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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.IdentifiableServiceConfiguratorImpl;
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import eu.etaxonomy.cdm.api.service.config.IncludedTaxonConfiguration;
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import eu.etaxonomy.cdm.api.service.config.MatchingTaxonConfigurator;
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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.api.service.pager.Pager;
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import eu.etaxonomy.cdm.model.agent.Person;
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import eu.etaxonomy.cdm.model.common.Annotation;
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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.Language;
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import eu.etaxonomy.cdm.model.common.LanguageString;
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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.description.CommonTaxonName;
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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.description.TextData;
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import eu.etaxonomy.cdm.model.metadata.SecReferenceHandlingEnum;
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import eu.etaxonomy.cdm.model.metadata.SecReferenceHandlingSwapEnum;
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import eu.etaxonomy.cdm.model.name.IBotanicalName;
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import eu.etaxonomy.cdm.model.name.INonViralName;
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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.NomenclaturalCode;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
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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.occurrence.DerivationEvent;
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import eu.etaxonomy.cdm.model.occurrence.DerivationEventType;
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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.OriginalSourceType;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.SynonymType;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.taxon.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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private static String[] genera = {"Carex", "Abies", "Belladonna", "Dracula", "Maria", "Calendula", "Polygala", "Vincia"};
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private static String[] epitheta = {"vulgaris", "magdalena", "officinalis", "alba", "negra", "communa", "alpina", "rotundifolia", "greutheriana", "helventica", "allemania", "franca"};
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private static String[] ranks = {"subsp", "var", "f"};
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public static UUID GENUS_NAME_UUID = UUID.fromString("8d761fc4-b509-42f4-9568-244161934336");
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public static UUID GENUS_UUID = UUID.fromString("bf4298a8-1735-4353-a210-244442e1bd62");
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public static UUID BASIONYM_UUID = UUID.fromString("7911c51d-ccb7-4708-8992-639eae58a0e3");
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public static UUID SPECIES1_UUID = UUID.fromString("f0eb77d9-76e0-47f4-813f-9b5605b78685");
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public static UUID SPECIES1_NAME_UUID = UUID.fromString("efd78713-126f-42e1-9070-a1ff83f12abf");
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public static UUID SYNONYM_NAME_UUID = UUID.fromString("b9cbaa74-dbe0-4930-8050-b7754ce85dc0");
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public static UUID SPECIES2_NAME_UUID = UUID.fromString("0267ab67-483e-4da5-b654-11013b242c22");
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public static UUID SPECIES2_UUID = UUID.fromString("e20eb549-ced6-4e79-9d74-44f0792a4929");
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public static UUID SYNONYM2_NAME_UUID = UUID.fromString("7c17c811-4201-454b-8108-7be7c91c0938");
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public static UUID SYNONYM2_UUID = UUID.fromString("2520b103-bd89-4ac1-99e4-e3bfcedfd4eb");
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public static UUID SPECIES5_NAME_UUID = UUID.fromString("0c6ecaac-804d-49e5-a33f-1b7ee77439e3");
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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#getTaxonByUuid(java.util.UUID)}.
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*/
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@Test
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public final void testGetTaxonByTitle() {
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TaxonName name = TaxonName.NewInstance(NomenclaturalCode.ICNAFP, Rank.SPECIES(), "Abies", null, "alba", null, null, null, null, null);
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Taxon expectedTaxon = Taxon.NewInstance(name, null);
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expectedTaxon.setDoubtful(true);
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service.save(expectedTaxon);
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IdentifiableServiceConfiguratorImpl<TaxonBase> config = new IdentifiableServiceConfiguratorImpl<TaxonBase>();
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config.setTitleSearchString("Abies alba*");
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//doubtful taxa should be found
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Pager<TaxonBase> actualTaxa = service.findByTitle(config);
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assertEquals(expectedTaxon, actualTaxa.getRecords().get(0));
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//and other taxa as well
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expectedTaxon.setDoubtful(false);
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service.saveOrUpdate(expectedTaxon);
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actualTaxa = service.findByTitle(config);
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assertEquals(expectedTaxon, actualTaxa.getRecords().get(0));
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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(TaxonNameFactory.NewBotanicalInstance(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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@Test
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public final void testSaveOrUpdateTaxonWithMisappliedName() {
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Taxon expectedTaxon = Taxon.NewInstance(null, null);
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TaxonName misappliedNameName = TaxonName.NewInstance(NomenclaturalCode.ICNAFP, Rank.SPECIES(), "Abies", null, "alba", null, null, null, null, null);
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UUID misappliedNameNameUuid = nameService.save(misappliedNameName).getUuid();
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misappliedNameName = nameService.find(misappliedNameNameUuid);
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SpecimenTypeDesignation typedes = SpecimenTypeDesignation.NewInstance();
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DerivedUnit derivedUnit = DerivedUnit.NewPreservedSpecimenInstance();
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FieldUnit fieldUnit = FieldUnit.NewInstance();
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DerivationEvent derivationEvent = DerivationEvent.NewSimpleInstance(fieldUnit, derivedUnit, DerivationEventType.ACCESSIONING());
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// derivedUnit.addDerivationEvent(derivationEvent);
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typedes.setTypeSpecimen(derivedUnit);
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misappliedNameName.addTypeDesignation(typedes, false);
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Taxon misappliedName = Taxon.NewInstance(misappliedNameName, null);
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UUID misappliedNameUuid = service.save(misappliedName).getUuid();
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misappliedName = (Taxon) service.find(misappliedNameUuid);
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expectedTaxon.addMisappliedName(misappliedName, 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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misappliedName.setSec(ReferenceFactory.newArticle());
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try{
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service.saveOrUpdate(actualTaxon);
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misappliedName = (Taxon)service.find(misappliedNameUuid);
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Assert.assertNotNull(misappliedName.getSec());
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}catch(Exception e){
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Assert.fail();
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}
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commitAndStartNewTransaction(null);
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actualTaxon = service.find(uuid);
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((Taxon)actualTaxon).getTaxonRelations(misappliedName).iterator().next().getFromTaxon().setSec(null);
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try{
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service.saveOrUpdate(actualTaxon);
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misappliedName = (Taxon)service.find(misappliedNameUuid);
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Assert.assertNull(misappliedName.getSec());
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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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@Test
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public final void testSwapSynonymAndAcceptedTaxon() throws FileNotFoundException{
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createTestDataSet();
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synonym.setSec(ReferenceFactory.newArticle());
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service.saveOrUpdate(synonym);
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UpdateResult result = service.swapSynonymAndAcceptedTaxon(synonym, taxWithSyn, true, false, SecReferenceHandlingSwapEnum.AlwaysDelete, null, null);
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// find forces flush
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Taxon tax = (Taxon)service.find(result.getCdmEntity().getUuid());
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MatchingTaxonConfigurator configurator = MatchingTaxonConfigurator.NewInstance();
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configurator.setTaxonNameTitle("Test3");
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List<TaxonBase> synList = service.findTaxaByName(configurator);
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if (synList.size() > 0){
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TaxonBase<?> syn = synList.get(0);
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assertTrue(tax.getSynonyms().contains(syn));
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}else{
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Assert.fail("There should be a synonym with name Test3");
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}
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assertTrue(tax.getName().getTitleCache().equals("Test2"));
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}
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@Test
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public final void testSwapSynonymAndAcceptedTaxonNewUuid() throws FileNotFoundException{
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createTestDataSet();
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synonym.setSec(ReferenceFactory.newArticle());
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service.saveOrUpdate(synonym);
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UpdateResult result = service.swapSynonymAndAcceptedTaxon(synonym, taxWithSyn, true, true, SecReferenceHandlingSwapEnum.AlwaysDelete, null, null);
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// find forces flush
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Taxon tax = (Taxon)service.find(result.getCdmEntity().getUuid());
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MatchingTaxonConfigurator configurator = MatchingTaxonConfigurator.NewInstance();
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configurator.setTaxonNameTitle("Test3");
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@SuppressWarnings("rawtypes")
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List<TaxonBase> synList = service.findTaxaByName(configurator);
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if (synList.size() > 0){
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TaxonBase<?> syn = synList.get(0);
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assertTrue(tax.getSynonyms().contains(syn));
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}else{
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Assert.fail("There should be a synonym with name Test3");
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}
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assertTrue(tax.getName().getTitleCache().equals("Test2"));
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}
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@Test
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public final void testChangeSynonymToAcceptedTaxon() throws FileNotFoundException{
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createTestDataSet();
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UpdateResult result = new UpdateResult();
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try {
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result = service.changeSynonymToAcceptedTaxon(synonym, taxWithSyn, null, null, null, true);
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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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313
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taxWithSyn = (Taxon)service.find(uuidTaxWithSyn);
|
|
314
|
Taxon taxNew = (Taxon)service.find(result.getCdmEntity().getUuid());
|
|
315
|
assertNull(syn);
|
|
316
|
assertNotNull(taxWithSyn);
|
|
317
|
assertNotNull(taxNew);
|
|
318
|
|
|
319
|
Assert.assertEquals("New taxon should have 1 synonym relationship (the old homotypic synonym)", 1, ((Taxon)result.getCdmEntity()).getSynonyms().size());
|
|
320
|
}
|
|
321
|
|
|
322
|
@Test
|
|
323
|
public final void testChangeSynonymToAcceptedTaxonWithSecHandlingAlwaysDelete(){
|
|
324
|
Taxon genus = getTestTaxon();
|
|
325
|
TaxonNode node = genus.getTaxonNodes().iterator().next();
|
|
326
|
|
|
327
|
UpdateResult result = new UpdateResult();
|
|
328
|
try {
|
|
329
|
result = service.changeSynonymToAcceptedTaxon(SYNONYM2_UUID, SPECIES2_UUID, node.getUuid(), null, null, SecReferenceHandlingEnum.AlwaysDelete, true);
|
|
330
|
} catch (HomotypicalGroupChangeException e) {
|
|
331
|
Assert.fail("Invocation of change method should not throw an exception");
|
|
332
|
}
|
|
333
|
taxWithSyn = null;
|
|
334
|
//test flush (resave deleted object)
|
|
335
|
TaxonBase<?> syn = service.find(SYNONYM2_UUID);
|
|
336
|
taxWithSyn = (Taxon)service.find(SPECIES2_UUID);
|
|
337
|
TaxonNode taxNodeNew = nodeService.find(result.getCdmEntity().getUuid());
|
|
338
|
Taxon taxNew = taxNodeNew.getTaxon();
|
|
339
|
assertNull(syn);
|
|
340
|
assertNotNull(taxWithSyn);
|
|
341
|
assertNotNull(taxNew);
|
|
342
|
assertNull(taxNew.getSec());
|
|
343
|
|
|
344
|
|
|
345
|
}
|
|
346
|
|
|
347
|
|
|
348
|
|
|
349
|
@Test
|
|
350
|
public final void testChangeSynonymToAcceptedTaxonWithSecHandlingUseNewParentSec(){
|
|
351
|
Taxon genus = getTestTaxon();
|
|
352
|
TaxonNode node = genus.getTaxonNodes().iterator().next();
|
|
353
|
UpdateResult result = new UpdateResult();
|
|
354
|
TaxonBase<?> syn = service.find(SYNONYM2_UUID);
|
|
355
|
Reference sec = ReferenceFactory.newBook();
|
|
356
|
sec.setTitleCache("Flora Cuba", true);
|
|
357
|
syn.setSec(sec);
|
|
358
|
service.saveOrUpdate(syn);
|
|
359
|
try {
|
|
360
|
result = service.changeSynonymToAcceptedTaxon(SYNONYM2_UUID, SPECIES2_UUID, node.getUuid(), null, null, SecReferenceHandlingEnum.UseNewParentSec, true);
|
|
361
|
} catch (HomotypicalGroupChangeException e) {
|
|
362
|
Assert.fail("Invocation of change method should not throw an exception");
|
|
363
|
}
|
|
364
|
taxWithSyn = null;
|
|
365
|
//test flush (resave deleted object)
|
|
366
|
syn = service.find(SYNONYM2_UUID);
|
|
367
|
taxWithSyn = (Taxon)service.find(SPECIES2_UUID);
|
|
368
|
TaxonNode taxNodeNew = nodeService.find(result.getCdmEntity().getUuid());
|
|
369
|
Taxon taxNew = taxNodeNew.getTaxon();
|
|
370
|
assertNull(syn);
|
|
371
|
assertNotNull(taxWithSyn);
|
|
372
|
assertNotNull(taxNew);
|
|
373
|
assertNotNull(taxNew.getSec());
|
|
374
|
assertEquals(taxWithSyn.getSec(), taxNew.getSec());
|
|
375
|
|
|
376
|
}
|
|
377
|
|
|
378
|
@Test
|
|
379
|
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="TaxonServiceImplTest.testMoveSynonymToAnotherTaxon.xml")
|
|
380
|
public final void testChangeSynonymToAcceptedTaxonWithSecHandlingWarningSelect(){
|
|
381
|
Taxon genus = getTestTaxon();
|
|
382
|
TaxonNode node = genus.getTaxonNodes().iterator().next();
|
|
383
|
|
|
384
|
UpdateResult result = new UpdateResult();
|
|
385
|
TaxonBase<?> syn = service.find(SYNONYM2_UUID);
|
|
386
|
Reference sec = ReferenceFactory.newBook();
|
|
387
|
sec.setTitleCache("Flora Cuba", true);
|
|
388
|
Reference newSec = ReferenceFactory.newBook();
|
|
389
|
newSec.setTitleCache("Flora Hawaii", true);
|
|
390
|
UUID newSecUuid = referenceService.saveOrUpdate(newSec);
|
|
391
|
syn.setSec(sec);
|
|
392
|
service.saveOrUpdate(syn);
|
|
393
|
try {
|
|
394
|
result = service.changeSynonymToAcceptedTaxon(SYNONYM2_UUID, SPECIES2_UUID, node.getUuid(), newSecUuid, "23", SecReferenceHandlingEnum.KeepOrSelect, true);
|
|
395
|
} catch (HomotypicalGroupChangeException e) {
|
|
396
|
Assert.fail("Invocation of change method should not throw an exception");
|
|
397
|
}
|
|
398
|
taxWithSyn = null;
|
|
399
|
//test flush (resave deleted object)
|
|
400
|
syn = service.find(SYNONYM2_UUID);
|
|
401
|
taxWithSyn = (Taxon)service.find(SPECIES2_UUID);
|
|
402
|
TaxonNode taxNodeNew = nodeService.find(result.getCdmEntity().getUuid());
|
|
403
|
Taxon taxNew = taxNodeNew.getTaxon();
|
|
404
|
assertNull(syn);
|
|
405
|
assertNotNull(taxWithSyn);
|
|
406
|
assertNotNull(taxNew);
|
|
407
|
assertNotNull(taxNew.getSec());
|
|
408
|
assertEquals(newSec, taxNew.getSec());
|
|
409
|
|
|
410
|
}
|
|
411
|
|
|
412
|
|
|
413
|
@Test
|
|
414
|
public final void testChangeSynonymToAcceptedTaxonSynonymForTwoTaxa(){
|
|
415
|
try {
|
|
416
|
createTestDataSet();
|
|
417
|
} catch (FileNotFoundException e1) {
|
|
418
|
// TODO Auto-generated catch block
|
|
419
|
e1.printStackTrace();
|
|
420
|
}
|
|
421
|
|
|
422
|
|
|
423
|
Taxon taxon = null;
|
|
424
|
UpdateResult result = new UpdateResult();
|
|
425
|
try {
|
|
426
|
result = service.changeSynonymToAcceptedTaxon(synonym, taxWithSyn, null, null, null, true);
|
|
427
|
service.save(taxon);
|
|
428
|
} catch (HomotypicalGroupChangeException e) {
|
|
429
|
Assert.fail("Invocation of change method should not throw an exception");
|
|
430
|
}
|
|
431
|
taxWithSyn = null;
|
|
432
|
tax2WithSyn = null;
|
|
433
|
|
|
434
|
//test flush (resave deleted object)
|
|
435
|
TaxonBase<?> syn = service.find(uuidSyn);
|
|
436
|
taxWithSyn = (Taxon)service.find(uuidTaxWithSyn);
|
|
437
|
Taxon taxNew = (Taxon)service.find(((Taxon)result.getCdmEntity()).getUuid());
|
|
438
|
assertNull(syn);
|
|
439
|
assertNotNull(taxWithSyn);
|
|
440
|
assertNotNull(taxNew);
|
|
441
|
|
|
442
|
// Assert.assertEquals("New taxon should have 1 synonym relationship (the old homotypic synonym)", 1, taxon.getSynonymRelations().size());
|
|
443
|
}
|
|
444
|
|
|
445
|
/**
|
|
446
|
* Old implementation taken from {@link TaxonServiceImplBusinessTest} for old version of method.
