
|
|
1082
|
|
|
1083
|
//tbc
|
|
1084
|
}
|
|
1085
|
|
|
1086
|
private Rank getSpeciesRank() {
|
|
1087
|
return (Rank)termService.find(Rank.uuidSpecies);
|
|
1088
|
}
|
|
1089
|
|
|
1090
|
private Rank getGenusRank() {
|
|
1091
|
return (Rank)termService.find(Rank.uuidGenus);
|
|
1092
|
}
|
|
1093
|
|
|
1094
|
@Override
|
|
1095
|
public void createTestDataSet() throws FileNotFoundException {}
|
|
1096
|
}
|