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/**
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* Copyright (C) 2007 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.persistence.dao.hibernate.common;
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import static org.junit.Assert.assertEquals;
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import java.io.FileNotFoundException;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.List;
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import java.util.Map;
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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.hibernate.MappingException;
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import org.hibernate.internal.SessionFactoryImpl;
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import org.hibernate.persister.collection.CollectionPersister;
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import org.hibernate.stat.Statistics;
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import org.hibernate.type.Type;
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import org.junit.Assert;
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import org.junit.Before;
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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.dbunit.annotation.DataSets;
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import org.unitils.spring.annotation.SpringBeanByType;
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import eu.etaxonomy.cdm.common.URI;
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import eu.etaxonomy.cdm.model.agent.Address;
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import eu.etaxonomy.cdm.model.agent.AgentBase;
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import eu.etaxonomy.cdm.model.agent.Contact;
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import eu.etaxonomy.cdm.model.agent.Institution;
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import eu.etaxonomy.cdm.model.agent.InstitutionalMembership;
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import eu.etaxonomy.cdm.model.agent.Person;
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import eu.etaxonomy.cdm.model.agent.Team;
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import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
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import eu.etaxonomy.cdm.model.common.Annotation;
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import eu.etaxonomy.cdm.model.common.AnnotationType;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.Credit;
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import eu.etaxonomy.cdm.model.common.Extension;
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import eu.etaxonomy.cdm.model.common.ExtensionType;
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import eu.etaxonomy.cdm.model.common.ICdmBase;
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import eu.etaxonomy.cdm.model.common.IdentifiableSource;
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import eu.etaxonomy.cdm.model.common.Identifier;
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import eu.etaxonomy.cdm.model.common.IntextReference;
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import eu.etaxonomy.cdm.model.common.LSIDAuthority;
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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.common.RelationshipTermBase;
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import eu.etaxonomy.cdm.model.common.TimePeriod;
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import eu.etaxonomy.cdm.model.common.VerbatimTimePeriod;
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import eu.etaxonomy.cdm.model.description.CategoricalData;
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import eu.etaxonomy.cdm.model.description.CommonTaxonName;
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import eu.etaxonomy.cdm.model.description.DescriptionBase;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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import eu.etaxonomy.cdm.model.description.Distribution;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
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import eu.etaxonomy.cdm.model.description.MeasurementUnit;
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import eu.etaxonomy.cdm.model.description.MediaKey;
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import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
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import eu.etaxonomy.cdm.model.description.QuantitativeData;
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import eu.etaxonomy.cdm.model.description.SpecimenDescription;
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import eu.etaxonomy.cdm.model.description.State;
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import eu.etaxonomy.cdm.model.description.StateData;
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import eu.etaxonomy.cdm.model.description.StatisticalMeasure;
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import eu.etaxonomy.cdm.model.description.StatisticalMeasurementValue;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.description.TaxonInteraction;
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import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
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import eu.etaxonomy.cdm.model.description.TextData;
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import eu.etaxonomy.cdm.model.description.TextFormat;
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import eu.etaxonomy.cdm.model.location.Country;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.location.NamedAreaLevel;
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import eu.etaxonomy.cdm.model.location.NamedAreaType;
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import eu.etaxonomy.cdm.model.location.Point;
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import eu.etaxonomy.cdm.model.location.ReferenceSystem;
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import eu.etaxonomy.cdm.model.media.AudioFile;
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import eu.etaxonomy.cdm.model.media.ImageFile;
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import eu.etaxonomy.cdm.model.media.Media;
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import eu.etaxonomy.cdm.model.media.MediaRepresentation;
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import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;
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import eu.etaxonomy.cdm.model.media.MovieFile;
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import eu.etaxonomy.cdm.model.media.Rights;
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import eu.etaxonomy.cdm.model.media.RightsType;
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import eu.etaxonomy.cdm.model.metadata.CdmPreference;
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import eu.etaxonomy.cdm.model.molecular.Amplification;
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import eu.etaxonomy.cdm.model.molecular.DnaSample;
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import eu.etaxonomy.cdm.model.molecular.PhylogeneticTree;
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import eu.etaxonomy.cdm.model.molecular.Primer;
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import eu.etaxonomy.cdm.model.molecular.Sequence;
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import eu.etaxonomy.cdm.model.molecular.SingleRead;
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import eu.etaxonomy.cdm.model.molecular.SingleReadAlignment;
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import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