|
|
447
|
*/
|
|
448
|
@Test
|
|
449
|
public final void testMoveSynonymToAnotherTaxon_OLD() {
|
|
450
|
SynonymType heteroTypicSynonymType = SynonymType.HETEROTYPIC_SYNONYM_OF();
|
|
451
|
Reference reference = ReferenceFactory.newGeneric();
|
|
452
|
String referenceDetail = "test";
|
|
453
|
|
|
454
|
INonViralName t1n = TaxonNameFactory.NewNonViralInstance(null);
|
|
455
|
Taxon t1 = Taxon.NewInstance(t1n, reference);
|
|
456
|
INonViralName t2n = TaxonNameFactory.NewNonViralInstance(null);
|
|
457
|
Taxon t2 = Taxon.NewInstance(t2n, reference);
|
|
458
|
INonViralName s1n = TaxonNameFactory.NewNonViralInstance(null);
|
|
459
|
Synonym s1 = Synonym.NewInstance(s1n, reference);
|
|
460
|
t1.addSynonym(s1, heteroTypicSynonymType);
|
|
461
|
service.saveOrUpdate(t1);
|
|
462
|
|
|
463
|
Synonym synonym = t1.getSynonyms().iterator().next();
|
|
464
|
|
|
465
|
boolean keepReference = false;
|
|
466
|
boolean moveHomotypicGroup = false;
|
|
467
|
try {
|
|
468
|
service.moveSynonymToAnotherTaxon(synonym, t2, moveHomotypicGroup, heteroTypicSynonymType, reference.getUuid(), referenceDetail, keepReference);
|
|
469
|
} catch (HomotypicalGroupChangeException e) {
|
|
470
|
Assert.fail("Method call should not throw exception");
|
|
471
|
}
|
|
472
|
|
|
473
|
Assert.assertTrue("t1 should have no synonyms", t1.getSynonyms().isEmpty());
|
|
474
|
|
|
475
|
Set<Synonym> synonyms = t2.getSynonyms();
|
|
476
|
Assert.assertTrue("t2 should have exactly one synonym", synonyms.size() == 1);
|
|
477
|
|
|
478
|
synonym = synonyms.iterator().next();
|
|
479
|
|
|
480
|
Assert.assertEquals(t2, synonym.getAcceptedTaxon());
|
|
481
|
Assert.assertEquals(heteroTypicSynonymType, synonym.getType());
|
|
482
|
Assert.assertEquals(reference, synonym.getSec());
|
|
483
|
Assert.assertEquals(referenceDetail, synonym.getSecMicroReference());
|
|
484
|
}
|
|
485
|
|
|
486
|
@Test
|
|
487
|
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="TaxonServiceImplTest.testMoveSynonymToAnotherTaxon.xml")
|
|
488
|
public final void testMoveSynonymToAnotherTaxon() throws Exception {
|
|
489
|
final String[] tableNames = new String[]{};
|
|
490
|
|
|
491
|
// printDataSet(System.err, new String[]{"AgentBase", "TaxonBase"});
|
|
492
|
// printDataSet(System.err, new String[]{"TaxonNode"});
|
|
493
|
|
|
494
|
UUID uuidNewTaxon = UUID.fromString("2d9a642d-5a82-442d-8fec-95efa978e8f8");
|
|
495
|
UUID uuidOldTaxon = UUID.fromString("c47fdb72-f32c-452e-8305-4b44f01179d0");
|
|
496
|
UUID uuidSyn1 = UUID.fromString("7da85381-ad9d-4886-9d4d-0eeef40e3d88");
|
|
497
|
UUID uuidSyn3 = UUID.fromString("3fba2b22-22ae-4291-af67-faab748a5232");
|
|
498
|
UUID uuidSyn4 = UUID.fromString("f9b589c7-50cf-4df2-a52e-1b85eb7e4805");
|
|
499
|
UUID uuidSyn5 = UUID.fromString("fcc0bcf8-8bac-43bd-9508-1e97821587dd");
|
|
500
|
UUID uuidSyn6 = UUID.fromString("0ccd4e7c-6fbd-4b7c-bd47-29e45b92f34b");
|
|
501
|
UUID uuidRef1 = UUID.fromString("336f9b38-698c-45d7-be7b-993ed3355bdc");
|
|
502
|
UUID uuidRef2 = UUID.fromString("c8f49d1a-69e1-48a3-98bb-45d61f3da3e7");
|
|
503
|
|
|
504
|
|
|
505
|
boolean moveHomotypicGroup = true;
|
|
506
|
SynonymType newSynonymType = null;
|
|
507
|
boolean keepReference = true;
|
|
508
|
Reference newReference = null;
|
|
509
|
String newReferenceDetail = null;
|
|
510
|
|
|
511
|
Taxon newTaxon = (Taxon)service.load(uuidNewTaxon);
|
|
512
|
Synonym homotypicSynonym = (Synonym)service.load(uuidSyn1);
|
|
513
|
Assert.assertNotNull("Synonym should exist", homotypicSynonym);
|
|
514
|
Assert.assertNotNull("Synonym should have 1 relation", homotypicSynonym.getAcceptedTaxon());
|
|
515
|
Assert.assertEquals("Accepted taxon of single relation should be the old taxon", uuidOldTaxon, homotypicSynonym.getAcceptedTaxon().getUuid());
|
|
516
|
Taxon oldTaxon = homotypicSynonym.getAcceptedTaxon();
|
|
517
|
|
|
518
|
try {
|
|
519
|
service.moveSynonymToAnotherTaxon(homotypicSynonym, newTaxon, moveHomotypicGroup, newSynonymType, null, newReferenceDetail, keepReference);
|
|
520
|
Assert.fail("Homotypic synonym move to other taxon should throw an exception");
|
|
521
|
} catch (HomotypicalGroupChangeException e) {
|
|
522
|
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")){
|
|
523
|
//OK
|
|
524
|
commitAndStartNewTransaction(tableNames);
|
|
525
|
}else{
|
|
526
|
Assert.fail("Unexpected exception occurred: " + e.getMessage());
|
|
527
|
}
|
|
528
|
}
|
|
529
|
//Asserts
|
|
530
|
homotypicSynonym = (Synonym)service.load(uuidSyn1);
|
|
531
|
Assert.assertNotNull("Synonym should still exist", homotypicSynonym);
|
|
532
|
Assert.assertNotNull("Synonym should still have 1 relation", homotypicSynonym.getAcceptedTaxon());
|
|
533
|
Assert.assertEquals("Accepted taxon of single relation should be the old taxon", oldTaxon, homotypicSynonym.getAcceptedTaxon());
|
|
534
|
|
|
535
|
//test heterotypic synonym with other synonym in homotypic group
|
|
536
|
newTaxon = (Taxon)service.load(uuidNewTaxon);
|
|
537
|
Synonym heterotypicSynonym = (Synonym)service.load(uuidSyn3);
|
|
538
|
Assert.assertNotNull("Synonym should exist", heterotypicSynonym);
|
|
539
|
Assert.assertNotNull("Synonym should have 1 relation", heterotypicSynonym.getAcceptedTaxon());
|
|
540
|
Assert.assertEquals("Accepted taxon of single relation should be the old taxon", uuidOldTaxon, heterotypicSynonym.getAcceptedTaxon().getUuid());
|
|
541
|
oldTaxon = heterotypicSynonym.getAcceptedTaxon();
|
|
542
|
moveHomotypicGroup = false;
|
|
543
|
|
|
544
|
try {
|
|
545
|
service.moveSynonymToAnotherTaxon(heterotypicSynonym, newTaxon, moveHomotypicGroup, newSynonymType, null, newReferenceDetail, keepReference);
|
|
546
|
Assert.fail("Heterotypic synonym move to other taxon should throw an exception");
|
|
547
|
} catch (HomotypicalGroupChangeException e) {
|
|
548
|
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")){
|
|
549
|
//OK
|
|
550
|
commitAndStartNewTransaction(tableNames);
|
|
551
|
}else{
|
|
552
|
Assert.fail("Unexpected exception occurred: " + e.getMessage());
|
|
553
|
}
|
|
554
|
}
|
|
555
|
//Asserts
|
|
556
|
heterotypicSynonym = (Synonym)service.load(uuidSyn3);
|
|
557
|
Assert.assertNotNull("Synonym should still exist", heterotypicSynonym);
|
|
558
|
Assert.assertNotNull("Synonym should have accepted taxon", heterotypicSynonym.getAcceptedTaxon());
|
|
559
|
Assert.assertEquals("Accepted taxon of single relation should still be the old taxon", oldTaxon, heterotypicSynonym.getAcceptedTaxon());
|
|
560
|
|
|
561
|
|
|
562
|
//test heterotypic synonym with no other synonym in homotypic group
|
|
563
|
//+ keep reference
|
|
564
|
|
|
565
|
newTaxon = (Taxon)service.load(uuidNewTaxon);
|
|
566
|
heterotypicSynonym = (Synonym)service.load(uuidSyn5);
|
|
567
|
Assert.assertNotNull("Synonym should exist", heterotypicSynonym);
|
|
568
|
Assert.assertNotNull("Synonym should have accepted taxon", heterotypicSynonym.getAcceptedTaxon());
|
|
569
|
Assert.assertEquals("Accepted taxon of single relation should be the old taxon", uuidOldTaxon, heterotypicSynonym.getAcceptedTaxon().getUuid());
|
|
570
|
oldTaxon = heterotypicSynonym.getAcceptedTaxon();
|
|
571
|
moveHomotypicGroup = false;
|
|
572
|
|
|
573
|
try {
|
|
574
|
service.moveSynonymToAnotherTaxon(heterotypicSynonym, newTaxon, moveHomotypicGroup, newSynonymType, null, newReferenceDetail, keepReference);
|
|
575
|
} catch (HomotypicalGroupChangeException e) {
|
|
576
|
Assert.fail("Move of single heterotypic synonym should not throw exception: " + e.getMessage());
|
|
577
|
}
|
|
578
|
//Asserts
|
|
579
|
commitAndStartNewTransaction(tableNames);
|
|
580
|
|
|
581
|
heterotypicSynonym = (Synonym)service.load(uuidSyn5);
|
|
582
|
Assert.assertNotNull("Synonym should still exist", heterotypicSynonym);
|
|
583
|
Assert.assertNotNull("Synonym should have accepted taxon", heterotypicSynonym.getAcceptedTaxon());
|
|
584
|
Assert.assertEquals("Accepted taxon of single relation should be new taxon", newTaxon, heterotypicSynonym.getAcceptedTaxon());
|
|
585
|
Assert.assertEquals("Old detail should be kept", "rel5", heterotypicSynonym.getSecMicroReference());
|
|
586
|
|
|
587
|
//test heterotypic synonym with other synonym in homotypic group and moveHomotypicGroup="true"
|
|
588
|
//+ new detail
|
|
589
|
newTaxon = (Taxon)service.load(uuidNewTaxon);
|
|
590
|
heterotypicSynonym = (Synonym)service.load(uuidSyn3);
|
|
591
|
Reference ref1 = referenceService.load(uuidRef1);
|
|
592
|
Assert.assertNotNull("Synonym should exist", heterotypicSynonym);
|
|
593
|
Assert.assertNotNull("Synonym should have 1 relation", heterotypicSynonym.getAcceptedTaxon());
|
|
594
|
Assert.assertEquals("Accepted taxon of single relation should be the old taxon", uuidOldTaxon, heterotypicSynonym.getAcceptedTaxon().getUuid());
|
|
595
|
oldTaxon = heterotypicSynonym.getAcceptedTaxon();
|
|
596
|
Assert.assertEquals("Detail should be ref1", ref1, heterotypicSynonym.getSec());
|
|
597
|
Assert.assertEquals("Detail should be 'rel3'", "rel3", heterotypicSynonym.getSecMicroReference());
|
|
598
|
TaxonName oldSynName3 = heterotypicSynonym.getName();
|
|
599
|
|
|
600
|
Synonym heterotypicSynonym4 = (Synonym)service.load(uuidSyn4);
|
|
601
|
Assert.assertNotNull("Synonym should exist", heterotypicSynonym4);
|
|
602
|
Assert.assertNotNull("Synonym should have accepted taxon", heterotypicSynonym4.getAcceptedTaxon());
|
|
603
|
Assert.assertEquals("Accepted taxon of other synonym in group should be the old taxon", uuidOldTaxon, heterotypicSynonym4.getAcceptedTaxon().getUuid());
|
|
604
|
Assert.assertSame("Homotypic group of both synonyms should be same", oldSynName3.getHomotypicalGroup() , heterotypicSynonym4.getName().getHomotypicalGroup() );
|
|
605
|
|
|
606
|
moveHomotypicGroup = true;
|
|
607
|
keepReference = false;
|
|
608
|
|
|
609
|
try {
|
|
610
|
service.moveSynonymToAnotherTaxon(heterotypicSynonym4, newTaxon, moveHomotypicGroup, newSynonymType, null, newReferenceDetail, keepReference);
|
|
611
|
} catch (HomotypicalGroupChangeException e) {
|
|
612
|
Assert.fail("Move with 'moveHomotypicGroup = true' should not throw exception: " + e.getMessage());
|
|
613
|
}
|
|
614
|
//Asserts
|
|
615
|
commitAndStartNewTransaction(tableNames);
|
|
616
|
heterotypicSynonym = (Synonym)service.load(uuidSyn3);
|
|
617
|
Assert.assertNotNull("Synonym should still exist", heterotypicSynonym);
|
|
618
|
Assert.assertNotNull("Synonym should still have accepted taxon", heterotypicSynonym.getAcceptedTaxon());
|
|
619
|
Assert.assertEquals("Accepted taxon of relation should be new taxon now", newTaxon, heterotypicSynonym.getAcceptedTaxon());
|
|
620
|
TaxonName synName3 = heterotypicSynonym.getName();
|
|
621
|
|
|
622
|
heterotypicSynonym = (Synonym)service.load(uuidSyn4);
|
|
623
|
Assert.assertNotNull("Synonym should still exist", heterotypicSynonym);
|
|
624
|
Assert.assertNotNull("Synonym should still have accepted taxon", heterotypicSynonym.getAcceptedTaxon());
|
|
625
|
Assert.assertEquals("Accepted taxon of relation should be new taxon now", newTaxon, heterotypicSynonym.getAcceptedTaxon());
|
|
626
|
Assert.assertNull("Old citation should be removed", heterotypicSynonym.getSec());
|
|
627
|
Assert.assertNull("Old detail should be removed", heterotypicSynonym.getSecMicroReference());
|
|
628
|
TaxonName synName4 = heterotypicSynonym.getName();
|
|
629
|
Assert.assertEquals("Homotypic group of both synonyms should be equal", synName3.getHomotypicalGroup() , synName4.getHomotypicalGroup() );
|
|
630
|
Assert.assertSame("Homotypic group of both synonyms should be same", synName3.getHomotypicalGroup() , synName4.getHomotypicalGroup() );
|
|
631
|
Assert.assertEquals("Homotypic group of both synonyms should be equal to old homotypic group", oldSynName3.getHomotypicalGroup() , synName3.getHomotypicalGroup() );
|
|
632
|
|
|
633
|
//test single heterotypic synonym to homotypic synonym of new taxon
|
|
634
|
//+ new reference
|
|
635
|
newTaxon = (Taxon)service.load(uuidNewTaxon);
|
|
636
|
Reference ref2 = referenceService.load(uuidRef2);
|
|
637
|
heterotypicSynonym = (Synonym)service.load(uuidSyn6);
|
|
638
|
Assert.assertNotNull("Synonym should exist", heterotypicSynonym);
|
|
639
|
Assert.assertNotNull("Synonym should have accepted taxon", heterotypicSynonym.getAcceptedTaxon());
|
|
640
|
Assert.assertEquals("Accepted taxon of single relation should be the old taxon", uuidOldTaxon, heterotypicSynonym.getAcceptedTaxon().getUuid());
|
|
641
|
oldTaxon = heterotypicSynonym.getAcceptedTaxon();
|
|
642
|
moveHomotypicGroup = false;
|
|
643
|
keepReference = false;
|
|
644
|
newReference = ref2;
|
|
645
|
newReferenceDetail = "newRefDetail";
|
|
646
|
newSynonymType = SynonymType.HOMOTYPIC_SYNONYM_OF();
|
|
647
|
|
|
648
|
try {
|
|
649
|
service.moveSynonymToAnotherTaxon(heterotypicSynonym, newTaxon, moveHomotypicGroup, newSynonymType, newReference.getUuid(), newReferenceDetail, keepReference);
|
|
650
|
} catch (HomotypicalGroupChangeException e) {
|
|
651
|