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import eu.etaxonomy.cdm.model.name.HybridRelationship;
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import eu.etaxonomy.cdm.model.name.HybridRelationshipType;
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import eu.etaxonomy.cdm.model.name.IBotanicalName;
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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.NameTypeDesignation;
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import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
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import eu.etaxonomy.cdm.model.name.TypeDesignationBase;
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import eu.etaxonomy.cdm.model.occurrence.Collection;
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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.GatheringEvent;
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import eu.etaxonomy.cdm.model.occurrence.PreservationMethod;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
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import eu.etaxonomy.cdm.model.permission.GrantedAuthorityImpl;
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import eu.etaxonomy.cdm.model.permission.Group;
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import eu.etaxonomy.cdm.model.permission.User;
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import eu.etaxonomy.cdm.model.reference.IBook;
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import eu.etaxonomy.cdm.model.reference.IBookSection;
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import eu.etaxonomy.cdm.model.reference.OriginalSourceBase;
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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.model.term.DefinedTerm;
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import eu.etaxonomy.cdm.model.term.DefinedTermBase;
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import eu.etaxonomy.cdm.model.term.OrderedTermBase;
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import eu.etaxonomy.cdm.model.term.OrderedTermVocabulary;
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import eu.etaxonomy.cdm.model.term.Representation;
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import eu.etaxonomy.cdm.model.term.TermNode;
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import eu.etaxonomy.cdm.model.term.TermTree;
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import eu.etaxonomy.cdm.model.term.TermVocabulary;
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import eu.etaxonomy.cdm.model.view.AuditEvent;
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import eu.etaxonomy.cdm.persistence.dao.agent.IAgentDao;
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import eu.etaxonomy.cdm.persistence.dao.common.ICdmGenericDao;
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import eu.etaxonomy.cdm.persistence.dao.name.ITaxonNameDao;
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import eu.etaxonomy.cdm.persistence.dao.occurrence.IOccurrenceDao;
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import eu.etaxonomy.cdm.persistence.dao.reference.IReferenceDao;
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import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao;
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import eu.etaxonomy.cdm.persistence.dto.ReferencingObjectDto;
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import eu.etaxonomy.cdm.strategy.match.DefaultMatchStrategy;
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import eu.etaxonomy.cdm.strategy.match.IMatchStrategyEqual;
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import eu.etaxonomy.cdm.strategy.match.MatchException;
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import eu.etaxonomy.cdm.strategy.merge.DefaultMergeStrategy;
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import eu.etaxonomy.cdm.strategy.merge.IMergeStrategy;
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import eu.etaxonomy.cdm.strategy.merge.MergeException;
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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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* @since 27.07.2009
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*/
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public class CdmGenericDaoImplTest extends CdmTransactionalIntegrationTest {
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private static final Logger logger = Logger.getLogger(CdmGenericDaoImplTest.class);
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@SpringBeanByType
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private ICdmGenericDao cdmGenericDao;
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@SpringBeanByType
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private ITaxonDao taxonDao;
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@SpringBeanByType
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private IOccurrenceDao occurrenceDao;
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@SpringBeanByType
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private ITaxonNameDao nameDao;
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@SpringBeanByType
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private IAgentDao agentDao;
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@SpringBeanByType
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private IReferenceDao referenceDao;
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@Before
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public void setUp() throws Exception {}
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// ***************** TESTS **************************************************
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@Test
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@DataSets({
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@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="/eu/etaxonomy/cdm/database/ClearDB_with_Terms_DataSet.xml"),
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@DataSet("/eu/etaxonomy/cdm/database/TermsDataSet-with_auditing_info.xml")}
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)
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public void testDelete(){
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Reference ref1 = ReferenceFactory.newBook();
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Reference ref2 = ReferenceFactory.newBook();
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Annotation annotation = Annotation.NewInstance("Anno1", null);
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ref1.addAnnotation(annotation);
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cdmGenericDao.saveOrUpdate(ref1);
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cdmGenericDao.saveOrUpdate(ref2);
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List<Reference> list = cdmGenericDao.list(Reference.class, 10, 0, null, null);
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try {
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cdmGenericDao.merge(ref2, ref1, null);
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} catch (MergeException e) {
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Assert.fail();
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}
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commitAndStartNewTransaction(null);
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list = cdmGenericDao.list(Reference.class, 10, 0, null, null);
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Assert.assertEquals(1, list.size());
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}
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@Test
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public void testGetCdmBasesByFieldAndClass() {
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logger.warn("Not yet implemented");
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}
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@Test
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public void testGetCdmBasesWithItemInCollection() {
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logger.warn("Not yet implemented");
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}
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@Test
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public void testGetAllPersistedClasses() {
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Class<?>[] existingClassesArray = {
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Address.class,
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AgentBase.class,
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Institution.class,
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InstitutionalMembership.class,
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Person.class,
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Team.class,
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TeamOrPersonBase.class,
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Annotation.class,
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AnnotationType.class,
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Credit.class,
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DefinedTermBase.class,
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Extension.class,
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ExtensionType.class,
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GrantedAuthorityImpl.class,
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Group.class,
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IdentifiableSource.class,
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Identifier.class,
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IntextReference.class,
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Language.class,
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LanguageString.class,
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LSIDAuthority.class,
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Marker.class,
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MarkerType.class,
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OrderedTermBase.class,
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OrderedTermVocabulary.class,
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OriginalSourceBase.class,
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RelationshipTermBase.class,
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Representation.class,
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TermVocabulary.class,
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User.class,
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DefinedTerm.class,
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CategoricalData.class,
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CommonTaxonName.class,
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DescriptionBase.class,
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DescriptionElementBase.class,
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Distribution.class,
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Feature.class,
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TermNode.class,
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TermTree.class,
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MediaKey.class,
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IndividualsAssociation.class,
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MeasurementUnit.class,
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PresenceAbsenceTerm.class,
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QuantitativeData.class,
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SpecimenDescription.class,
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State.class,
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StateData.class,
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StatisticalMeasure.class,
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StatisticalMeasurementValue.class,
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TaxonDescription.class,
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TaxonInteraction.class,
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TaxonNameDescription.class,
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TextData.class,
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TextFormat.class,
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NamedArea.class,
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NamedAreaLevel.class,
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NamedAreaType.class,
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ReferenceSystem.class,
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Country.class,
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AudioFile.class,
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ImageFile.class,
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Media.class,
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MediaRepresentation.class,
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MediaRepresentationPart.class,
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MovieFile.class,
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Rights.class,
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RightsType.class,
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Amplification.class,
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DnaSample.class,
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SingleRead.class,
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SingleReadAlignment.class,
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Primer.class,
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Sequence.class,
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PhylogeneticTree.class,
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Sequence.class,
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HomotypicalGroup.class,
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HybridRelationship.class,
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HybridRelationshipType.class,
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NameRelationship.class,
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NameRelationshipType.class,
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NameTypeDesignation.class,
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NameTypeDesignationStatus.class,
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323
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NomenclaturalStatus.class,
|
|
324
|
NomenclaturalStatusType.class,
|
|
325
|
Rank.class,
|
|
326
|
SpecimenTypeDesignation.class,
|
|
327
|
SpecimenTypeDesignationStatus.class,
|
|
328
|
TaxonName.class,
|
|
329
|
TypeDesignationBase.class,
|
|
330
|
Collection.class,
|
|
331
|
DerivationEvent.class,
|
|
332
|
DerivationEventType.class,
|
|
333
|
DerivedUnit.class,
|
|
334
|
DeterminationEvent.class,
|
|
335
|
FieldUnit.class,
|
|
336
|
GatheringEvent.class,
|
|
337
|
PreservationMethod.class,
|
|
338
|
SpecimenOrObservationBase.class,
|
|
339
|
Reference.class,
|
|
340
|
Synonym.class,
|
|
341
|
SynonymType.class,
|
|
342
|
Taxon.class,
|
|
343
|
TaxonBase.class,
|
|
344
|
TaxonNode.class,
|
|
345
|
Classification.class,
|
|
346
|
TaxonRelationship.class,
|
|
347
|
TaxonRelationshipType.class ,
|
|
348
|
//Contact.class, //these are embedabble classes
|
|
349
|
//LSID.class,
|
|
350
|
//Point.class,
|
|
351
|
//NomenclaturalCode.class,
|
|
352
|
} ;
|
|
353
|
List<Class<?>> existingClassesList = new ArrayList<>();
|
|
354
|
existingClassesList.addAll(Arrays.asList(existingClassesArray));