Assert.fail("Move of single heterotypic synonym should not throw exception: " + e.getMessage());
|
|
652
|
}
|
|
653
|
//Asserts
|
|
654
|
commitAndStartNewTransaction(tableNames);
|
|
655
|
heterotypicSynonym = (Synonym)service.load(uuidSyn6);
|
|
656
|
Assert.assertNotNull("Synonym should still exist", heterotypicSynonym);
|
|
657
|
Assert.assertNotNull("Synonym should still have accepted taxon", heterotypicSynonym.getAcceptedTaxon());
|
|
658
|
Assert.assertEquals("Relationship type should be 'homotypic synonym'", newSynonymType, heterotypicSynonym.getType());
|
|
659
|
Assert.assertEquals("Accepted taxon of single relation should be new taxon", newTaxon, heterotypicSynonym.getAcceptedTaxon());
|
|
660
|
Assert.assertEquals("New citation should be ref2", ref2 ,heterotypicSynonym.getSec());
|
|
661
|
Assert.assertEquals("New detail should be kept", "newRefDetail", heterotypicSynonym.getSecMicroReference());
|
|
662
|
|
|
663
|
Assert.assertEquals("New taxon and new synonym should have equal homotypical group", heterotypicSynonym.getHomotypicGroup(), heterotypicSynonym.getAcceptedTaxon().getHomotypicGroup());
|
|
664
|
Assert.assertSame("New taxon and new synonym should have same homotypical group", heterotypicSynonym.getHomotypicGroup(), heterotypicSynonym.getAcceptedTaxon().getHomotypicGroup());
|
|
665
|
}
|
|
666
|
|
|
667
|
@Test
|
|
668
|
public final void testGetHeterotypicSynonymyGroups(){
|
|
669
|
Rank rank = Rank.SPECIES();
|
|
670
|
Reference ref1 = ReferenceFactory.newGeneric();
|
|
671
|
//HomotypicalGroup group = HomotypicalGroup.NewInstance();
|
|
672
|
Taxon taxon1 = Taxon.NewInstance(TaxonNameFactory.NewBotanicalInstance(rank, "Test3", null, null, null, null, null, null, null), null);
|
|
673
|
Synonym synonym0 = Synonym.NewInstance(TaxonNameFactory.NewBotanicalInstance(rank, "Test2", null, null, null, null, null, null, null), null);
|
|
674
|
Synonym synonym1 = Synonym.NewInstance(TaxonNameFactory.NewBotanicalInstance(rank, "Test2", null, null, null, null, null, null, null), null);
|
|
675
|
Synonym synonym2 = Synonym.NewInstance(TaxonNameFactory.NewBotanicalInstance(rank, "Test4", null, null, null, null, null, null, null), null);
|
|
676
|
synonym0.getName().setHomotypicalGroup(taxon1.getHomotypicGroup());
|
|
677
|
synonym2.getName().setHomotypicalGroup(synonym1.getHomotypicGroup());
|
|
678
|
//tax2.addHeterotypicSynonymName(synonym.getName());
|
|
679
|
taxon1.addSynonym(synonym1, SynonymType.HETEROTYPIC_SYNONYM_OF());
|
|
680
|
taxon1.addSynonym(synonym2, SynonymType.HETEROTYPIC_SYNONYM_OF());
|
|
681
|
|
|
682
|
service.save(synonym1);
|
|
683
|
service.save(synonym2);
|
|
684
|
service.save(taxon1);
|
|
685
|
|
|
686
|
List<List<Synonym>> heteroSyns = service.getHeterotypicSynonymyGroups(taxon1, null);
|
|
687
|
Assert.assertEquals("There should be 1 heterotypic group", 1, heteroSyns.size());
|
|
688
|
List<Synonym> synList = heteroSyns.get(0);
|
|
689
|
Assert.assertEquals("There should be 2 heterotypic syns in group 1", 2, synList.size());
|
|
690
|
|
|
691
|
//test sec
|
|
692
|
synonym2.setSec(ref1);
|
|
693
|
heteroSyns = service.getHeterotypicSynonymyGroups(taxon1, null);
|
|
694
|
Assert.assertEquals("There should be 1 heterotypic group", 1, heteroSyns.size());
|
|
695
|
synList = heteroSyns.get(0);
|
|
696
|
Assert.assertEquals("getHeterotypicSynonymyGroups should be independent of sec reference", 2, synList.size());
|
|
697
|
}
|
|
698
|
|
|
699
|
@Test
|
|
700
|
public final void testGetHomotypicSynonymsByHomotypicGroup(){
|
|
701
|
Rank rank = Rank.SPECIES();
|
|
702
|
Reference ref1 = ReferenceFactory.newGeneric();
|
|
703
|
//HomotypicalGroup group = HomotypicalGroup.NewInstance();
|
|
704
|
Taxon taxon1 = Taxon.NewInstance(TaxonNameFactory.NewBotanicalInstance(rank, "Test3", null, null, null, null, null, null, null), null);
|
|
705
|
Synonym synonym0 = Synonym.NewInstance(TaxonNameFactory.NewBotanicalInstance(rank, "Test2", null, null, null, null, null, null, null), null);
|
|
706
|
Synonym synonym1 = Synonym.NewInstance(TaxonNameFactory.NewBotanicalInstance(rank, "Test2", null, null, null, null, null, null, null), null);
|
|
707
|
Synonym synonym2 = Synonym.NewInstance(TaxonNameFactory.NewBotanicalInstance(rank, "Test4", null, null, null, null, null, null, null), null);
|
|
708
|
synonym0.getName().setHomotypicalGroup(taxon1.getHomotypicGroup());
|
|
709
|
synonym2.getName().setHomotypicalGroup(synonym1.getHomotypicGroup());
|
|
710
|
//tax2.addHeterotypicSynonymName(synonym.getName());
|
|
711
|
taxon1.addSynonym(synonym0, SynonymType.HOMOTYPIC_SYNONYM_OF());
|
|
712
|
taxon1.addSynonym(synonym1, SynonymType.HETEROTYPIC_SYNONYM_OF());
|
|
713
|
taxon1.addSynonym(synonym2, SynonymType.HETEROTYPIC_SYNONYM_OF());
|
|
714
|
|
|
715
|
service.save(synonym1);
|
|
716
|
service.save(synonym2);
|
|
717
|
service.save(taxon1);
|
|
718
|
|
|
719
|
List<Synonym> homoSyns = service.getHomotypicSynonymsByHomotypicGroup(taxon1, null);
|
|
720
|
Assert.assertEquals("There should be 1 heterotypic group", 1, homoSyns.size());
|
|
721
|
Assert.assertSame("The homotypic synonym should be synonym0", synonym0, homoSyns.get(0));
|
|
722
|
|
|
723
|
//test sec
|
|
724
|
synonym0.setSec(ref1);
|
|
725
|
homoSyns = service.getHomotypicSynonymsByHomotypicGroup(taxon1, null);
|
|
726
|
Assert.assertEquals("getHeterotypicSynonymyGroups should be independent of sec reference", 1, homoSyns.size());
|
|
727
|
}
|
|
728
|
|
|
729
|
@Test
|
|
730
|
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="TaxonServiceImplTest.testDeleteSynonym.xml")
|
|
731
|
//test delete synonym, but the name will not be deleted
|
|
732
|
public final void testDeleteSynonymSynonymTaxonDontDeleteName(){
|
|
733
|
final String[]tableNames = {
|
|
734
|
// "TaxonBase","TaxonBase_AUD", "TaxonName","TaxonName_AUD",
|
|
735
|
// "HomotypicalGroup","HomotypicalGroup_AUD"
|
|
736
|
};
|
|
737
|
|
|
738
|
int nSynonyms = service.count(Synonym.class);
|
|
739
|
Assert.assertEquals("There should be 2 synonyms in the database", 2, nSynonyms);
|
|
740
|
int nNames = nameService.count(TaxonName.class);
|
|
741
|
Assert.assertEquals("There should be 4 names in the database", 4, nNames);
|
|
742
|
long nRelations = service.countSynonyms(true);
|
|
743
|
Assert.assertEquals("There should be two relationship left in the database", 2, nRelations);
|
|
744
|
|
|
745
|
UUID uuidSynonym1=UUID.fromString("7da85381-ad9d-4886-9d4d-0eeef40e3d88");
|
|
746
|
|
|
747
|
Synonym synonym1 = (Synonym)service.load(uuidSynonym1);
|
|
748
|
SynonymDeletionConfigurator config = new SynonymDeletionConfigurator();
|
|
749
|
config.setDeleteNameIfPossible(false);
|
|
750
|
config.setNewHomotypicGroupIfNeeded(true);
|
|
751
|
service.deleteSynonym(synonym1, config);
|
|
752
|
|
|
753
|
this.commitAndStartNewTransaction(tableNames);
|
|
754
|
|
|
755
|
nSynonyms = service.count(Synonym.class);
|
|
756
|
Assert.assertEquals("There should be 1 synonym left in the database", 1, nSynonyms);
|
|
757
|
nNames = nameService.count(TaxonName.class);
|
|
758
|
Assert.assertEquals("There should be 4 names left in the database", 4, nNames);
|
|
759
|
nRelations = service.countSynonyms(true);
|
|
760
|
Assert.assertEquals("There should be no relationship left in the database", 1, nRelations);
|
|
761
|
}
|
|
762
|
|
|
763
|
@Test
|
|
764
|
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="TaxonServiceImplTest.testDeleteSynonym.xml")
|
|
765
|
//test delete synonym and his name
|
|
766
|
public final void testDeleteSynonymSynonymTaxonDeleteName(){
|
|
767
|
final String[]tableNames = {"TaxonBase","TaxonBase_AUD", "TaxonName","TaxonName_AUD",
|
|
768
|
"HomotypicalGroup","HomotypicalGroup_AUD"};
|
|
769
|
|
|
770
|
int nSynonyms = service.count(Synonym.class);
|
|
771
|
Assert.assertEquals("There should be 2 synonyms in the database", 2, nSynonyms);
|
|
772
|
int nNames = nameService.count(TaxonName.class);
|
|
773
|
Assert.assertEquals("There should be 4 names in the database", 4, nNames);
|
|
774
|
long nRelations = service.countSynonyms(true);
|
|
775
|
Assert.assertEquals("There should be 2 relationship left in the database", 2, nRelations);
|
|
776
|
|
|
777
|
UUID uuidSynonym1=UUID.fromString("7da85381-ad9d-4886-9d4d-0eeef40e3d88");
|
|
778
|
Synonym synonym1 = (Synonym)service.load(uuidSynonym1);
|
|
779
|
service.deleteSynonym(synonym1, new SynonymDeletionConfigurator());
|
|
780
|
|
|
781
|
this.commitAndStartNewTransaction(tableNames);
|
|
782
|
|
|
783
|
nSynonyms = service.count(Synonym.class);
|
|
784
|
Assert.assertEquals("There should be 1 synonym left in the database", 1, nSynonyms);
|
|
785
|
nNames = nameService.count(TaxonName.class);
|
|
786
|
Assert.assertEquals("There should be 3 names left in the database", 3, nNames);
|
|
787
|
nRelations = service.countSynonyms(true);
|
|
788
|
Assert.assertEquals("There should be 1 relationship left in the database", 1, nRelations);
|
|
789
|
}
|
|
790
|
|
|
791
|
@Test
|
|
792
|
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="TaxonServiceImplTest.testDeleteSynonym.xml")
|
|
793
|
//test remove synonym from taxon -> synonym and name still in the db and the synonymrelationship to the other taxon
|
|
794
|
//test delete synonym -> all relationships are deleted, the name is deleted and the synonym itself
|
|
795
|
public final void testDeleteSynonymSynonymTaxonBooleanRelToOneTaxon(){
|
|
796
|
final String[]tableNames = {"TaxonBase","TaxonBase_AUD", "TaxonName","TaxonName_AUD",
|
|
797
|
"HomotypicalGroup","HomotypicalGroup_AUD"};
|
|
798
|
|
|
799
|
int nSynonyms = service.count(Synonym.class);
|
|
800
|
Assert.assertEquals("There should be 2 synonyms in the database", 2, nSynonyms);
|
|
801
|
int nNames = nameService.count(TaxonName.class);
|
|
802
|
Assert.assertEquals("There should be 4 names in the database", 4, nNames);
|
|
803
|
|
|
804
|
UUID uuidTaxon1=UUID.fromString("c47fdb72-f32c-452e-8305-4b44f01179d0");
|
|
805
|
UUID uuidSynonym1=UUID.fromString("7da85381-ad9d-4886-9d4d-0eeef40e3d88");
|
|
806
|
|
|
807
|
Taxon taxon2 = (Taxon)service.load(uuidTaxon1);
|
|
808
|
|
|
809
|
List<String> initStrat = new ArrayList<>();
|
|
810
|
initStrat.add("markers");
|
|
811
|
Synonym synonym1 = (Synonym)service.load(uuidSynonym1, initStrat);
|
|
812
|
long nRelations = service.countSynonyms(true);
|
|
813
|
Assert.assertEquals("There should be 2 relationship left in the database", 2, nRelations);
|
|
814
|
|
|
815
|
taxon2.removeSynonym(synonym1, false);
|
|
816
|
service.saveOrUpdate(taxon2);
|
|
817
|
|
|
818
|
commitAndStartNewTransaction(null);
|
|
819
|
|
|
820
|
nSynonyms = service.count(Synonym.class);
|
|
821
|
Assert.assertEquals("There should be 2 synonyms in the database", 2, nSynonyms);
|
|
822
|
nNames = nameService.count(TaxonName.class);
|
|
823
|
Assert.assertEquals("There should be 4 names in the database", 4, nNames);
|
|
824
|
nRelations = service.countSynonyms(true);
|
|
825
|
Assert.assertEquals("There should be 1 relationship left in the database", 1, nRelations);
|
|
826
|
Marker marker1 = Marker.NewInstance(MarkerType.IMPORTED(), true);
|
|
827
|
Marker marker2 = Marker.NewInstance(MarkerType.COMPUTED(), true);
|
|
828
|
synonym1.addMarker(marker1);
|
|
829
|
synonym1.addMarker(marker2);
|
|
830
|
service.update(synonym1);
|
|
831
|
synonym1 =(Synonym) service.load(uuidSynonym1);
|
|
832
|
|
|
833
|
Set<Marker> markers = synonym1.getMarkers();
|
|
834
|
Marker marker = markers.iterator().next();
|
|
835
|
UUID markerUUID = marker.getUuid();
|
|
836
|
// taxon2 = (Taxon)service.load(uuidTaxon2);
|
|
837
|
synonym1 = (Synonym)service.load(uuidSynonym1);
|
|
838
|
//the marker should not prevent the deletion
|
|
839
|
DeleteResult result = service.deleteSynonym(synonym1, new SynonymDeletionConfigurator());
|
|
840
|
if (!result.isOk()){
|
|
841
|
Assert.fail();
|
|
842
|
}
|
|
843
|
|
|
844
|
commitAndStartNewTransaction(tableNames);
|
|
845
|
nSynonyms = service.count(Synonym.class);
|
|
846
|
Assert.assertEquals("There should be 1 synonym left in the database", 1, nSynonyms);
|
|
847
|
nNames = nameService.count(TaxonName.class);
|
|
848
|
Assert.assertEquals("There should be 3 names left in the database", 3, nNames);
|
|
849
|
nRelations = service.countSynonyms(true);
|
|
850
|
Assert.assertEquals("There should be no relationship left in the database", 1, nRelations);
|
|
851
|
marker = markerService.load(markerUUID);
|
|
852
|
assertNull(marker);
|
|
853
|
}
|
|
854
|
|
|
855
|
@Test
|
|
856
|
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="TaxonServiceImplTest.testDeleteSynonym.xml")
|
|
857
|
//this test is more or less obsolete since we have no synonym relationships anymore
|
|
858
|
//test delete synonym, only for a special taxon, but because of other relationships it will not be deleted at all
|
|
859
|
public final void testDeleteSynonymSynonymTaxonBooleanDeleteOneTaxon(){
|
|
860
|
final String[]tableNames = {
|
|
861
|
// "TaxonBase","TaxonBase_AUD", "TaxonName","TaxonName_AUD",
|
|
862
|