|
|
355
|
boolean includeAbstractClasses = true;
|
|
356
|
Set<Class<? extends CdmBase>> foundClasses = cdmGenericDao.getAllPersistedClasses(includeAbstractClasses);
|
|
357
|
|
|
358
|
//for debugging only
|
|
359
|
// for (Class existingClass : existingClassesList){
|
|
360
|
// if (! foundClasses.contains(existingClass)){
|
|
361
|
// logger.warn("Class not found: " + existingClass.getCanonicalName());
|
|
362
|
// }
|
|
363
|
// }
|
|
364
|
|
|
365
|
//All classes must be found
|
|
366
|
Assert.assertTrue("all classes must be found by getAllCdmClasses() method", foundClasses.containsAll(existingClassesList));
|
|
367
|
|
|
368
|
//No extra classes must be found
|
|
369
|
for (Class<?> clazz : foundClasses){
|
|
370
|
if (! CdmBase.class.isAssignableFrom(clazz)&& !( AuditEvent.class == clazz) && !( CdmPreference.class == clazz) ){ //OLD: && !( LSID.class == clazz)&& !( NomenclaturalCode.class == clazz) && !( Point.class == clazz) && !( Modifier.class == clazz) && !( Contact.class == clazz)
|
|
371
|
Assert.fail("Class " + clazz.getName() + " is not assignable from CdmBase");
|
|
372
|
}
|
|
373
|
}
|
|
374
|
|
|
375
|
includeAbstractClasses = false;
|
|
376
|
Set<Class<? extends CdmBase>> noAbstractClasses = cdmGenericDao.getAllPersistedClasses(includeAbstractClasses);
|
|
377
|
Class<?> abstractClassToTest = TaxonBase.class;
|
|
378
|
Assert.assertFalse("Abstract class " + abstractClassToTest.getName() + " may not be in set ", noAbstractClasses.contains(abstractClassToTest));
|
|
379
|
}
|
|
380
|
|
|
381
|
@Test
|
|
382
|
@DataSets({
|
|
383
|
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="/eu/etaxonomy/cdm/database/ClearDB_with_Terms_DataSet.xml"),
|
|
384
|
@DataSet("/eu/etaxonomy/cdm/database/TermsDataSet-with_auditing_info.xml")})
|
|
385
|
public void testGetReferencingObjectsCdmBase() {
|
|
386
|
IBotanicalName name = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
387
|
name.setTitleCache("A name", true);
|
|
388
|
Reference ref1 = ReferenceFactory.newArticle();
|
|
389
|
Taxon taxon = Taxon.NewInstance(name, ref1);
|
|
390
|
Person author = Person.NewInstance();
|
|
391
|
author.setTitleCache("Author", true);
|
|
392
|
ref1.addAnnotation(Annotation.NewInstance("A1", Language.DEFAULT()));
|
|
393
|
ref1.setAuthorship(author);
|
|
394
|
name.setBasionymAuthorship(author);
|
|
395
|
|
|
396
|
name.setNomenclaturalReference(ref1);
|
|
397
|
|
|
398
|
taxonDao.save(taxon);
|
|
399
|
// UUID uuid = UUID.fromString("613980ac-9bd5-43b9-a374-d71e1794688f");
|
|
400
|
// Reference ref1 = referenceService.findByUuid(uuid);
|
|
401
|
commitAndStartNewTransaction(null);
|
|
402
|
|
|
403
|
Set<CdmBase> referencedObjects = cdmGenericDao.getReferencingObjects(ref1);
|
|
404
|
String debug = "############## RESULT ###################";
|
|
405
|
for (CdmBase obj: referencedObjects){
|
|
406
|
debug += "Object1: " + obj.getClass().getSimpleName() + " - " + obj;
|
|
407
|
}
|
|
408
|
//was 3 before bidirectionality was removed for supplemental data
|
|
409
|
assertEquals(2, referencedObjects.size());
|
|
410
|
debug += "############## END ###################";
|
|
411
|
|
|
412
|
// UUID uuidAuthor = UUID.fromString("4ce66544-a5a3-4601-ab0b-1f0a1338327b");
|
|
413
|
// AgentBase author = agentService.findByUuid(uuidAuthor);
|
|
414
|
|
|
415
|
referencedObjects = cdmGenericDao.getReferencingObjects(author);
|
|
416
|
debug += "############## RESULT ###################";
|
|
417
|
for (CdmBase obj: referencedObjects){
|
|
418
|
debug += "Object2: " + obj.getClass().getSimpleName() + " - " + obj;
|
|
419
|
}
|
|
420
|
assertEquals(2, referencedObjects.size());
|
|
421
|
debug += "############## END ###################";
|
|
422
|
logger.info(debug);
|
|
423
|
}
|
|
424
|
|
|
425
|
|
|
426
|
//similar to testGetReferencingObjectsCdmBase but with DTO
|
|
427
|
@Test
|
|
428
|
@DataSets({
|
|
429
|
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="/eu/etaxonomy/cdm/database/ClearDB_with_Terms_DataSet.xml"),
|
|
430
|
@DataSet("/eu/etaxonomy/cdm/database/TermsDataSet-with_auditing_info.xml")})
|
|
431
|
public void testGetReferencingObjectsDto() {
|
|
432
|
|
|
433
|
IBotanicalName name = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
434
|
name.setTitleCache("A name", true);
|
|
435
|
Reference ref1 = ReferenceFactory.newArticle();
|
|
436
|
Taxon taxon = Taxon.NewInstance(name, ref1);
|
|
437
|
Person author = Person.NewInstance();
|
|
438
|
author.setTitleCache("Author", true);
|
|
439
|
ref1.addAnnotation(Annotation.NewInstance("A1", Language.DEFAULT()));
|
|
440
|
ref1.setAuthorship(author);
|
|
441
|
name.setCombinationAuthorship(author);
|
|
442
|
name.setBasionymAuthorship(author); //to test deduplication
|
|
443
|
|
|
444
|
name.setNomenclaturalReference(ref1);
|
|
445
|
|
|
446
|
taxonDao.save(taxon);
|
|
447
|
// UUID uuid = UUID.fromString("613980ac-9bd5-43b9-a374-d71e1794688f");
|
|
448
|
// Reference ref1 = referenceService.findByUuid(uuid);
|
|
449
|
commitAndStartNewTransaction(null);
|
|
450
|
|
|
451
|
int i = 1;
|
|
452
|
Set<ReferencingObjectDto> referencedObjects = cdmGenericDao.getReferencingObjectsDto(ref1);
|
|
453
|
String debug = "############## RESULT for ref1 ###################\n";
|
|
454
|
for (ReferencingObjectDto dto: referencedObjects){
|
|
455
|
debug += "Object"+ i++ +": " + dto.getType().getSimpleName() + " - " + dto + "\n";
|
|
456
|
}
|
|
457
|
//was 3 before bidirectionality was removed for supplemental data
|
|
458
|
assertEquals(2, referencedObjects.size());
|
|
459
|
debug += "############## END ###################\n";
|
|
460
|
|
|
461
|
// UUID uuidAuthor = UUID.fromString("4ce66544-a5a3-4601-ab0b-1f0a1338327b");
|
|
462
|
// AgentBase author = agentService.findByUuid(uuidAuthor);
|
|
463
|
|
|
464
|
referencedObjects = cdmGenericDao.getReferencingObjectsDto(author);
|
|
465
|
i = 1;
|
|
466
|
debug += "############## RESULT for author ###################\n";
|
|
467
|
for (ReferencingObjectDto dto: referencedObjects){
|
|
468
|
debug += "Object"+ i++ +": " + dto.getType().getSimpleName() + " - " + dto + "\n";
|
|
469
|
}
|
|
470
|
assertEquals("The both taxon names should be dedulicated", 2, referencedObjects.size());
|
|
471
|
debug += "############## END ###################\n";
|
|
472
|
logger.warn(debug);
|
|
473
|
}
|
|
474
|
|
|
475
|
/**
|
|
476
|
* 2nd test method for {@link eu.etaxonomy.cdm.persistence.dao.hibernate.common.CdmGenericDaoImpl#getReferencingObjects(CdmBase)}.
|
|
477
|
*/
|
|
478
|
@Test
|
|
479
|
@DataSet
|
|
480
|
public final void testGetReferencingObjects2() {
|
|
481
|
// SpecimenDescription desc1 = SpecimenDescription.NewInstance();
|
|
482
|
// desc1.setTitleCache("desc1");
|
|
483
|
// SpecimenDescription desc2 = SpecimenDescription.NewInstance();
|
|
484
|
// desc2.setTitleCache("desc2");
|
|
485
|
//
|
|
486
|
// SpecimenOrObservationBase spec1 = Specimen.NewInstance();
|
|
487
|
//
|
|
488
|
// desc1.addDescribedSpecimenOrObservation(spec1);
|
|
489
|
// //Taxon taxon = Taxon.NewInstance(taxonName, sec)
|
|
490
|
// spec1.addDescription(desc2);
|
|
491
|
//
|
|
492
|
// occurrenceService.save(spec1);
|
|
493
|
|
|
494
|
UUID uuidSpec = UUID.fromString("41539e9c-3764-4f14-9712-2d07d00c8e4c");
|
|
495
|
SpecimenOrObservationBase<?> spec1 = occurrenceDao.findByUuid(uuidSpec);
|
|
496
|
|
|
497
|
Set<CdmBase> referencingObjects = cdmGenericDao.getReferencingObjects(spec1);
|
|
498
|
// System.out.println("############## RESULT ###################");
|
|
499
|
// for (CdmBase obj: referencingObjects){
|
|
500
|
// System.out.println("Object: " + obj.getClass().getSimpleName() + " - " + obj);
|
|
501
|
// }
|
|
502
|
// System.out.println("############## END ###################");
|
|
503
|
assertEquals("Number of referencing objects must be 2.", 2, referencingObjects.size());
|
|
504
|
}
|
|
505
|
|
|
506
|
/**
|
|
507
|
* Test method for {@link eu.etaxonomy.cdm.persistence.dao.hibernate.common.CdmGenericDaoImpl#merge(CdmBase, CdmBase)}.
|
|
508
|
* @throws MergeException
|
|
509
|
*/
|
|
510
|
@Test
|
|
511
|
public void testMergeCdmBaseReferenceAndIdentifiable() throws MergeException {
|
|
512
|
|
|
513
|
TaxonName name1 = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
514
|
name1.setTitleCache("BotanicalName1", true);
|
|
515
|
|
|
516
|
TaxonName name2 = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
517
|
name2.setTitleCache("BotanicalName2", true);
|
|
518
|
|
|
519
|
TaxonName zooName1 = TaxonNameFactory.NewZoologicalInstance(Rank.SPECIES());
|
|
520
|
name1.setTitleCache("ZoologicalName1", true);
|
|
521
|
|
|
522
|
Reference article1 = ReferenceFactory.newArticle();
|
|
523
|
Reference article2 = ReferenceFactory.newArticle();
|
|
524
|
|
|
525
|
name1.setNomenclaturalReference(article1);
|
|
526
|
name2.setNomenclaturalReference(article2);
|
|
527
|
|
|
528
|
Taxon taxon1 = Taxon.NewInstance(name1, article1);
|
|
529
|
Taxon taxon2 = Taxon.NewInstance(name2, article2);
|
|
530
|
|
|
531
|
// Person author = Person.NewInstance();
|
|
532
|
// author.setTitleCache("Author");
|
|
533
|
Annotation annotation1 = Annotation.NewInstance("A1", Language.DEFAULT());
|
|
534
|
Annotation annotation2 = Annotation.NewInstance("A2", Language.DEFAULT());
|
|
535
|
|
|
536
|
article1.addAnnotation(annotation1);
|
|
537
|
article2.addAnnotation(annotation2);
|
|
538
|
|
|
539
|
Marker marker1 = Marker.NewInstance(MarkerType.COMPLETE(), false);
|
|
540
|
Marker marker2 = Marker.NewInstance(MarkerType.IMPORTED(), false);
|
|
541
|
|
|
542
|
article1.addMarker(marker1);
|
|
543
|
article2.addMarker(marker2);
|
|
544
|
|
|
545
|
Rights rights1 = Rights.NewInstance();
|
|
546
|
Rights rights2 = Rights.NewInstance();
|
|
547
|
|
|
548
|
article1.addRights(rights1);
|
|
549
|
article2.addRights(rights2);
|
|
550
|
|
|
551
|
Credit credit1 = Credit.NewInstance(Team.NewInstance(), "credit1");
|
|
552
|
Credit credit2 = Credit.NewInstance(Team.NewInstance(), "credit2");
|
|
553
|
|
|
554
|
article1.addCredit(credit1);
|
|
555
|
article2.addCredit(credit2);
|
|
556
|
|
|
557
|
Extension extension1 = Extension.NewInstance();
|
|
558
|
Extension extension2 = Extension.NewInstance();
|
|
559
|
|
|
560
|
article1.addExtension(extension1);
|
|
561
|
article2.addExtension(extension2);
|
|
562
|
|
|
563
|
IdentifiableSource source1 = IdentifiableSource.NewInstance(OriginalSourceType.Unknown);
|
|
564
|
IdentifiableSource source2 = IdentifiableSource.NewInstance(OriginalSourceType.Unknown);
|
|
565
|
|
|
566
|
article1.addSource(source1);
|
|
567
|
article2.addSource(source2);
|
|
568
|
|
|
569
|
Media media1 = Media.NewInstance();
|
|
570
|
Media media2 = Media.NewInstance();
|
|
571
|
|
|
572
|
article1.addMedia(media1);
|
|
573
|
article2.addMedia(media2);
|
|
574
|
|
|
575
|
// ref1.setAuthorship(author);
|
|
576
|
// name1.setBasionymAuthorship(author);
|
|
577
|
|
|
578
|
name1.setNomenclaturalReference(article1);
|
|
579
|
|
|
580
|
nameDao.save(name1);
|
|
581
|
nameDao.save(name2);
|
|
582
|
nameDao.save(zooName1);
|
|
583
|
|
|
584
|
TaxonDescription taxDesc = TaxonDescription.NewInstance(taxon1);
|
|
585
|
taxDesc.setTitleCache("taxDesc", true);
|
|
586
|
taxDesc.addSource(OriginalSourceType.Unknown, null, null, article2, null);
|
|
587
|
|
|
588
|
taxonDao.save(taxon1);
|
|
589
|
|
|
590
|
//unidircetional reference to the merged object should be redirected
|
|
591
|
cdmGenericDao.merge(article1, article2, null);
|
|
592
|
Assert.assertEquals("Name2 must have article 1 as new nomRef", article1 ,name2.getNomenclaturalReference());
|
|
593
|
//TODO microCitations!! -> warning
|
|
594
|
|
|
595
|
//Annotations
|
|
596
|
Assert.assertEquals("Annotation number should be 2 (1 from each of the merged objects)", 2, article1.getAnnotations().size());
|
|
597
|
|
|
598
|
//Marker
|
|
599
|
Assert.assertEquals("Marker number should be 2 (1 from each of the merged objects)", 2, article1.getMarkers().size());
|
|
600
|
|
|
601
|
//Rights
|
|
602
|
Assert.assertEquals("Rights number should be 2 (1 from each of the merged objects)", 2, article1.getRights().size());
|
|
603
|
|
|
604
|
//Credits
|
|
605
|
Assert.assertEquals("Credits number should be 2 (1 from each of the merged objects)", 2, article1.getCredits().size());
|
|
606
|
|
|
607
|
//Extensions
|
|
608
|
Assert.assertEquals("Extensions number should be 2 (1 from each of the merged objects)", 2, article1.getExtensions().size());
|
|
609
|
|
|
610
|
//Sources
|
|
611
|
Assert.assertEquals("Sources number should be 2 (1 from each of the merged objects)", 2, article1.getSources().size());
|
|
612
|
|
|
613
|
//Media
|
|
614
|
Assert.assertEquals("Media number should be 2 (1 from each of the merged objects)", 2, article1.getMedia().size());
|
|
615
|
|
|
616
|
//Description sources
|
|
617
|
Assert.assertEquals("Number of sources for taxon description must be 1", 1, taxDesc.getSources().size());
|
|
618
|
Assert.assertEquals("Taxon description must have article1 as source", taxDesc.getSources().iterator().next().getCitation(),article1);
|
|
619
|
|
|
620
|
//test exceptions
|
|
621
|
|
|
622
|
testMergeExceptions(name1, name2, taxon1, zooName1);
|
|
623
|
|
|
624
|
//FIXME TO BE IMPLEMENTED
|
|
625
|
//current defalt implementation for rights, credits and media is ADD_CLONE and therefore the below tests don't work
|
|
626
|
//TODO is this the wanted default behaviour?