// "HomotypicalGroup","HomotypicalGroup_AUD"
|
|
863
|
};
|
|
864
|
int nSynonyms = service.count(Synonym.class);
|
|
865
|
Assert.assertEquals("There should be 2 synonyms in the database", 2, nSynonyms);
|
|
866
|
int nNames = nameService.count(TaxonName.class);
|
|
867
|
Assert.assertEquals("There should be 4 names in the database", 4, nNames);
|
|
868
|
|
|
869
|
UUID uuidTaxon2=UUID.fromString("2d9a642d-5a82-442d-8fec-95efa978e8f8");
|
|
870
|
UUID uuidSynonym1=UUID.fromString("7da85381-ad9d-4886-9d4d-0eeef40e3d88");
|
|
871
|
|
|
872
|
Taxon taxon2 = (Taxon)service.load(uuidTaxon2);
|
|
873
|
Synonym synonym1 = (Synonym)service.load(uuidSynonym1);
|
|
874
|
synonym1.setSec(ReferenceFactory.newArticle());
|
|
875
|
|
|
876
|
taxon2.addSynonym(synonym1, SynonymType.HETEROTYPIC_SYNONYM_OF());
|
|
877
|
service.saveOrUpdate(synonym1);
|
|
878
|
long nRelations = service.countSynonyms(true);
|
|
879
|
//this was "3" when we still had synonym relationships
|
|
880
|
Assert.assertEquals("There should be 2 relationship left in the database", 2, nRelations);
|
|
881
|
service.deleteSynonym(synonym1, new SynonymDeletionConfigurator());
|
|
882
|
|
|
883
|
this.commitAndStartNewTransaction(tableNames);
|
|
884
|
|
|
885
|
nSynonyms = service.count(Synonym.class);
|
|
886
|
//this was "2" when we still had synonym relationships
|
|
887
|
Assert.assertEquals("There should still be 1 synonym left in the database", 1, nSynonyms);
|
|
888
|
nNames = nameService.count(TaxonName.class);
|
|
889
|
//was 3
|
|
890
|
Assert.assertEquals("There should be 3 names left in the database", 3, nNames);
|
|
891
|
nRelations = service.countSynonyms(true);
|
|
892
|
Assert.assertEquals("There should be 1 related synonym left in the database", 1, nRelations);
|
|
893
|
}
|
|
894
|
|
|
895
|
@Test
|
|
896
|
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="TaxonServiceImplTest.testDeleteSynonym.xml")
|
|
897
|
|
|
898
|
public final void testDeleteSynonymWithAnnotations(){
|
|
899
|
final String[]tableNames = {
|
|
900
|
// "TaxonBase","TaxonBase_AUD", "TaxonName","TaxonName_AUD",
|
|
901
|
// "HomotypicalGroup","HomotypicalGroup_AUD"
|
|
902
|
};
|
|
903
|
|
|
904
|
UUID uuidTaxon2=UUID.fromString("2d9a642d-5a82-442d-8fec-95efa978e8f8");
|
|
905
|
UUID uuidSynonym1=UUID.fromString("7da85381-ad9d-4886-9d4d-0eeef40e3d88");
|
|
906
|
|
|
907
|
Taxon taxon2 = (Taxon)service.load(uuidTaxon2);
|
|
908
|
Synonym synonym1 = (Synonym)service.load(uuidSynonym1);
|
|
909
|
taxon2.addSynonym(synonym1, SynonymType.HETEROTYPIC_SYNONYM_OF());
|
|
910
|
|
|
911
|
Annotation annotation = Annotation.NewDefaultLanguageInstance("test");
|
|
912
|
synonym1.addAnnotation(annotation);
|
|
913
|
service.saveOrUpdate(synonym1);
|
|
914
|
|
|
915
|
DeleteResult result = service.deleteSynonym(synonym1, new SynonymDeletionConfigurator());
|
|
916
|
if (result.isError()){
|
|
917
|
Assert.fail();
|
|
918
|
}
|
|
919
|
this.commitAndStartNewTransaction(tableNames);
|
|
920
|
}
|
|
921
|
|
|
922
|
@Test
|
|
923
|
@DataSet("TaxonServiceImplTest.testDeleteSynonym.xml")
|
|
924
|
|
|
925
|
public final void testDeleteSynonymSynonymTaxonBooleanWithRelatedName(){
|
|
926
|
final String[]tableNames = {"TaxonBase","TaxonBase_AUD", "TaxonName","TaxonName_AUD",
|
|
927
|
"HomotypicalGroup","HomotypicalGroup_AUD"};
|
|
928
|
|
|
929
|
int nSynonyms = service.count(Synonym.class);
|
|
930
|
Assert.assertEquals("There should be 2 synonyms in the database", 2, nSynonyms);
|
|
931
|
int nNames = nameService.count(TaxonName.class);
|
|
932
|
Assert.assertEquals("There should be 4 names in the database", 4, nNames);
|
|
933
|
|
|
934
|
UUID uuidSynonym1=UUID.fromString("7da85381-ad9d-4886-9d4d-0eeef40e3d88");
|
|
935
|
UUID uuidSynonymName2=UUID.fromString("613f3c93-013e-4ffc-aadc-1c98d71c335e");
|
|
936
|
|
|
937
|
Synonym synonym1 = (Synonym)service.load(uuidSynonym1);
|
|
938
|
TaxonName name2 = nameService.load(uuidSynonymName2);
|
|
939
|
UUID name3Uuid = synonym1.getName().getUuid();
|
|
940
|
TaxonName name3 = nameService.load(name3Uuid);
|
|
941
|
name3.addRelationshipFromName(name2, NameRelationshipType.LATER_HOMONYM(), null, null);
|
|
942
|
|
|
943
|
service.saveOrUpdate(synonym1);
|
|
944
|
|
|
945
|
long nRelations = nameService.listNameRelationships(null, 1000, 0, null, null).size();
|
|
946
|
logger.info("number of name relations: " + nRelations);
|
|
947
|
Assert.assertEquals("There should be 1 name relationship left in the database", 1, nRelations);
|
|
948
|
SynonymDeletionConfigurator config = new SynonymDeletionConfigurator();
|
|
949
|
|
|
950
|
service.deleteSynonym(synonym1, config);
|
|
951
|
|
|
952
|
this.commitAndStartNewTransaction(tableNames);
|
|
953
|
//synonym is deleted, but the name can not be deleted because of a name relationship
|
|
954
|
nSynonyms = service.count(Synonym.class);
|
|
955
|
Assert.assertEquals("There should still be 1 synonyms left in the database", 1, nSynonyms);
|
|
956
|
nNames = nameService.count(TaxonName.class);
|
|
957
|
Assert.assertEquals("There should be 4 names left in the database (name is related to synonymName2)", 4, nNames);
|
|
958
|
nRelations = service.countSynonyms(true);
|
|
959
|
//may change with better implementation of countAllRelationships (see #2653)
|
|
960
|
nRelations = nameService.listNameRelationships(null, 1000, 0, null, null).size();
|
|
961
|
logger.info("number of name relations: " + nRelations);
|
|
962
|
Assert.assertEquals("There should be 1 name relationship left in the database", 1, nRelations);
|
|
963
|
|
|
964
|
//clean up database
|
|
965
|
name2 = nameService.load(uuidSynonymName2);
|
|
966
|
NameRelationship rel = CdmBase.deproxy(name2.getNameRelations().iterator().next(), NameRelationship.class);
|
|
967
|
name2.removeNameRelationship(rel);
|
|
968
|
nameService.save(name2);
|
|
969
|
this.setComplete();
|
|
970
|
this.endTransaction();
|
|
971
|
}
|
|
972
|
|
|
973
|
@Test
|
|
974
|
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="TaxonServiceImplTest.testDeleteSynonym.xml")
|
|
975
|
public final void testDeleteSynonymSynonymTaxonBooleanWithRelatedNameDeleteAllNameRelations(){
|
|
976
|
final String[]tableNames = {"TaxonBase","TaxonBase_AUD", "TaxonName","TaxonName_AUD",
|
|
977
|
"HomotypicalGroup","HomotypicalGroup_AUD"};
|
|
978
|
|
|
979
|
int nSynonyms = service.count(Synonym.class);
|
|
980
|
Assert.assertEquals("There should be 2 synonyms in the database", 2, nSynonyms);
|
|
981
|
int nNames = nameService.count(TaxonName.class);
|
|
982
|
Assert.assertEquals("There should be 4 names in the database", 4, nNames);
|
|
983
|
|
|
984
|
UUID uuidSynonym1=UUID.fromString("7da85381-ad9d-4886-9d4d-0eeef40e3d88");
|
|
985
|
UUID uuidSynonymName2=UUID.fromString("613f3c93-013e-4ffc-aadc-1c98d71c335e");
|
|
986
|
|
|
987
|
Synonym synonym1 = (Synonym)service.load(uuidSynonym1);
|
|
988
|
TaxonName name2 = nameService.load(uuidSynonymName2);
|
|
989
|
UUID name3Uuid = synonym1.getName().getUuid();
|
|
990
|
TaxonName name3 = nameService.load(name3Uuid);
|
|
991
|
name3.addRelationshipFromName(name2, NameRelationshipType.LATER_HOMONYM(), null, null);
|
|
992
|
|
|
993
|
service.saveOrUpdate(synonym1);
|
|
994
|
|
|
995
|
long nRelations = nameService.listNameRelationships(null, 1000, 0, null, null).size();
|
|
996
|
logger.info("number of name relations: " + nRelations);
|
|
997
|
Assert.assertEquals("There should be 1 name relationship left in the database", 1, nRelations);
|
|
998
|
SynonymDeletionConfigurator config = new SynonymDeletionConfigurator();
|
|
999
|
NameDeletionConfigurator nameDeletionConfig = new NameDeletionConfigurator();
|
|
1000
|
nameDeletionConfig.setRemoveAllNameRelationships(true);
|
|
1001
|
config.setNameDeletionConfig(nameDeletionConfig);
|
|
1002
|
|
|
1003
|
service.deleteSynonym(synonym1, config);
|
|
1004
|
|
|
1005
|
this.commitAndStartNewTransaction(tableNames);
|
|
1006
|
|
|
1007
|
nSynonyms = service.count(Synonym.class);
|
|
1008
|
Assert.assertEquals("There should still be 1 synonyms left in the database", 1, nSynonyms);
|
|
1009
|
nNames = nameService.count(TaxonName.class);
|
|
1010
|
Assert.assertEquals("There should be 3 names left in the database ", 3, nNames);
|
|
1011
|
nRelations = service.countSynonyms(true);
|
|
1012
|
//may change with better implementation of countAllRelationships (see #2653)
|
|
1013
|
nRelations = nameService.listNameRelationships(null, 1000, 0, null, null).size();
|
|
1014
|
logger.info("number of name relations: " + nRelations);
|
|
1015
|
Assert.assertEquals("There should be no name relationship left in the database", 0, nRelations);
|
|
1016
|
}
|
|
1017
|
|
|
1018
|
@Test
|
|
1019
|
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="TaxonServiceImplTest.testDeleteSynonym.xml")
|
|
1020
|
public final void testDeleteSynonymSynonymTaxonBooleanWithRelatedNameIgnoreIsBasionym(){
|
|
1021
|
final String[]tableNames = {"TaxonBase","TaxonBase_AUD", "TaxonName","TaxonName_AUD",
|
|
1022
|
"HomotypicalGroup","HomotypicalGroup_AUD"};
|
|
1023
|
|
|
1024
|
int nSynonyms = service.count(Synonym.class);
|
|
1025
|
Assert.assertEquals("There should be 2 synonyms in the database", 2, nSynonyms);
|
|
1026
|
int nNames = nameService.count(TaxonName.class);
|
|
1027
|
Assert.assertEquals("There should be 4 names in the database", 4, nNames);
|
|
1028
|
|
|
1029
|
UUID uuidSynonym1=UUID.fromString("7da85381-ad9d-4886-9d4d-0eeef40e3d88");
|
|
1030
|
UUID uuidSynonymName2=UUID.fromString("613f3c93-013e-4ffc-aadc-1c98d71c335e");
|
|
1031
|
|
|
1032
|
Synonym synonym1 = (Synonym)service.load(uuidSynonym1);
|
|
1033
|
TaxonName synName2 = nameService.load(uuidSynonymName2);
|
|
1034
|
UUID name3Uuid = synonym1.getName().getUuid();
|
|
1035
|
TaxonName synName1 = nameService.load(name3Uuid);
|
|
1036
|
synName1.addRelationshipFromName(synName2, NameRelationshipType.BASIONYM(), null, null);
|
|
1037
|
|
|
1038
|
service.saveOrUpdate(synonym1);
|
|
1039
|
|
|
1040
|
long nRelations = nameService.listNameRelationships(null, 1000, 0, null, null).size();
|
|
1041
|
logger.info("number of name relations: " + nRelations);
|
|
1042
|
Assert.assertEquals("There should be 1 name relationship left in the database", 1, nRelations);
|
|
1043
|
SynonymDeletionConfigurator config = new SynonymDeletionConfigurator();
|
|
1044
|
NameDeletionConfigurator nameDeletionConfig = new NameDeletionConfigurator();
|
|
1045
|
nameDeletionConfig.setIgnoreIsBasionymFor(true);
|
|
1046
|
config.setNameDeletionConfig(nameDeletionConfig);
|
|
1047
|
|
|
1048
|
DeleteResult result =service.deleteSynonym(synonym1, config);
|
|
1049
|
if (!result.isOk()){
|
|
1050
|
Assert.fail();
|
|
1051
|
}
|
|
1052
|
|
|
1053
|
logger.debug(result);
|
|
1054
|
this.commitAndStartNewTransaction(tableNames);
|
|
1055
|
|
|
1056
|
nSynonyms = service.count(Synonym.class);
|
|
1057
|
Assert.assertEquals("There should still be 1 synonyms left in the database", 1, nSynonyms);
|
|
1058
|
nNames = nameService.count(TaxonName.class);
|
|
1059
|
Assert.assertEquals("There should be 3 names left in the database ", 3, nNames);
|
|
1060
|
nRelations = service.countSynonyms(true);
|
|
1061
|
//may change with better implementation of countAllRelationships (see #2653)
|
|
1062
|
nRelations = nameService.listNameRelationships(null, 1000, 0, null, null).size();
|
|
1063
|
logger.info("number of name relations: " + nRelations);
|
|
1064
|
Assert.assertEquals("There should be no name relationship left in the database", 0, nRelations);
|
|
1065
|
}
|
|
1066
|
|
|
1067
|
@Test
|
|
1068
|
@DataSet("TaxonServiceImplTest.testDeleteSynonym.xml")
|
|
1069
|
public final void testDeleteSynonymSynonymTaxonBooleanWithRollback(){
|
|
1070
|
// final String[]tableNames = {"TaxonBase","TaxonBase_AUD", "TaxonName","TaxonName_AUD",
|
|
1071
|
// "HomotypicalGroup","HomotypicalGroup_AUD"};
|
|
1072
|
|
|
1073
|
int nSynonyms = service.count(Synonym.class);
|
|
1074
|
Assert.assertEquals("There should be 2 synonyms in the database", 2, nSynonyms);
|
|
1075
|
int nNames = nameService.count(TaxonName.class);
|
|
1076
|
Assert.assertEquals("There should be 4 names in the database", 4, nNames);
|
|
1077
|
long nRelations = service.countSynonyms(true);
|
|
1078
|
|
|
1079
|
//may change with better implementation of countAllRelationships (see #2653)
|
|
1080
|
|
|
1081
|
logger.debug("");
|
|
1082
|
Assert.assertEquals("There should be 2 relationships in the database (the 2 synonym relationship) but no name relationship", 2, nRelations);
|
|
1083
|
|
|
1084
|
UUID uuidSynonym1=UUID.fromString("7da85381-ad9d-4886-9d4d-0eeef40e3d88");
|
|
1085
|
UUID uuidSynonymName2=UUID.fromString("613f3c93-013e-4ffc-aadc-1c98d71c335e");
|
|
1086
|
|
|
1087
|
Synonym synonym1 = (Synonym)service.load(uuidSynonym1);
|
|
1088
|
TaxonName name2 = nameService.load(uuidSynonymName2);
|
|
1089
|
synonym1.getName().addRelationshipFromName(name2, NameRelationshipType.LATER_HOMONYM(), null, null);
|
|
1090
|
|
|
1091
|
service.deleteSynonym(synonym1, new SynonymDeletionConfigurator());