|
|
627
|
// Assert.assertTrue("Rights2 must be contained in the rights", article1.getRights().contains(rights2));
|
|
628
|
// Assert.assertTrue("Credits2 must be contained in the credits", article1.getCredits().contains(credit2));
|
|
629
|
// Assert.assertTrue("Media2 must be contained in the media", article1.getMedia().contains(media2));
|
|
630
|
|
|
631
|
}
|
|
632
|
|
|
633
|
@Test
|
|
634
|
public void testMergeTaxonNameAndTaxon() throws MergeException {
|
|
635
|
TaxonName name1 = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
636
|
name1.setTitleCache("BotanicalName1", true);
|
|
637
|
|
|
638
|
TaxonName name2 = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
639
|
name2.setTitleCache("BotanicalName2", true);
|
|
640
|
|
|
641
|
IBotanicalName name3 = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
642
|
name3.setTitleCache("BotanicalName3", true);
|
|
643
|
|
|
644
|
Reference database = ReferenceFactory.newDatabase();
|
|
645
|
|
|
646
|
Taxon taxon1 = Taxon.NewInstance(name1, database);
|
|
647
|
Taxon taxon2 = Taxon.NewInstance(name2, database);
|
|
648
|
Taxon taxon3 = Taxon.NewInstance(name3, database);
|
|
649
|
|
|
650
|
taxonDao.save(taxon1);
|
|
651
|
taxonDao.save(taxon2);
|
|
652
|
taxonDao.save(taxon3);
|
|
653
|
|
|
654
|
cdmGenericDao.merge(name1, name2, null);
|
|
655
|
Assert.assertEquals("Name1 must have 2 taxa attached now.", 2 ,name1.getTaxonBases().size());
|
|
656
|
Assert.assertEquals("Taxon2 must have name1 as new name.", name1 ,taxon2.getName());
|
|
657
|
|
|
658
|
//TODO
|
|
659
|
// cdmGenericDao.merge(taxon1, taxon3, null);
|
|
660
|
// Assert.assertEquals("Name1 must have 3 taxa attached now.", 3 ,name1.getTaxonBases().size());
|
|
661
|
}
|
|
662
|
|
|
663
|
@Test
|
|
664
|
public void testMergeAuthors() throws MergeException {
|
|
665
|
|
|
666
|
IBotanicalName name1 = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
667
|
name1.setTitleCache("BotanicalName1", true);
|
|
668
|
|
|
669
|
IBotanicalName name2 = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
670
|
name2.setTitleCache("BotanicalName2", true);
|
|
671
|
|
|
672
|
IBook book1 = ReferenceFactory.newBook();
|
|
673
|
IBook book2 = ReferenceFactory.newBook();
|
|
674
|
|
|
675
|
Team team1 = Team.NewInstance();
|
|
676
|
Team team2 = Team.NewInstance();
|
|
677
|
Team team3 = Team.NewInstance();
|
|
678
|
team1.setTitleCache("team1", true);
|
|
679
|
team2.setTitleCache("team2", true);
|
|
680
|
team3.setTitleCache("team3", true);
|
|
681
|
|
|
682
|
Person person1 = Person.NewTitledInstance("person1");
|
|
683
|
Person person2 = Person.NewTitledInstance("person2");
|
|
684
|
Person person3 = Person.NewTitledInstance("person3");
|
|
685
|
|
|
686
|
team1.setNomenclaturalTitleCache("T.1", true);
|
|
687
|
String street1 = "Strasse1";
|
|
688
|
team1.setContact(Contact.NewInstance(street1, "12345", "Berlin", Country.ARGENTINAARGENTINEREPUBLIC(),"pobox" , "Region", "a@b.de", "f12345", "+49-30-123456", URI.create("www.abc.de"), Point.NewInstance(2.4, 3.2, ReferenceSystem.WGS84(), 3)));
|
|
689
|
team2.setContact(Contact.NewInstance("Street2", null, "London", null, null, null, null, "874599873", null, null, null));
|
|
690
|
String street3 = "Street3";
|
|
691
|
team2.addAddress(street3, null, null, null, null, null, Point.NewInstance(1.1, 2.2, null, 4));
|
|
692
|
String emailAddress1 = "Email1";
|
|
693
|
team1.addEmailAddress(emailAddress1);
|
|
694
|
|
|
695
|
team2.addTeamMember(person1);
|
|
696
|
team2.addTeamMember(person2);
|
|
697
|
String emailAddress2 = "Email2";
|
|
698
|
team2.addEmailAddress(emailAddress2);
|
|
699
|
|
|
700
|
team3.addTeamMember(person3);
|
|
701
|
team3.addEmailAddress("emailAddress3");
|
|
702
|
|
|
703
|
book1.setAuthorship(team2);
|
|
704
|
book2.setAuthorship(team3);
|
|
705
|
|
|
706
|
Credit credit1 = Credit.NewInstance(team3, "credit1");
|
|
707
|
book2.addCredit(credit1);
|
|
708
|
|
|
709
|
agentDao.save(team1);
|
|
710
|
agentDao.save(team2);
|
|
711
|
agentDao.save(team3);
|
|
712
|
cdmGenericDao.save((Reference)book1);
|
|
713
|
cdmGenericDao.save((Reference)book2);
|
|
714
|
|
|
715
|
cdmGenericDao.merge(team2, team3, null);
|
|
716
|
|
|
717
|
Assert.assertSame("Author of book1 must be team2.", team2, book1.getAuthorship());
|
|
718
|
Assert.assertSame("Author of book2 must be team2.", team2, book2.getAuthorship());
|
|
719
|
Assert.assertSame("Agent of credit1 must be team2.", team2, credit1.getAgent());
|
|
720
|
|
|
721
|
Assert.assertEquals("Team2 must have 3 persons as members.",3, team2.getTeamMembers().size());