|
|
1092
|
|
|
1093
|
this.rollback();
|
|
1094
|
// printDataSet(System.out, tableNames);
|
|
1095
|
this.startNewTransaction();
|
|
1096
|
|
|
1097
|
nSynonyms = service.count(Synonym.class);
|
|
1098
|
Assert.assertEquals("There should still be 2 synonyms left in the database", 2, nSynonyms);
|
|
1099
|
nNames = nameService.count(TaxonName.class);
|
|
1100
|
Assert.assertEquals("There should be 4 names left in the database", 4, nNames);
|
|
1101
|
nRelations = service.countSynonyms(true);
|
|
1102
|
//may change with better implementation of countAllRelationships (see #2653)
|
|
1103
|
Assert.assertEquals("There should be 2 relationship in the database (the 2 synonym relationship) but no name relationship", 2, nRelations);
|
|
1104
|
}
|
|
1105
|
|
|
1106
|
@Test
|
|
1107
|
@DataSet("TaxonServiceImplTest.testDeleteSynonym.xml")
|
|
1108
|
public final void testDeleteSynonymSynonymTaxonBooleanWithoutTransaction(){
|
|
1109
|
@SuppressWarnings("unused")
|
|
1110
|
final String[]tableNames = {"TaxonBase","TaxonBase_AUD", "TaxonName","TaxonName_AUD",
|
|
1111
|
"HomotypicalGroup","HomotypicalGroup_AUD"};
|
|
1112
|
|
|
1113
|
int nSynonyms = service.count(Synonym.class);
|
|
1114
|
Assert.assertEquals("There should be 2 synonyms in the database", 2, nSynonyms);
|
|
1115
|
int nNames = nameService.count(TaxonName.class);
|
|
1116
|
Assert.assertEquals("There should be 4 names in the database", 4, nNames);
|
|
1117
|
long nRelations = service.countSynonyms(true);
|
|
1118
|
//may change with better implementation of countAllRelationships (see #2653)
|
|
1119
|
Assert.assertEquals("There should be 2 relationship in the database (the 2 synonym relationships) but no name relationship", 2, nRelations);
|
|
1120
|
|
|
1121
|
UUID uuidSynonym1=UUID.fromString("7da85381-ad9d-4886-9d4d-0eeef40e3d88");
|
|
1122
|
UUID uuidSynonymName2=UUID.fromString("613f3c93-013e-4ffc-aadc-1c98d71c335e");
|
|
1123
|
|
|
1124
|
Synonym synonym1 = (Synonym)service.load(uuidSynonym1);
|
|
1125
|
TaxonName name2 = nameService.load(uuidSynonymName2);
|
|
1126
|
synonym1.getName().addRelationshipFromName(name2, NameRelationshipType.LATER_HOMONYM(), null, null);
|
|
1127
|
|
|
1128
|
service.saveOrUpdate(synonym1);
|
|
1129
|
nRelations = service.countSynonyms(true);
|
|
1130
|
Assert.assertEquals("There should be two relationships in the database", 2, nRelations);
|
|
1131
|
this.setComplete();
|
|
1132
|
this.endTransaction();
|
|
1133
|
|
|
1134
|
// printDataSet(System.out, tableNames);
|
|
1135
|
|
|
1136
|
//out of wrapping transaction
|
|
1137
|
service.deleteSynonym(synonym1, new SynonymDeletionConfigurator());
|
|
1138
|
|
|
1139
|
this.startNewTransaction();
|
|
1140
|
|
|
1141
|
nSynonyms = service.count(Synonym.class);
|
|
1142
|
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);
|
|
1143
|
nNames = nameService.count(TaxonName.class);
|
|
1144
|
Assert.assertEquals("There should be 4 names left in the database", 4, nNames);
|
|
1145
|
nRelations = service.countSynonyms(true);
|
|
1146
|
Assert.assertEquals("There should be no taxon or synonym relationship in the database", 1, nRelations);
|
|
1147
|
nRelations = nameService.listNameRelationships(null, 1000, 0, null, null).size();
|
|
1148
|
Assert.assertEquals("There should be one name relationship in the database", 1, nRelations);
|
|
1149
|
}
|
|
1150
|
|
|
1151
|
@Test
|
|
1152
|
@DataSet("TaxonServiceImplTest.testInferredSynonyms.xml")
|
|
1153
|
public void testCreateInferredSynonymy(){
|
|
1154
|
|
|
1155
|
UUID classificationUuid = UUID.fromString("aeee7448-5298-4991-b724-8d5b75a0a7a9");
|
|
1156
|
Classification tree = classificationService.find(classificationUuid);
|
|
1157
|
UUID taxonUuid = UUID.fromString("bc09aca6-06fd-4905-b1e7-cbf7cc65d783");
|
|
1158
|
TaxonBase<?> taxonBase = service.find(taxonUuid);
|
|
1159
|
List <Synonym> synonyms = service.list(Synonym.class, null, null, null, null);
|
|
1160
|
assertEquals("Number of synonyms should be 2",2,synonyms.size());
|
|
1161
|
Taxon taxon = (Taxon)taxonBase;
|
|
1162
|
|
|
1163
|
//synonyms = taxonDao.getAllSynonyms(null, null);
|
|
1164
|
//assertEquals("Number of synonyms should be 2",2,synonyms.size());
|
|
1165
|
List<Synonym> inferredSynonyms = service.createInferredSynonyms(taxon, tree, SynonymType.INFERRED_EPITHET_OF(), true);
|
|
1166
|
assertNotNull("there should be a new synonym ", inferredSynonyms);
|
|
1167
|
assertEquals ("the name of inferred epithet should be SynGenus lachesis", "SynGenus lachesis syn. sec. Sp. Pl.", inferredSynonyms.get(0).getTitleCache());
|
|
1168
|
|
|
1169
|
inferredSynonyms = service.createInferredSynonyms(taxon, tree, SynonymType.INFERRED_GENUS_OF(), true);
|
|
1170
|
assertNotNull("there should be a new synonym ", inferredSynonyms);
|
|
1171
|
assertEquals ("the name of inferred epithet should be SynGenus lachesis", "Acherontia ciprosus syn. sec. Sp. Pl.", inferredSynonyms.get(0).getTitleCache());
|
|
1172
|
|
|
1173
|
inferredSynonyms = service.createInferredSynonyms(taxon, tree, SynonymType.POTENTIAL_COMBINATION_OF(), true);
|
|
1174
|
assertNotNull("there should be a new synonym ", inferredSynonyms);
|
|
1175
|
assertEquals ("the name of inferred epithet should be SynGenus lachesis", "SynGenus ciprosus syn. sec. Sp. Pl.", inferredSynonyms.get(0).getTitleCache());
|
|
1176
|
//assertTrue("set of synonyms should contain an inferred Synonym ", synonyms.contains(arg0))
|
|
1177
|
}
|
|
1178
|
|
|
1179
|
@Test
|
|
1180
|
@DataSet("../../database/ClearDBDataSet.xml")
|
|
1181
|
public final void testTaxonDeletionConfig(){
|
|
1182
|
final String[]tableNames = {}
|
|
1183
|
// "Classification", "Classification_AUD",
|
|
1184
|
// "TaxonBase","TaxonBase_AUD",
|
|
1185
|
// "TaxonNode","TaxonNode_AUD",
|
|
1186
|
// "TaxonName","TaxonName_AUD",
|
|
1187
|
// "TaxonRelationship", "TaxonRelationship_AUD",
|
|
1188
|
// "TaxonDescription", "TaxonDescription_AUD",
|
|
1189
|
// "HomotypicalGroup","HomotypicalGroup_AUD",
|
|
1190
|
// "PolytomousKey","PolytomousKey_AUD",
|
|
1191
|
// "PolytomousKeyNode","PolytomousKeyNode_AUD",
|
|
1192
|
// "Media","Media_AUD",
|
|
1193
|
// "DescriptiveDataSet","DescriptiveDataSet_AUD",
|
|
1194
|
// "DescriptionElementBase","DescriptionElementBase_AUD",
|
|
1195
|
// "DeterminationEvent","DeterminationEvent_AUD",
|
|
1196
|
// "SpecimenOrObservationBase","SpecimenOrObservationBase_AUD"}
|
|
1197
|
;
|
|
1198
|
|
|
1199
|
commitAndStartNewTransaction(tableNames);
|
|
1200
|
getTestTaxon();
|
|
1201
|
commitAndStartNewTransaction(tableNames);
|
|
1202
|
int nTaxa = service.count(Taxon.class);
|
|
1203
|
|
|
1204
|
Assert.assertEquals("There should be 4 taxa in the database", 4, nTaxa);
|
|
1205
|
Taxon parent = (Taxon)service.find(GENUS_UUID);
|
|
1206
|
Assert.assertNotNull("Parent taxon should exist", parent);
|
|
1207
|
Taxon child1 = (Taxon)service.find(SPECIES1_UUID);
|
|
1208
|
Assert.assertNotNull("Child taxon should exist", child1);
|
|
1209
|
TaxonDeletionConfigurator config = new TaxonDeletionConfigurator();
|
|
1210
|
config.setDeleteTaxonNodes(false);
|
|
1211
|
config.setDeleteMisappliedNames(false);
|
|
1212
|
//try {
|
|
1213
|
//commitAndStartNewTransaction(tableNames);
|
|
1214
|
|
|
1215
|
DeleteResult result = service.deleteTaxon(child1.getUuid(), config, null);
|
|
1216
|
if (result.isOk()){
|
|
1217
|
Assert.fail("Delete should throw an error as long as name is used in classification.");
|
|
1218
|
}
|
|
1219
|
|
|
1220
|
nTaxa = service.count(Taxon.class);
|
|
1221
|
Assert.assertEquals("There should be 4 taxa in the database", 4, nTaxa);
|
|
1222
|
child1 = (Taxon)service.find(SPECIES1_UUID);
|
|
1223
|
Assert.assertNotNull("Child taxon should exist", child1);
|
|
1224
|
Assert.assertEquals("Child should belong to 1 node", 1, child1.getTaxonNodes().size());
|
|
1225
|
|
|
1226
|
TaxonNode node = child1.getTaxonNodes().iterator().next();
|
|
1227
|
child1.addSource(IdentifiableSource.NewInstance(OriginalSourceType.Import));
|
|
1228
|
|
|
1229
|
SpecimenOrObservationBase<?> identifiedUnit = DerivedUnit.NewInstance(SpecimenOrObservationType.DerivedUnit);
|
|
1230
|
DeterminationEvent.NewInstance(child1, identifiedUnit);
|
|
1231
|
//UUID eventUUID = eventService.save(determinationEvent);
|
|
1232
|
UUID identifiedUnitUUID = occurenceService.save(identifiedUnit).getUuid();
|
|
1233
|
|
|
1234
|
TaxonNode parentNode = node.getParent();
|
|
1235
|
parentNode =CdmBase.deproxy(parentNode, TaxonNode.class);
|
|
1236
|
parentNode.deleteChildNode(node);
|
|
1237
|
nodeService.save(parentNode);
|
|
1238
|
//commitAndStartNewTransaction(tableNames);
|
|
1239
|
|
|
1240
|
// try {
|
|
1241
|
|
|
1242
|
result = service.deleteTaxon(child1
|
|
1243
|
.getUuid(), config, null);
|
|
1244
|
if (result.isOk()){
|
|
1245
|
Assert.fail("Delete should throw an exception because of the determination event");
|
|
1246
|
}
|
|
1247
|
|
|
1248
|
//determinationEvent = (DeterminationEvent)eventService.load(eventUUID);
|
|
1249
|
commitAndStartNewTransaction(tableNames);
|
|
1250
|
identifiedUnit = occurenceService.load(identifiedUnitUUID);
|
|
1251
|
|
|
1252
|
occurenceService.delete(identifiedUnit);
|
|
1253
|
|
|
1254
|
commitAndStartNewTransaction(tableNames);
|
|
1255
|
child1 = (Taxon)service.find(SPECIES1_UUID);
|
|
1256
|
|
|
1257
|
assertEquals(0, child1.getTaxonNodes().size());
|
|
1258
|
// try {
|
|
1259
|
|
|
1260
|
result = service.deleteTaxon(child1.getUuid(), config, null);
|
|
1261
|
|
|
1262
|
if (!result.isOk()){
|
|
1263
|
Assert.fail("Delete should not throw an exception anymore");
|
|
1264
|
}
|
|
1265
|
|
|
1266
|
nTaxa = service.count(Taxon.class);
|
|
1267
|
Assert.assertEquals("There should be 3 taxa in the database", 3, nTaxa);
|
|
1268
|
|
|
1269
|
config.setDeleteTaxonNodes(true);
|
|
1270
|
Taxon child2 =(Taxon) service.find(SPECIES2_UUID);
|
|
1271
|
|
|
1272
|
// try {
|
|
1273
|
result = service.deleteTaxon(child2.getUuid(), config, child2.getTaxonNodes().iterator().next().getClassification().getUuid());
|
|
1274
|
if (!result.isOk()){
|
|
1275
|
Assert.fail("Delete should not throw an exception");
|
|
1276
|
}
|
|
1277
|
|
|
1278
|
//service.find(uuid);
|
|
1279
|
|
|
1280
|
nTaxa = service.count(Taxon.class);
|
|
1281
|
Assert.assertEquals("There should be 2 taxa in the database",2, nTaxa);
|
|
1282
|
// nNames = nameService.count(TaxonName.class);
|
|
1283
|
// Assert.assertEquals("There should be 3 names left in the database", 3, nNames);
|
|
1284
|
// int nRelations = service.countAllRelationships();
|
|
1285
|
// Assert.assertEquals("There should be no relationship left in the database", 0, nRelations);
|
|
1286
|
}
|
|
1287
|
|
|
1288
|
@Test
|
|
1289
|
@DataSet(value="../../database/ClearDBDataSet.xml")
|
|
1290
|
public final void testDeleteTaxon(){
|
|
1291
|
|
|
1292
|
//create a small classification
|
|
1293
|
Taxon testTaxon = getTestTaxon();
|
|
1294
|
service.save(testTaxon).getUuid();
|
|
1295
|
|
|
1296
|
Taxon speciesTaxon = (Taxon)service.find(SPECIES1_UUID);
|
|
1297
|
Iterator<TaxonDescription> descriptionIterator = speciesTaxon.getDescriptions().iterator();
|
|
1298
|
UUID descrUUID = null;
|
|
1299
|
UUID descrElementUUID = null;
|
|
1300
|
if (descriptionIterator.hasNext()){
|
|
1301
|
TaxonDescription descr = descriptionIterator.next();
|
|
1302
|
descrUUID = descr.getUuid();
|
|
1303
|
descrElementUUID = descr.getElements().iterator().next().getUuid();
|
|
1304
|
}
|
|
1305
|
IBotanicalName taxonName = nameService.find(SPECIES1_NAME_UUID);
|
|
1306
|
assertNotNull(taxonName);
|
|
1307
|
|
|
1308
|
TaxonDeletionConfigurator config = new TaxonDeletionConfigurator();
|
|
1309
|
config.setDeleteNameIfPossible(false);
|
|
1310
|
|
|
1311
|
DeleteResult result = service.deleteTaxon(speciesTaxon.getUuid(), config, speciesTaxon.getTaxonNodes().iterator().next().getClassification().getUuid());
|
|
1312
|
if (!result.isOk()){
|
|
1313
|
Assert.fail();
|
|
1314
|
}
|
|
1315
|
commitAndStartNewTransaction(null);
|
|
1316
|
|
|
1317
|
taxonName = nameService.find(SPECIES1_NAME_UUID);
|
|
1318
|
Taxon taxon = (Taxon)service.find(SPECIES1_UUID);
|
|
1319
|
|
|
1320
|
//descriptionService.find(descrUUID);
|
|
1321
|
assertNull(descriptionService.find(descrUUID));
|
|
1322
|
assertNull(descriptionService.getDescriptionElementByUuid(descrElementUUID));
|
|
1323
|
//assertNull(synName);
|
|
1324
|
assertNotNull(taxonName);
|
|
1325
|
assertNull(taxon);
|
|
1326
|
config.setDeleteNameIfPossible(true);
|
|
1327
|
Taxon newTaxon = Taxon.NewInstance(TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES()), null);
|
|
1328
|
service.save(newTaxon);
|
|
1329
|
result = service.deleteTaxon(newTaxon.getUuid()
|
|
1330
|
, config, null);
|
|
1331
|
if (!result.isOk()){
|
|
1332
|
Assert.fail();
|
|
1333
|
}
|
|
1334
|
}
|
|
1335
|
|
|
1336
|
@Test
|
|
1337
|
@DataSet(value="../../database/ClearDBDataSet.xml")
|
|
1338
|
public final void testDeleteTaxonWithAnnotations(){
|
|
1339
|
|
|
1340
|
//create a small classification
|
|
1341
|
Taxon testTaxon = getTestTaxon();
|
|
1342
|
service.save(testTaxon).getUuid();
|
|
1343
|
|
|
1344
|
Taxon speciesTaxon = (Taxon)service.find(SPECIES1_UUID);
|
|
1345
|
Iterator<TaxonDescription> descriptionIterator = speciesTaxon.getDescriptions().iterator();
|
|
1346
|
UUID descrUUID = null;
|
|
1347
|
UUID descrElementUUID = null;
|
|
1348
|
if (descriptionIterator.hasNext()){
|
|
1349
|
TaxonDescription descr = descriptionIterator.next();
|
|
1350
|
descrUUID = descr.getUuid();
|
|
1351
|
descrElementUUID = descr.getElements().iterator().next().getUuid();
|
|
1352
|
}
|
|
1353
|
IBotanicalName taxonName = nameService.find(SPECIES1_NAME_UUID);
|
|
1354
|
assertNotNull(taxonName);
|
|
1355
|
|
|
1356
|
TaxonDeletionConfigurator config = new TaxonDeletionConfigurator();
|
|
1357
|
config.setDeleteNameIfPossible(false);
|
|
1358
|
Annotation annotation = Annotation.NewDefaultLanguageInstance("test");
|
|
1359
|
speciesTaxon.addAnnotation(annotation);
|
|
1360
|
|
|
1361
|
|
|
1362
|
DeleteResult result = service.deleteTaxon(speciesTaxon.getUuid(), config, speciesTaxon.getTaxonNodes().iterator().next().getClassification().getUuid());
|
|
1363
|
if (!result.isOk()){
|
|
1364
|
Assert.fail();
|
|
1365
|
}
|
|
1366
|
commitAndStartNewTransaction(null);
|
|
1367
|
|
|
1368
|
taxonName = nameService.find(SPECIES1_NAME_UUID);
|
|
1369
|
Taxon taxon = (Taxon)service.find(SPECIES1_UUID);
|
|
1370
|
|
|
1371
|
//descriptionService.find(descrUUID);
|
|
1372
|
assertNull(descriptionService.find(descrUUID));
|
|
1373
|
assertNull(descriptionService.getDescriptionElementByUuid(descrElementUUID));
|
|
1374
|
//assertNull(synName);
|
|
1375
|
assertNotNull(taxonName);
|
|
1376
|
assertNull(taxon);
|
|
1377
|
config.setDeleteNameIfPossible(true);
|
|
1378
|
Taxon newTaxon = Taxon.NewInstance(TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES()), null);
|
|
1379
|
service.save(newTaxon);
|
|
1380
|
result = service.deleteTaxon(newTaxon.getUuid()
|
|
1381
|
, config, null);
|
|
1382
|
if (!result.isOk()){
|
|
1383
|
Assert.fail();
|
|
1384
|
}
|
|
1385
|
}
|
|
1386
|
|
|
1387
|
@Test
|
|
1388
|
@DataSet(value="../../database/ClearDBDataSet.xml")
|
|
1389
|
public final void testDeleteTaxonUsedInTaxonRelation(){
|
|
1390
|
|
|
1391
|
//create a small classification
|
|
1392
|
Taxon testTaxon = getTestTaxon();
|
|
1393
|
service.save(testTaxon).getUuid();
|
|
1394
|
|
|
1395
|
Taxon speciesTaxon = (Taxon)service.find(SPECIES1_UUID);
|
|
1396
|
Taxon speciesTaxon2 = (Taxon)service.find(SPECIES2_UUID);
|
|
1397
|
speciesTaxon.addTaxonRelation(speciesTaxon2, TaxonRelationshipType.MISAPPLIED_NAME_FOR(), null, null);
|
|
1398
|
|
|
1399
|
IBotanicalName taxonName = nameService.find(SPECIES1_NAME_UUID);
|
|
1400
|
assertNotNull(taxonName);
|
|
1401
|
|
|
1402
|
TaxonDeletionConfigurator config = new TaxonDeletionConfigurator();
|
|
1403
|
config.setDeleteNameIfPossible(false);
|
|
1404
|
config.setDeleteTaxonRelationships(false);
|
|
1405
|
|
|
1406
|
|
|
1407
|
DeleteResult result = service.deleteTaxon(speciesTaxon.getUuid(), config, speciesTaxon.getTaxonNodes().iterator().next().getClassification().getUuid());
|
|
1408
|
if (result.isOk()){
|
|
1409
|
Assert.fail();
|
|
1410
|
}
|
|
1411
|
commitAndStartNewTransaction(null);
|
|
1412
|
|
|
1413
|
taxonName = nameService.find(SPECIES1_NAME_UUID);
|
|
1414
|
Taxon taxon = (Taxon)service.find(SPECIES1_UUID);
|
|
1415
|
|
|
1416
|
assertNotNull(taxonName);
|
|
1417
|
assertNotNull(taxon);
|
|
1418
|
|
|
1419
|
config.setDeleteNameIfPossible(false);
|
|
1420
|
config.setDeleteTaxonRelationships(true);
|
|
1421
|
|
|
1422
|
|
|
1423
|
result = service.deleteTaxon(speciesTaxon.getUuid(), config, speciesTaxon.getTaxonNodes().iterator().next().getClassification().getUuid());
|
|
1424
|
if (!result.isOk()){
|
|
1425
|
Assert.fail();
|
|
1426
|
}
|
|
1427
|
commitAndStartNewTransaction(null);
|
|
1428
|
|
|
1429
|
config.setDeleteNameIfPossible(true);
|
|
1430
|
Taxon newTaxon = Taxon.NewInstance(TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES()), null);
|
|
1431
|
service.save(newTaxon);
|
|
1432
|
result = service.deleteTaxon(newTaxon.getUuid()
|
|
1433
|
, config, null);
|
|
1434
|
if (!result.isOk()){
|
|
1435
|
Assert.fail();
|
|
1436
|
}
|
|
1437
|
}
|
|
1438
|
|
|
1439
|
@Test
|
|
1440
|
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="../../database/ClearDBDataSet.xml")
|
|
1441
|
public final void testDeleteTaxonDeleteSynonymRelations(){
|
|
1442
|
|
|
1443
|
final String[]tableNames = {
|
|
1444
|
"Classification", "Classification_AUD",
|
|
1445
|
"TaxonBase","TaxonBase_AUD",
|
|
1446
|
"TaxonNode","TaxonNode_AUD",
|
|
1447
|
"TaxonName","TaxonName_AUD"};
|
|
1448
|
commitAndStartNewTransaction(tableNames);
|
|
1449
|
//create a small classification
|
|
1450
|
Taxon testTaxon = getTestTaxon();
|
|
1451
|
service.save(testTaxon).getUuid();
|
|
1452
|
Taxon speciesTaxon = (Taxon)service.find(SPECIES2_UUID);
|
|
1453
|
|
|
1454
|
Synonym synonym = speciesTaxon.getSynonyms().iterator().next();
|
|
1455
|
UUID synonymUuid = synonym.getUuid();
|
|
1456
|
service.countSynonyms(true);
|
|
1457
|
|
|
1458
|
TaxonDeletionConfigurator config = new TaxonDeletionConfigurator();
|
|
1459
|
config.setDeleteSynonymsIfPossible(false);
|
|
1460
|
|
|
1461
|
|
|
1462
|
DeleteResult result = service.deleteTaxon(speciesTaxon.getUuid(), config, speciesTaxon.getTaxonNodes().iterator().next().getClassification().getUuid());
|
|
1463
|
if (!result.isOk()){
|
|
1464
|
Assert.fail();
|
|
1465
|
}
|
|
1466
|
commitAndStartNewTransaction(null);
|
|
1467
|
|
|
1468
|
Taxon taxon = (Taxon)service.find(SPECIES2_UUID);
|
|
1469
|
assertNull("The deleted taxon should no longer exist", taxon);
|
|
1470
|
|
|
1471
|
Synonym syn = (Synonym)service.find(synonymUuid);
|
|
1472
|
assertNotNull("The synonym should still exist since DeleteSynonymsIfPossible was false", service.find(synonymUuid));
|
|
1473
|
assertNull("The synonym should not be attached to an accepted taxon anymore", syn.getAcceptedTaxon());
|
|
1474
|
}
|
|
1475
|
|
|
1476
|
@Test
|
|
1477
|
@DataSet(value="../../database/ClearDBDataSet.xml")
|
|
1478
|
public final void testDeleteTaxonNameUsedInOtherContext(){
|
|
1479
|
|
|
1480
|
//create a small classification
|
|
1481
|
Taxon testTaxon = getTestTaxon();
|
|
1482
|
service.save(testTaxon).getUuid();
|
|
1483
|
Taxon speciesTaxon = (Taxon)service.find(SPECIES1_UUID);
|
|
1484
|
|
|
1485
|
IBotanicalName taxonName = nameService.find(SPECIES1_NAME_UUID);
|
|
1486
|
assertNotNull(taxonName);
|
|
1487
|
TaxonName fromName = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
1488
|
taxonName.addRelationshipFromName(fromName, NameRelationshipType.VALIDATED_BY_NAME(), null, null);
|
|
1489
|
nameService.save(fromName);
|
|
1490
|
|
|
1491
|
TaxonDeletionConfigurator config = new TaxonDeletionConfigurator();
|
|
1492
|
config.setDeleteNameIfPossible(true);
|
|
1493
|
DeleteResult result = service.deleteTaxon(speciesTaxon.getUuid(), config, speciesTaxon.getTaxonNodes().iterator().next().getClassification().getUuid());
|
|
1494
|
if (!result.isOk()){
|
|
1495
|
Assert.fail();
|
|
1496
|
}
|
|
1497
|
commitAndStartNewTransaction(null);
|
|
1498
|
|
|
1499
|
taxonName = nameService.find(SPECIES1_NAME_UUID);
|
|
1500
|
Taxon taxon = (Taxon)service.find(SPECIES1_UUID);
|
|
1501
|
//because of the namerelationship the name cannot be deleted
|
|
1502
|
assertNotNull(taxonName);
|
|
1503
|
assertNull(taxon);
|
|
1504
|
}
|
|
1505
|
|
|
1506
|
@Test
|
|
1507
|
@DataSet(value="../../database/ClearDBDataSet.xml")
|
|
1508
|
public final void testDeleteTaxonNameUsedInTwoClassificationsDeleteAllNodes(){
|
|
1509
|
commitAndStartNewTransaction(null);
|
|
1510
|
TaxonDeletionConfigurator config = new TaxonDeletionConfigurator();
|
|
1511
|
//create a small classification
|
|
1512
|
Taxon testTaxon = getTestTaxon();
|
|
1513
|
|
|
1514
|
UUID uuid = service.save(testTaxon).getUuid();
|
|
1515
|
//BotanicalName name = nameService.find(uuid);
|
|
1516
|
Set<TaxonNode> nodes = testTaxon.getTaxonNodes();
|
|
1517
|
TaxonNode node = nodes.iterator().next();
|
|
1518
|
List<TaxonNode> childNodes = node.getChildNodes();
|
|
1519
|
TaxonNode childNode = childNodes.iterator().next();
|
|
1520
|
UUID childUUID = childNode.getTaxon().getUuid();
|
|
1521
|
Classification secondClassification = getTestClassification("secondClassification");
|
|
1522
|
|
|
1523
|
secondClassification.addChildTaxon(testTaxon, null, null);
|
|
1524
|
//delete the taxon in all classifications
|
|
1525
|
config.setDeleteInAllClassifications(true);
|
|
1526
|
DeleteResult result = service.deleteTaxon(testTaxon.getUuid(), config, null);
|
|
1527
|
if (!result.isOk()){
|
|
1528
|
Assert.fail();
|
|
1529
|
}
|
|
1530
|
commitAndStartNewTransaction(null);
|
|
1531
|
Taxon tax = (Taxon)service.find(uuid);
|
|
1532
|
assertNull(tax);
|
|
1533
|
Taxon childTaxon = (Taxon)service.find(childUUID);
|
|
1534
|
assertNull(tax);
|
|
1535
|
commitAndStartNewTransaction(null);
|
|
1536
|
}
|
|
1537
|
|
|
1538
|
@Test
|
|
1539
|
@DataSet(value="../../database/ClearDBDataSet.xml")
|
|
1540
|
public final void testDeleteTaxonNameUsedInTwoClassificationsDoNotDeleteAllNodes(){
|
|
1541
|
// delete the taxon only in second classification, this should delete only the nodes, not the taxa
|
|
1542
|
Taxon testTaxon = getTestTaxon();
|
|
1543
|
UUID uuid = service.save(testTaxon).getUuid();
|
|
1544
|
Classification secondClassification = getTestClassification("secondClassification");
|
|
1545
|
Set<TaxonNode> nodes = testTaxon.getTaxonNodes();
|
|
1546
|
TaxonNode node = nodes.iterator().next();
|
|
1547
|
List<TaxonNode> childNodes = node.getChildNodes();
|
|
1548
|
TaxonNode childNode = childNodes.iterator().next();
|
|
1549
|
UUID childUUID = childNode.getTaxon().getUuid();
|
|
1550
|
childNode = secondClassification.addChildTaxon(testTaxon, null, null);
|
|
1551
|
UUID childNodeUUID = childNode.getUuid();
|
|
1552
|
|
|
1553
|
TaxonDeletionConfigurator config = new TaxonDeletionConfigurator() ;
|
|
1554
|
config.setDeleteInAllClassifications(false);
|
|
1555
|
// try {
|
|
1556
|
DeleteResult result = service.deleteTaxon(testTaxon.getUuid(), config, secondClassification.getUuid());
|
|
1557
|
/* Assert.fail("The taxon should not be deletable because it is used in a second classification and the configuration is set to deleteInAllClassifications = false");
|
|
1558
|
} catch (DataChangeNoRollbackException e) {
|
|
1559
|
logger.debug(e.getMessage());
|
|
1560
|
}
|
|
1561
|
*/
|
|
1562
|
|
|
1563
|
if (result.isOk()){
|
|
1564
|
Assert.fail("The taxon should not be deletable because it is used in a second classification and the configuration is set to deleteInAllClassifications = false");
|
|
1565
|
}
|
|
1566
|
|
|
1567
|
//commitAndStartNewTransaction(null);
|
|
1568
|
Taxon tax = (Taxon)service.find(uuid);
|
|
1569
|
assertNotNull(tax);
|
|
1570
|
Taxon childTaxon = (Taxon)service.find(childUUID);
|
|
1571
|
assertNotNull(tax);
|
|
1572
|
//when calling delete taxon and the taxon can not be deleted the children should not be deleted as well. If children should be deleted call delete taxonnode
|
|
1573
|
node = nodeService.find(childNodeUUID);
|
|
1574
|
assertNotNull(node);
|
|
1575
|
}
|
|
1576
|
|
|
1577
|
@Test
|
|
1578
|
@DataSet(value="../../database/ClearDBDataSet.xml")
|
|
1579
|
public final void testTaxonNodeDeletionConfiguratorMoveToParent(){
|
|
1580
|
//test childHandling MOVE_TO_PARENT:
|
|
1581
|
Taxon testTaxon = getTestTaxon();
|
|
1582
|
UUID uuid = service.save(testTaxon).getUuid();
|
|
1583
|
|
|
1584
|
Taxon topMost = Taxon.NewInstance(TaxonNameFactory.NewBotanicalInstance(Rank.FAMILY()), null);
|
|
1585
|
|
|
1586
|
Iterator<TaxonNode> nodes = testTaxon.getTaxonNodes().iterator();
|
|
1587
|
TaxonNode node =nodes.next();
|
|
1588
|
Classification classification = node.getClassification();
|
|
1589
|
classification.addParentChild(topMost, testTaxon, null, null);
|
|
1590
|
UUID topMostUUID = service.save(topMost).getUuid();
|
|
1591
|
|
|
1592
|
TaxonDeletionConfigurator config = new TaxonDeletionConfigurator() ;
|
|
1593
|
config.getTaxonNodeConfig().setChildHandling(ChildHandling.MOVE_TO_PARENT);
|
|
1594
|
|
|
1595
|
|
|
1596
|
DeleteResult result = service.deleteTaxon(testTaxon.getUuid(), config, classification.getUuid());
|
|
1597
|
if(!result.isOk()){
|
|
1598
|
Assert.fail();
|
|
1599
|
}
|
|
1600
|
|
|
1601
|
commitAndStartNewTransaction(null);
|
|
1602
|
Taxon tax = (Taxon)service.find(uuid);
|
|
1603
|
assertNull(tax);
|
|
1604
|
tax = (Taxon)service.find(topMostUUID);
|
|
1605
|
Set<TaxonNode> topMostNodes = tax.getTaxonNodes();
|
|
1606
|
assertNotNull(topMostNodes);
|
|
1607
|
assertEquals("there should be one taxon node", 1, topMostNodes.size());
|
|
1608
|
nodes = topMostNodes.iterator();
|
|
1609
|
TaxonNode topMostNode = nodes.next();
|
|
1610
|
int size = topMostNode.getChildNodes().size();
|
|
1611
|
|
|
1612
|