|
|
722
|
Assert.assertTrue("Team2 must have person3 as new member.", team2.getTeamMembers().contains(person3));
|
|
723
|
Assert.assertSame("Team2 must have person3 as third member.",person3, team2.getTeamMembers().get(2));
|
|
724
|
|
|
725
|
//Contact
|
|
726
|
cdmGenericDao.merge(team2, team1, null);
|
|
727
|
Contact team2Contact = team2.getContact();
|
|
728
|
Assert.assertNotNull("team2Contact must not be null", team2Contact);
|
|
729
|
Assert.assertNotNull("Addresses must not be null", team2Contact.getAddresses());
|
|
730
|
Assert.assertEquals("Number of addresses must be 3", 3, team2Contact.getAddresses().size());
|
|
731
|
Assert.assertEquals("Number of email addresses must be 4", 4, team2Contact.getEmailAddresses().size());
|
|
732
|
|
|
733
|
boolean street1Exists = false;
|
|
734
|
boolean street3Exists = false;
|
|
735
|
boolean country1Exists = false;
|
|
736
|
for (Address address : team2Contact.getAddresses()){
|
|
737
|
if (street1.equals(address.getStreet())){
|
|
738
|
street1Exists = true;
|
|
739
|
}
|
|
740
|
if (street3.equals(address.getStreet())){
|
|
741
|
street3Exists = true;
|
|
742
|
}
|
|
743
|
if (Country.ARGENTINAARGENTINEREPUBLIC() == address.getCountry()){
|
|
744
|
country1Exists = true;
|
|
745
|
}
|
|
746
|
}
|
|
747
|
Assert.assertTrue("Street1 must be one of the streets in team2's addresses", street1Exists);
|
|
748
|
Assert.assertTrue("Street3 must be one of the streets in team2's addressesss", street3Exists);
|
|
749
|
Assert.assertTrue("Argentina must be one of the countries in team2's addresses", country1Exists);
|
|
750
|
|
|
751
|
//Person
|
|
752
|
Institution institution1 = Institution.NewInstance();
|
|
753
|
institution1.setTitleCache("inst1", true);
|
|
754
|
Institution institution2 = Institution.NewInstance();
|
|
755
|
institution2.setTitleCache("inst2", true);
|
|
756
|
|
|
757
|
TimePeriod period1 = TimePeriod.NewInstance(2002, 2004);
|
|
758
|
TimePeriod period2 = TimePeriod.NewInstance(2004, 2006);
|
|
759
|
|
|
760
|
person1.addInstitutionalMembership(institution1, period1, "departement1", "role1");
|
|
761
|
person2.addInstitutionalMembership(institution2, period2, "departement2", "role2");
|
|
762
|
|
|
763
|
IMergeStrategy personMergeStrategy = DefaultMergeStrategy.NewInstance(Person.class);
|
|
764
|
personMergeStrategy.invoke(person1, person2);
|
|
765
|
|
|
766
|
Assert.assertEquals("Number of institutional memberships must be 2", 2, person1.getInstitutionalMemberships().size());
|
|
767
|
for (InstitutionalMembership institutionalMembership : person1.getInstitutionalMemberships()){
|
|
768
|
Assert.assertSame("Person of institutional memebership must be person1", person1, institutionalMembership.getPerson());
|
|
769
|
}
|
|
770
|
}
|
|
771
|
|
|
772
|
/**
|
|
773
|
* Test method for {@link eu.etaxonomy.cdm.persistence.dao.hibernate.common.CdmGenericDaoImpl#merge(CdmBase, CdmBase)}.
|
|
774
|
*
|
|
775
|
* Test for https://dev.e-taxonomy.eu/redmine/issues/5652
|
|
776
|
*
|
|
777
|
* @throws MergeException
|
|
778
|
*/
|
|
779
|
@Test
|
|
780
|
public void testMergePersons() throws MergeException {
|
|
781
|
Team team1 = Team.NewInstance();
|
|
782
|
Team team2 = Team.NewInstance();
|
|
783
|
Team team3 = Team.NewInstance();
|
|
784
|
team1.setTitleCache("team1", true);
|
|
785
|
team2.setTitleCache("team2", true);
|
|
786
|
team3.setTitleCache("team3", true);
|
|
787
|
|
|
788
|
Person person1a = Person.NewTitledInstance("person1a");
|
|
789
|
Person person1b = Person.NewTitledInstance("person1b");
|
|
790
|
Person person2 = Person.NewTitledInstance("person2");
|
|
791
|
Person person3 = Person.NewTitledInstance("person3");
|
|
792
|
|
|
793
|
team1.addTeamMember(person1a);
|
|
794
|
team1.addTeamMember(person2);
|
|
795
|
|
|
796
|
team2.addTeamMember(person2);
|
|
797
|
team2.addTeamMember(person1a);
|
|
798
|
team2.addTeamMember(person3);
|
|
799
|
|
|
800
|
team3.addTeamMember(person3);
|
|
801
|
|
|
802
|
agentDao.save(team1);
|
|
803
|
agentDao.save(team2);
|
|
804
|
agentDao.save(team3);
|
|
805
|
agentDao.save(person1b);
|
|
806
|
commitAndStartNewTransaction(null);
|
|
807
|
|
|
808
|
IMergeStrategy personMergeStrategy = DefaultMergeStrategy.NewInstance(Person.class);
|
|
809
|
cdmGenericDao.merge(person1b, person1a, personMergeStrategy);
|
|
810
|
|
|
811
|
team1 = (Team)agentDao.load(team1.getUuid());
|
|
812
|
team2 = (Team)agentDao.load(team2.getUuid());
|
|
813
|
|
|
814
|
//order should not change and 1a should be replaced by 1b
|
|
815
|