assertEquals(2, size);
|
|
1613
|
}
|
|
1614
|
|
|
1615
|
@Test
|
|
1616
|
@DataSet(value="../../database/ClearDBDataSet.xml")
|
|
1617
|
public final void testTaxonNodeDeletionConfiguratorDeleteChildren(){
|
|
1618
|
//test childHandling DELETE:
|
|
1619
|
Taxon testTaxon = getTestTaxon();
|
|
1620
|
UUID uuid = service.save(testTaxon).getUuid();
|
|
1621
|
|
|
1622
|
Taxon topMost = Taxon.NewInstance(TaxonNameFactory.NewBotanicalInstance(Rank.FAMILY()), null);
|
|
1623
|
|
|
1624
|
Iterator<TaxonNode> nodes = testTaxon.getTaxonNodes().iterator();
|
|
1625
|
TaxonNode node =nodes.next();
|
|
1626
|
UUID taxonNodeUUID = node.getUuid();
|
|
1627
|
Classification classification = node.getClassification();
|
|
1628
|
classification.addParentChild(topMost, testTaxon, null, null);
|
|
1629
|
UUID topMostUUID = service.save(topMost).getUuid();
|
|
1630
|
|
|
1631
|
TaxonDeletionConfigurator config = new TaxonDeletionConfigurator() ;
|
|
1632
|
config.getTaxonNodeConfig().setChildHandling(ChildHandling.DELETE);
|
|
1633
|
|
|
1634
|
// try {
|
|
1635
|
DeleteResult result = service.deleteTaxon(testTaxon.getUuid(), config, testTaxon.getTaxonNodes().iterator().next().getClassification().getUuid());
|
|
1636
|
if(!result.isOk()){
|
|
1637
|
Assert.fail();
|
|
1638
|
}
|
|
1639
|
commitAndStartNewTransaction(null);
|
|
1640
|
Taxon tax = (Taxon)service.find(uuid);
|
|
1641
|
assertNull(tax);
|
|
1642
|
tax = (Taxon)service.find(topMostUUID);
|
|
1643
|
Set<TaxonNode> topMostNodes = tax.getTaxonNodes();
|
|
1644
|
assertNotNull(topMostNodes);
|
|
1645
|
assertEquals("there should be one taxon node", 1, topMostNodes.size());
|
|
1646
|
nodes = topMostNodes.iterator();
|
|
1647
|
TaxonNode topMostNode = nodes.next();
|
|
1648
|
int size = topMostNode.getChildNodes().size();
|
|
1649
|
node = nodeService.find(taxonNodeUUID);
|
|
1650
|
assertNull(node);
|
|
1651
|
assertEquals(0, size);
|
|
1652
|
}
|
|
1653
|
|
|
1654
|
|
|
1655
|
@Test
|
|
1656
|
@DataSet(value="../../database/ClearDBDataSet.xml")
|
|
1657
|
public final void testTaxonDeletionConfiguratorDeleteMarker(){
|
|
1658
|
//test childHandling DELETE:
|
|
1659
|
Taxon testTaxon = getTestTaxon();
|
|
1660
|
UUID uuid = service.save(testTaxon).getUuid();
|
|
1661
|
|
|
1662
|
Taxon topMost = Taxon.NewInstance(TaxonNameFactory.NewBotanicalInstance(Rank.FAMILY()), null);
|
|
1663
|
|
|
1664
|
Iterator<TaxonNode> nodes = testTaxon.getTaxonNodes().iterator();
|
|
1665
|
TaxonNode node =nodes.next();
|
|
1666
|
Classification classification = node.getClassification();
|
|
1667
|
classification.addParentChild(topMost, testTaxon, null, null);
|
|
1668
|
UUID topMostUUID = service.save(topMost).getUuid();
|
|
1669
|
Marker marker = Marker.NewInstance(testTaxon, true, MarkerType.IS_DOUBTFUL());
|
|
1670
|
testTaxon.addMarker(marker);
|
|
1671
|
TaxonDeletionConfigurator config = new TaxonDeletionConfigurator() ;
|
|
1672
|
config.getTaxonNodeConfig().setChildHandling(ChildHandling.DELETE);
|
|
1673
|
|
|
1674
|
DeleteResult result = service.deleteTaxon(testTaxon.getUuid(), config, node.getClassification().getUuid());
|
|
1675
|
|
|
1676
|
if(!result.isOk()){
|
|
1677
|
Assert.fail();
|
|
1678
|
}
|
|
1679
|
commitAndStartNewTransaction(null);
|
|
1680
|
Taxon tax = (Taxon)service.find(uuid);
|
|
1681
|
assertNull(tax);
|
|
1682
|
tax = (Taxon)service.find(topMostUUID);
|
|
1683
|
Set<TaxonNode> topMostNodes = tax.getTaxonNodes();
|
|
1684
|
assertNotNull(topMostNodes);
|
|
1685
|
assertEquals("there should be one taxon node", 1, topMostNodes.size());
|
|
1686
|
nodes = topMostNodes.iterator();
|
|
1687
|
TaxonNode topMostNode = nodes.next();
|
|
1688
|
int size = topMostNode.getChildNodes().size();
|
|
1689
|
|
|
1690
|
assertEquals(0, size);
|
|
1691
|
}
|
|
1692
|
|
|
1693
|
|
|
1694
|
@Test
|
|
1695
|
@DataSet(value="../../database/ClearDBDataSet.xml")
|
|
1696
|
public final void testTaxonDeletionConfiguratorTaxonWithMisappliedName(){
|
|
1697
|
|
|
1698
|
Taxon testTaxon = getTestTaxon();
|
|
1699
|
UUID uuid = service.save(testTaxon).getUuid();
|
|
1700
|
|
|
1701
|
Taxon misappliedName = Taxon.NewInstance(TaxonNameFactory.NewBotanicalInstance(Rank.GENUS()), null);
|
|
1702
|
|
|
1703
|
Iterator<TaxonNode> nodes = testTaxon.getTaxonNodes().iterator();
|
|
1704
|
TaxonNode node =nodes.next();
|
|
1705
|
testTaxon.addMisappliedName(misappliedName, null, null);
|
|
1706
|
UUID misappliedNameUUID = service.save(misappliedName).getUuid();
|
|
1707
|
|
|
1708
|
TaxonDeletionConfigurator config = new TaxonDeletionConfigurator() ;
|
|
1709
|
config.setDeleteMisappliedNames(true);
|
|
1710
|
|
|
1711
|
DeleteResult result = service.deleteTaxon(testTaxon.getUuid(), config, node.getClassification().getUuid());
|
|
1712
|
if(!result.isOk()){
|
|
1713
|
Assert.fail();
|
|
1714
|
}
|
|
1715
|
commitAndStartNewTransaction(null);
|
|
1716
|
Taxon tax = (Taxon)service.find(uuid);
|
|
1717
|
assertNull(tax);
|
|
1718
|
tax = (Taxon)service.find(misappliedNameUUID);
|
|
1719
|
//TODO: is that correct or should it be deleted because there is no relation to anything
|
|
1720
|
assertNull(tax);
|
|
1721
|
|
|
1722
|
}
|
|
1723
|
@Test
|
|
1724
|
@DataSet(value="../../database/ClearDBDataSet.xml")
|
|
1725
|
public final void testTaxonDeletionConfiguratorTaxonWithMisappliedNameDoNotDelete(){
|
|
1726
|
|
|
1727
|
Taxon testTaxon = getTestTaxon();
|
|
1728
|
UUID uuid = service.save(testTaxon).getUuid();
|
|
1729
|
|
|
1730
|
Taxon misappliedName = Taxon.NewInstance(TaxonNameFactory.NewBotanicalInstance(Rank.GENUS()), null);
|
|
1731
|
|
|
1732
|
Iterator<TaxonNode> nodes = testTaxon.getTaxonNodes().iterator();
|
|
1733
|
TaxonNode node =nodes.next();
|
|
1734
|
testTaxon.addMisappliedName(misappliedName, null, null);
|
|
1735
|
UUID misappliedNameUUID = service.save(misappliedName).getUuid();
|
|
1736
|
|
|
1737
|
TaxonDeletionConfigurator config = new TaxonDeletionConfigurator() ;
|
|
1738
|
config.setDeleteMisappliedNames(false);
|
|
1739
|
|
|
1740
|
DeleteResult result = service.deleteTaxon(testTaxon.getUuid(), config, node.getClassification().getUuid());
|
|
1741
|
if(!result.isOk()){
|
|
1742
|
Assert.fail();
|
|
1743
|
}
|
|
1744
|
commitAndStartNewTransaction(null);
|
|
1745
|
Taxon tax = (Taxon)service.find(uuid);
|
|
1746
|
assertNull(tax);
|
|
1747
|
tax = (Taxon)service.find(misappliedNameUUID);
|
|
1748
|
//TODO: is that correct or should it be deleted because there is no relation to anything
|
|
1749
|
assertNotNull(tax);
|
|
1750
|
}
|
|
1751
|
|
|
1752
|
@Test
|
|
1753
|
@DataSet(value="../../database/ClearDBDataSet.xml")
|
|
1754
|
public final void testTaxonDeletionConfiguratorTaxonMisappliedName(){
|
|
1755
|
|
|
1756
|
Taxon testTaxon = getTestTaxon();
|
|
1757
|
UUID uuid = service.save(testTaxon).getUuid();
|
|
1758
|
|
|
1759
|
Taxon misappliedNameTaxon = Taxon.NewInstance(TaxonNameFactory.NewBotanicalInstance(Rank.GENUS()), null);
|
|
1760
|
|
|
1761
|
Iterator<TaxonNode> nodes = testTaxon.getTaxonNodes().iterator();
|
|
1762
|
TaxonNode node =nodes.next();
|
|
1763
|
testTaxon.addMisappliedName(misappliedNameTaxon, null, null);
|
|
1764
|
UUID misappliedNameUUID = service.save(misappliedNameTaxon).getUuid();
|
|
1765
|
misappliedNameTaxon = (Taxon)service.find(misappliedNameUUID);
|
|
1766
|
UUID misNameUUID = misappliedNameTaxon.getName().getUuid();
|
|
1767
|
|
|
1768
|
TaxonDeletionConfigurator config = new TaxonDeletionConfigurator() ;
|
|
1769
|
|
|
1770
|
service.deleteTaxon(misappliedNameTaxon.getUuid(), config,null);
|
|
1771
|
|
|
1772
|
commitAndStartNewTransaction(null);
|
|
1773
|
Taxon tax = (Taxon)service.find(uuid);
|
|
1774
|
assertNotNull(tax);
|
|
1775
|
tax = (Taxon)service.find(misappliedNameUUID);
|
|
1776
|
IBotanicalName name = nameService.find(misNameUUID);
|
|
1777
|
|
|
1778
|
assertNull(tax);
|
|
1779
|
assertNull(name);
|
|
1780
|
}
|
|
1781
|
|
|
1782
|
@Test
|
|
1783
|
@DataSet(value="../../database/ClearDBDataSet.xml")
|
|
1784
|
public final void testListIncludedTaxa(){
|
|
1785
|
Reference citation = null;
|
|
1786
|
String microcitation = null;
|
|
1787
|
|
|
1788
|
//Data
|
|
1789
|
Classification cl1 = Classification.NewInstance("testClassification1");
|
|
1790
|
Classification cl2 = Classification.NewInstance("testClassification2");
|
|
1791
|
Classification cl3 = Classification.NewInstance("testClassification3");
|
|
1792
|
|
|
1793
|
classificationService.save(cl1);
|
|
1794
|
classificationService.save(cl2);
|
|
1795
|
classificationService.save(cl3);
|
|
1796
|
|
|
1797
|
Taxon c1Genus = Taxon.NewInstance(null, null);c1Genus.setUuid(UUID.fromString("daa24f6f-7e38-4668-b385-10c789212e4e"));
|
|
1798
|
Taxon c1Species = Taxon.NewInstance(null, null);c1Species.setUuid(UUID.fromString("1c1d0566-67d0-4806-bf23-ecf55f4b9118"));
|
|
1799
|
Taxon c1SubSpecies1 = Taxon.NewInstance(null, null);c1SubSpecies1.setUuid(UUID.fromString("96ae2fad-76df-429f-b179-42e00838fea4"));
|
|
1800
|
Taxon c1SubSpecies2 = Taxon.NewInstance(null, null);c1SubSpecies2.setUuid(UUID.fromString("5d3f6147-ca72-40e0-be8a-6c835a09a579"));
|
|
1801
|
TaxonNode c1childNodeSpecies1 = cl1.addParentChild(c1Genus, c1Species, null, null);
|
|
1802
|
nodeService.saveOrUpdate(c1childNodeSpecies1.getParent());
|
|
1803
|
nodeService.saveOrUpdate(c1childNodeSpecies1);
|
|
1804
|
TaxonNode c1childNodeSubSpecies1 =cl1.addParentChild(c1Species, c1SubSpecies1, null, null);
|
|
1805
|
nodeService.saveOrUpdate(c1childNodeSubSpecies1);
|
|
1806
|
TaxonNode c1childNodeSubSpecies2 =cl1.addParentChild(c1Species, c1SubSpecies2, null, null);
|
|
1807
|
nodeService.saveOrUpdate(c1childNodeSubSpecies2);
|
|
1808
|
|
|
1809
|
Taxon c2Genus = Taxon.NewInstance(null, null);c2Genus.setUuid(UUID.fromString("ed0ec006-3ac8-4a12-ae13-fdf2a13dedbe"));
|
|
1810
|
Taxon c2Species = Taxon.NewInstance(null, null);c2Species.setUuid(UUID.fromString("1027eb18-1c26-450e-a299-981b775ebc3c"));
|
|
1811
|
Taxon c2SubSpecies1 = Taxon.NewInstance(null, null);c2SubSpecies1.setUuid(UUID.fromString("61f039c8-01f3-4f5d-8e16-1602139774e7"));
|
|
1812
|
Taxon c2SubSpecies2 = Taxon.NewInstance(null, null);c2SubSpecies2.setUuid(UUID.fromString("2ed6b6f8-05f9-459a-a075-2bca57e3013e"));
|
|
1813
|
TaxonNode c2childNodeSpecies1 = cl2.addParentChild(c2Genus, c2Species, null, null);
|
|
1814
|
nodeService.saveOrUpdate(c2childNodeSpecies1.getParent());
|
|
1815
|
nodeService.saveOrUpdate(c2childNodeSpecies1);
|
|
1816
|
TaxonNode c2childNodeSubSpecies1 = cl2.addParentChild(c2Species, c2SubSpecies1, null, null);
|
|
1817
|
nodeService.saveOrUpdate(c2childNodeSubSpecies1);
|
|
1818
|
TaxonNode c2childNodeSubSpecies2 = cl2.addParentChild(c2Species, c2SubSpecies2, null, null);
|
|
1819
|
nodeService.saveOrUpdate(c2childNodeSubSpecies2);
|
|
1820
|
|
|
1821
|
Taxon c3Genus = Taxon.NewInstance(null, null);c3Genus.setUuid(UUID.fromString("407dfc8d-7a4f-4370-ada4-76c1a8279d1f"));
|
|
1822
|
Taxon c3Species = Taxon.NewInstance(null, null);c3Species.setUuid(UUID.fromString("b6d34fc7-4aa7-41e5-b633-86f474edbbd5"));
|
|
1823
|
Taxon c3SubSpecies1 = Taxon.NewInstance(null, null);c3SubSpecies1.setUuid(UUID.fromString("01c07585-a422-40cd-9339-a74c56901d9f"));
|
|
1824
|
Taxon c3SubSpecies2 = Taxon.NewInstance(null, null);c3SubSpecies2.setUuid(UUID.fromString("390c8e23-e05f-4f89-b417-50cf080f4c91"));
|
|
1825
|
TaxonNode c3childNodeSpecies1 = cl3.addParentChild(c3Genus, c3Species, null, null);
|
|
1826
|
nodeService.saveOrUpdate(c3childNodeSpecies1.getParent());
|
|
1827
|
nodeService.saveOrUpdate(c3childNodeSpecies1);
|
|
1828
|
TaxonNode c3childNodeSubSpecies1 = cl3.addParentChild(c3Species, c3SubSpecies1, null, null);
|
|
1829
|
nodeService.saveOrUpdate(c3childNodeSubSpecies1);
|
|
1830
|
TaxonNode c3childNodeSubSpecies2 = cl3.addParentChild(c3Species, c3SubSpecies2, null, null);
|
|
1831
|
nodeService.saveOrUpdate(c3childNodeSubSpecies2);
|
|
1832
|
|
|
1833
|
Taxon c4Genus = Taxon.NewInstance(null, null);c4Genus.setUuid(UUID.fromString("bfd6bbdd-0116-4ab2-a781-9316224aad78"));
|
|
1834
|
Taxon c4Species = Taxon.NewInstance(null, null);c4Species.setUuid(UUID.fromString("9347a3d9-5ece-4d64-9035-e8aaf5d3ee02"));
|
|
1835
|
Taxon c4SubSpecies = Taxon.NewInstance(null, null);c4SubSpecies.setUuid(UUID.fromString("777aabbe-4c3a-449c-ab99-a91f2fec9f07"));
|
|
1836
|
|
|
1837
|
TaxonRelationship rel = c1Species.addTaxonRelation(c2Species, TaxonRelationshipType.CONGRUENT_TO(), citation, microcitation);
|
|
1838
|
rel.setDoubtful(true);
|
|
1839
|
c1Species.addTaxonRelation(c4Species, TaxonRelationshipType.INCLUDES(), citation, microcitation);
|
|
1840
|
c2Species.addTaxonRelation(c1SubSpecies2, TaxonRelationshipType.INCLUDES(), citation, microcitation);
|
|
1841
|
|
|
1842
|
service.saveOrUpdate(c1Species);
|
|
1843
|
service.saveOrUpdate(c2Species);
|
|
1844
|
service.save(c4Species);
|
|
1845
|
commitAndStartNewTransaction();
|
|
1846
|
|
|
1847
|
//Tests
|
|
1848
|
//default starting at species 1
|
|
1849
|
IncludedTaxaDTO dto = service.listIncludedTaxa(c1Species.getUuid(), new IncludedTaxonConfiguration(null, true, false));
|
|
1850
|
Assert.assertNotNull("IncludedTaxaDTO", dto);
|
|
1851
|
Assert.assertEquals("Result should contain 7 taxa: c1Species", 7, dto.getIncludedTaxa().size());
|
|
1852
|
Assert.assertNotNull("date should not be null", dto.getDate());
|
|
1853
|
// Assert.assertTrue(dto.contains(taxonUuid));
|
|
1854
|
//same without doubtful
|
|
1855
|
dto = service.listIncludedTaxa(c1Species.getUuid(), new IncludedTaxonConfiguration(null, false, false));
|
|
1856
|
Assert.assertEquals(4, dto.getIncludedTaxa().size());
|
|
1857
|
|
|
1858
|
//other example starting at Genus2
|
|
1859
|
dto = service.listIncludedTaxa(c2Genus.getUuid(), new IncludedTaxonConfiguration(null, true, false));
|
|
1860
|
Assert.assertEquals(8, dto.getIncludedTaxa().size());
|
|
1861
|
//same without doubtful
|
|
1862
|
dto = service.listIncludedTaxa(c2Genus.getUuid(), new IncludedTaxonConfiguration(null, false, false));
|
|
1863
|
Assert.assertEquals(5, dto.getIncludedTaxa().size());
|
|
1864
|
|
|
1865
|
//only congruent
|
|
1866
|
dto = service.listIncludedTaxa(c1Species.getUuid(), new IncludedTaxonConfiguration(null, true, true));
|
|
1867
|
Assert.assertEquals(2, dto.getIncludedTaxa().size());
|
|
1868
|
//same without doubtful
|
|
1869
|
dto = service.listIncludedTaxa(c1Species.getUuid(), new IncludedTaxonConfiguration(null, false, true));
|
|
1870
|
Assert.assertEquals(1, dto.getIncludedTaxa().size());
|
|
1871
|
}
|
|
1872
|
|
|
1873
|
@Test
|
|
1874
|
public void testDeleteDescriptions(){
|
|
1875
|
try {
|
|
1876
|
createTestDataSet();
|
|
1877
|
} catch (FileNotFoundException e) {
|
|
1878
|
// TODO Auto-generated catch block
|
|
1879
|
e.printStackTrace();
|
|
1880
|
}
|
|
1881
|
TaxonDescription description = TaxonDescription.NewInstance(taxWithoutSyn);
|
|
1882
|
SpecimenOrObservationBase<IIdentifiableEntityCacheStrategy<FieldUnit>> specimen = FieldUnit.NewInstance();
|
|
1883
|
UUID uuid = occurenceService.saveOrUpdate(specimen);
|
|
1884
|
DescriptionElementBase element = IndividualsAssociation.NewInstance(specimen);
|
|
1885
|
description.addElement(element);
|
|
1886
|
service.saveOrUpdate(taxWithoutSyn);
|
|
1887
|
|
|
1888
|
|
|
1889
|
Taxon tax = (Taxon)service.find(uuidTaxWithoutSyn);
|
|
1890
|
Set<TaxonDescription> descr = tax.getDescriptions();
|
|
1891
|
assertEquals(1, descr.size());
|
|
1892
|
description = descr.iterator().next();
|
|
1893
|
UUID uuidDescr = description.getUuid();
|
|
1894
|
UUID uuidDescEl = description.getElements().iterator().next().getUuid();
|
|
1895
|
|
|
1896
|
descriptionService.deleteDescription(description);
|
|
1897
|
service.saveOrUpdate(tax);
|
|
1898
|
|
|
1899
|
description = (TaxonDescription) descriptionService.find(uuidDescr);
|
|
1900
|
specimen = occurenceService.find(uuid);
|
|
1901
|
assertNull(description);
|
|
1902
|
DeleteResult result = occurenceService.delete(specimen);
|
|
1903
|
assertTrue(result.isOk());
|
|
1904
|
|
|
1905
|
}
|
|
1906
|
|
|
1907
|
@Test
|
|
1908
|
public void testRemoveDescriptionsFromTaxa(){
|
|
1909
|
try {
|
|
1910
|
createTestDataSet();
|
|
1911
|
} catch (FileNotFoundException e) {
|
|
1912
|
// TODO Auto-generated catch block
|
|
1913
|
e.printStackTrace();
|
|
1914
|
}
|
|
1915
|
TaxonDescription description = TaxonDescription.NewInstance(taxWithoutSyn);
|
|
1916
|
SpecimenOrObservationBase<IIdentifiableEntityCacheStrategy<FieldUnit>> specimen = FieldUnit.NewInstance();
|
|
1917
|
UUID uuid = occurenceService.saveOrUpdate(specimen);
|
|
1918
|
DescriptionElementBase element = IndividualsAssociation.NewInstance(specimen);
|
|
1919
|
description.addElement(element);
|
|
1920
|
service.saveOrUpdate(taxWithoutSyn);
|
|
1921
|
|
|
1922
|
|
|
1923
|
Taxon tax = (Taxon)service.find(uuidTaxWithoutSyn);
|
|
1924
|
Set<TaxonDescription> descr = tax.getDescriptions();
|
|
1925
|
assertEquals(1, descr.size());
|
|
1926
|
description = descr.iterator().next();
|
|
1927
|
UUID uuidDescr = description.getUuid();
|
|
1928
|
|
|
1929
|
|
|
1930
|
tax.removeDescription(description, true);
|
|
1931
|
service.saveOrUpdate(tax);
|
|
1932
|
|
|
1933
|
description = (TaxonDescription) descriptionService.find(uuidDescr);
|
|
1934
|
specimen = occurenceService.find(uuid);
|
|
1935
|
assertNotNull(description);
|
|
1936
|
DeleteResult result = occurenceService.delete(specimen);
|
|
1937
|
assertTrue(result.isOk());
|
|
1938
|
}
|
|
1939
|
|
|
1940
|
@Override
|
|
1941
|
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="ClearDBDataSet.xml")
|
|
1942
|
public void createTestDataSet() throws FileNotFoundException {
|
|
1943
|
Rank rank = Rank.SPECIES();
|
|
1944
|
taxWithoutSyn = Taxon.NewInstance(TaxonNameFactory.NewBotanicalInstance(rank, "Test1", null, null, null, null, null, null, null), null);
|
|
1945
|
taxWithSyn = Taxon.NewInstance(TaxonNameFactory.NewBotanicalInstance(rank, "Test3", null, null, null, null, null, null, null), null);
|
|
1946
|
tax2WithSyn = Taxon.NewInstance(TaxonNameFactory.NewBotanicalInstance(rank, "Test5", null, null, null, null, null, null, null), null);
|
|
1947
|
synonym = Synonym.NewInstance(TaxonNameFactory.NewBotanicalInstance(rank, "Test2", null, null, null, null, null, null, null), null);
|
|
1948
|
synonym2 = Synonym.NewInstance(TaxonNameFactory.NewBotanicalInstance(rank, "Test4", null, null, null, null, null, null, null), null);
|
|
1949
|
synonym2.getName().setHomotypicalGroup(synonym.getHomotypicGroup());
|
|
1950
|
|
|
1951
|
taxWithSyn.addSynonym(synonym, SynonymType.HETEROTYPIC_SYNONYM_OF());
|
|
1952
|
taxWithSyn.addSynonym(synonym2, SynonymType.HETEROTYPIC_SYNONYM_OF());
|
|
1953
|
|
|
1954
|
uuidTaxWithoutSyn = service.save(taxWithoutSyn).getUuid();
|
|
1955
|
uuidSyn = service.save(synonym).getUuid();
|
|
1956
|
uuidSyn2 = service.save(synonym2).getUuid();
|
|
1957
|
uuidTaxWithSyn =service.save(taxWithSyn).getUuid();
|
|
1958
|
|
|
1959
|
}
|
|
1960
|
|
|
1961
|
//public static UUID DESCRIPTION1_UUID = UUID.fromString("f3e061f6-c5df-465c-a253-1e18ab4c7e50");
|
|
1962
|
//public static UUID DESCRIPTION2_UUID = UUID.fromString("1b009a40-ebff-4f7e-9f7f-75a850ba995d");
|
|
1963
|
|
|
1964
|
public Taxon getTestTaxon(){
|
|
1965
|
int descrIndex = 6000;
|
|
1966
|
Person deCandolle = Person.NewInstance();
|
|
1967
|
deCandolle.setTitleCache("DC.", true);
|
|
1968
|
|
|
1969
|
Reference sec = ReferenceFactory.newDatabase();
|
|
1970
|
sec.setTitleCache("Flora lunaea", true);
|
|
1971
|
Reference citationRef = ReferenceFactory.newBook();
|
|
1972
|
citationRef.setTitleCache("Sp. lunarum", true);
|
|
1973
|
|
|
1974
|
//genus taxon with Name, combinationAuthor,
|
|
1975
|
IBotanicalName botName = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());
|
|
1976
|
botName.setTitleCache("Hieracium L.", true);
|
|
1977
|
botName.setGenusOrUninomial("Hieracium");
|
|
1978
|
botName.setCombinationAuthorship(Person.NewInstance());
|
|
1979
|
botName.getCombinationAuthorship().setNomenclaturalTitleCache("L.", true);
|
|
1980
|
botName.setUuid(GENUS_NAME_UUID);
|
|
1981
|
Taxon genusTaxon = Taxon.NewInstance(botName, sec);
|
|
1982
|
genusTaxon.setUuid(GENUS_UUID);
|
|
1983
|
service.save(genusTaxon);
|
|
1984
|
//a name that is the basionym of genusTaxon's name
|
|
1985
|
TaxonName basionym = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());
|
|
1986
|
basionym.setTitleCache("Hieracilla DC.", true);
|
|
1987
|
basionym.setGenusOrUninomial("Hieracilla");
|
|
1988
|
basionym.setCombinationAuthorship(deCandolle);
|
|
1989
|
basionym.setUuid(BASIONYM_UUID);
|
|
1990
|
botName.addBasionym(basionym, null, null,"216", null);
|
|
1991
|
nameService.saveOrUpdate(basionym);
|
|
1992
|
//species taxon that is the child of genus taxon
|
|
1993
|
IBotanicalName botSpecies = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
1994
|
botSpecies.setTitleCache("Hieracium asturianum Pau", true);
|
|
1995
|
botSpecies.setGenusOrUninomial("Hieracium");
|
|
1996
|
botSpecies.setSpecificEpithet("asturianum");
|
|
1997
|
botSpecies.setCombinationAuthorship(Person.NewInstance());
|
|
1998
|
botSpecies.getCombinationAuthorship().setNomenclaturalTitleCache("Pau", true);
|
|
1999
|
botSpecies.setUuid(SPECIES1_NAME_UUID);
|
|
2000
|
Taxon childTaxon = Taxon.NewInstance(botSpecies, sec);
|
|
2001
|
childTaxon.setUuid(SPECIES1_UUID);
|
|
2002
|
TaxonDescription taxDesc = getTestDescription(descrIndex++);
|
|
2003
|
//taxDesc.setUuid(DESCRIPTION1_UUID);
|
|
2004
|
childTaxon.addDescription(taxDesc);
|
|
2005
|
service.saveOrUpdate(childTaxon);
|
|
2006
|
Classification classification = getTestClassification("TestClassification");
|
|
2007
|
classification.addParentChild(genusTaxon, childTaxon, citationRef, "456");
|
|
2008
|
// childTaxon.setTaxonomicParent(genusTaxon, citationRef, "456");
|
|
2009
|
classificationService.save(classification);
|
|
2010
|
//homotypic synonym of childTaxon1
|
|
2011
|
IBotanicalName botSpecies4= TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
2012
|
botSpecies4.setTitleCache("Hieracium gueri DC.", true);
|
|
2013
|
botSpecies4.setGenusOrUninomial("Hieracium");
|
|
2014
|
botSpecies4.setSpecificEpithet("gueri");
|
|
2015
|
botSpecies4.setCombinationAuthorship(deCandolle);
|
|
2016
|
botSpecies4.setUuid(SYNONYM_NAME_UUID);
|
|
2017
|
Synonym homoSynonym = Synonym.NewInstance(botSpecies4, sec);
|
|
2018
|
|
|
2019
|
childTaxon.addSynonym(homoSynonym, SynonymType.HOMOTYPIC_SYNONYM_OF());
|
|
2020
|
service.saveOrUpdate(childTaxon);
|
|
2021
|
|
|
2022
|
//2nd child species taxon that is the child of genus taxon
|
|
2023
|
IBotanicalName botSpecies2= TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
2024
|
botSpecies2.setTitleCache("Hieracium wolffii Zahn", true);
|
|
2025
|
botSpecies2.setGenusOrUninomial("Hieracium");
|
|
2026
|
botSpecies2.setSpecificEpithet("wolffii");
|
|
2027
|
botSpecies2.setCombinationAuthorship(Person.NewInstance());
|
|
2028
|
botSpecies2.getCombinationAuthorship().setNomenclaturalTitleCache("Zahn", true);
|
|
2029
|
botSpecies2.setUuid(SPECIES2_NAME_UUID);
|
|
2030
|
Taxon childTaxon2 = Taxon.NewInstance(botSpecies2, sec);
|
|
2031
|
childTaxon2.setUuid(SPECIES2_UUID);
|
|
2032
|
classification.addParentChild(genusTaxon, childTaxon2, citationRef, "499");
|
|
2033
|
//childTaxon2.setTaxonomicParent(genusTaxon, citationRef, "499");
|
|
2034
|
service.saveOrUpdate(childTaxon2);
|
|
2035
|
//heterotypic synonym of childTaxon2
|
|
2036
|
IBotanicalName botSpecies3= TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
2037
|
botSpecies3.setTitleCache("Hieracium lupium DC.", true);
|
|
2038
|
botSpecies3.setGenusOrUninomial("Hieracium");
|
|
2039
|
botSpecies3.setSpecificEpithet("lupium");
|
|
2040
|
botSpecies3.setCombinationAuthorship(deCandolle);
|
|
2041
|
botSpecies3.setUuid(SYNONYM2_NAME_UUID);
|
|
2042
|
Synonym heteroSynonym = Synonym.NewInstance(botSpecies3, sec);
|
|
2043
|
heteroSynonym.setUuid(SYNONYM2_UUID);
|
|
2044
|
childTaxon2.addSynonym(heteroSynonym, SynonymType.HETEROTYPIC_SYNONYM_OF());
|
|
2045
|
service.saveOrUpdate(childTaxon2);
|
|
2046
|
//missaplied Name for childTaxon2
|
|
2047
|
IBotanicalName missName= TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
2048
|
missName.setTitleCache("Hieracium lupium DC.", true);
|
|
2049
|
missName.setGenusOrUninomial("Hieracium");
|
|
2050
|
missName.setSpecificEpithet("lupium");
|
|
2051
|
missName.setCombinationAuthorship(deCandolle);
|
|
2052
|
missName.setUuid(SPECIES5_NAME_UUID);
|
|
2053
|
Taxon misappliedNameTaxon = Taxon.NewInstance(missName, sec);
|
|
2054
|
childTaxon2.addMisappliedName(misappliedNameTaxon, citationRef, "125");
|
|
2055
|
taxDesc = getTestDescription(descrIndex++);
|
|
2056
|
// taxDesc.setUuid(DESCRIPTION2_UUID);
|
|
2057
|
genusTaxon.addDescription(taxDesc);
|
|
2058
|
service.saveOrUpdate(genusTaxon);
|
|
2059
|
service.save(misappliedNameTaxon);
|
|
2060
|
|
|
2061
|
return genusTaxon;
|
|
2062
|
}
|
|
2063
|
|
|
2064
|
public TaxonDescription getTestDescription(int index){
|
|
2065
|
TaxonDescription taxonDescription = TaxonDescription.NewInstance();
|
|
2066
|
Language language = Language.DEFAULT();
|
|
2067
|
//taxonDescription.setId(index);
|
|
2068
|
|
|
2069
|
//textData
|
|
2070
|
TextData textData = TextData.NewInstance();
|
|
2071
|
String descriptionText = "this is a desciption for a taxon";
|
|
2072
|
LanguageString languageString = LanguageString.NewInstance(descriptionText, language);
|
|
2073
|
textData.putText(languageString);
|
|
2074
|
taxonDescription.addElement(textData);
|
|
2075
|
|
|
2076
|
//commonName
|
|
2077
|
|
|
2078
|
String commonNameString = "Schönveilchen";
|
|
2079
|
CommonTaxonName commonName = CommonTaxonName.NewInstance(commonNameString, language);
|
|
2080
|
taxonDescription.addElement(commonName);
|
|
2081
|
|
|
2082
|
return taxonDescription;
|
|
2083
|
}
|
|
2084
|
|
|
2085
|
public Classification getTestClassification(String name){
|
|
2086
|
return Classification.NewInstance(name);
|
|
2087
|
}
|
|
2088
|
}
|