Assert.assertEquals("person1b", team1.getTeamMembers().get(0).getTitleCache());
|
|
816
|
Assert.assertEquals("person2", team1.getTeamMembers().get(1).getTitleCache());
|
|
817
|
|
|
818
|
Assert.assertEquals("person2", team2.getTeamMembers().get(0).getTitleCache());
|
|
819
|
Assert.assertEquals("person1b", team2.getTeamMembers().get(1).getTitleCache());
|
|
820
|
Assert.assertEquals("person3", team2.getTeamMembers().get(2).getTitleCache());
|
|
821
|
}
|
|
822
|
|
|
823
|
@Test
|
|
824
|
public void testReallocateIntextReferenceForReferenceAndLanguageString() throws MergeException {
|
|
825
|
UUID uuidRef1 = UUID.fromString("41743cec-b893-4e8b-b06c-91f9b9ba8fee");
|
|
826
|
UUID uuidRef2 = UUID.fromString("8fd56b43-7cca-4c3b-bb90-7576da81c072");
|
|
827
|
|
|
828
|
// CREATE DATA
|
|
829
|
|
|
830
|
Reference ref1 = ReferenceFactory.newGeneric();
|
|
831
|
ref1.setTitle("Reference1");
|
|
832
|
ref1.setUuid(uuidRef1);
|
|
833
|
Reference ref2 = ReferenceFactory.newGeneric();
|
|
834
|
ref2.setTitle("Reference2");
|
|
835
|
ref2.setUuid(uuidRef2);
|
|
836
|
referenceDao.save(ref2);
|
|
837
|
Taxon taxon = Taxon.NewInstance(null, null);
|
|
838
|
|
|
839
|
TaxonDescription desc = TaxonDescription.NewInstance(taxon);
|
|
840
|
Language language = Language.DEFAULT();
|
|
841
|
TextData textData = TextData.NewInstance(Feature.DESCRIPTION(), "And here is a citation" , language, null);
|
|
842
|
LanguageString languageString = textData.getLanguageText(language);
|
|
843
|
IntextReference intextRefRef = languageString.addIntextReference(ref1, 4, 8);
|
|
844
|
String uuidIntextRefRef = intextRefRef.getUuid().toString();
|
|
845
|
desc.addElement(textData);
|
|
846
|
Assert.assertEquals("And <cdm:reference cdmId='"+uuidRef1+"' intextId='"+uuidIntextRefRef+"'>here</cdm:reference> is a citation",
|
|
847
|
languageString.getText());
|
|
848
|
|
|
849
|
//SAVE AND COMMIT
|
|
850
|
taxonDao.save(taxon);
|
|
851
|
commitAndStartNewTransaction(null);
|
|
852
|
|
|
853
|
//MERGE
|
|
854
|
DefaultMergeStrategy strategy = DefaultMergeStrategy.NewInstance(Reference.class);
|
|
855
|
ref1 = referenceDao.findByUuid(uuidRef1);
|
|
856
|
ref2 = referenceDao.findByUuid(uuidRef2);
|
|
857
|
cdmGenericDao.merge(ref2, ref1, strategy);
|
|
858
|
|
|
859
|
taxon = (Taxon)taxonDao.findByUuid(taxon.getUuid());
|
|
860
|
textData = (TextData)taxon.getDescriptions().iterator().next().getElements().iterator().next();
|
|
861
|
languageString = textData.getLanguageText(language);
|
|
862
|
Assert.assertEquals("And <cdm:reference cdmId='"+uuidRef2+"' intextId='"+uuidIntextRefRef+"'>here</cdm:reference> is a citation",
|
|
863
|
languageString.getText());
|
|
864
|
}
|
|
865
|
|
|
866
|
@Test
|
|
867
|
public void testReallocateIntextReferenceForNameAndAnnotation() throws MergeException {
|
|
868
|
UUID uuidPinusAlba = UUID.fromString("52743cec-b893-4e8b-b06c-91f9b9ba8fee");
|
|
869
|
UUID uuidAbiesAlba = UUID.fromString("6ed56b43-7cca-4c3b-bb90-7576da81c072");
|
|
870
|
|
|
871
|
// CREATE DATA
|
|
872
|
TaxonName pinusAlba = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
873
|
pinusAlba.setTitleCache("BotanicalName1", true);
|
|
874
|
pinusAlba.setUuid(uuidPinusAlba);
|
|
875
|
|
|
876
|
TaxonName abiesAlba = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
877
|
abiesAlba.setTitleCache("Abies alba", true);
|
|
878
|
abiesAlba.setUuid(uuidAbiesAlba);
|
|
879
|
|
|
880
|
Taxon taxon = Taxon.NewInstance(null, null);
|
|
881
|
|
|
882
|
Annotation annotation = Annotation.NewDefaultLanguageInstance("My annotation on Abies alba and its habit.");
|
|
883
|
taxon.addAnnotation(annotation);
|
|
884
|
IntextReference intextRefName = annotation.addIntextReference(abiesAlba, "My annotation on ", "Abies alba", " and its habit.");
|
|
885
|
String uuidIntextRefName = intextRefName.getUuid().toString();
|
|
886
|
Assert.assertEquals("My annotation on <cdm:name cdmId='"+uuidAbiesAlba+"' intextId='"+uuidIntextRefName+"'>Abies alba</cdm:name> and its habit.",
|
|
887
|
annotation.getText());
|
|
888
|
|
|
889
|
//SAVE AND COMMIT
|
|
890
|
taxonDao.save(taxon);
|
|
891
|
nameDao.save(abiesAlba);
|
|
892
|
nameDao.save(pinusAlba);
|
|
893
|
commitAndStartNewTransaction(null);
|
|
894
|
|
|
895
|
//MERGE
|
|
896
|
DefaultMergeStrategy strategy = DefaultMergeStrategy.NewInstance(TaxonName.class);
|
|
897
|
abiesAlba = nameDao.findByUuid(uuidAbiesAlba);
|
|
898
|
pinusAlba = nameDao.findByUuid(uuidPinusAlba);
|
|
899
|
cdmGenericDao.merge(pinusAlba, abiesAlba, strategy);
|
|
900
|
|
|
901
|
taxon = (Taxon)taxonDao.findByUuid(taxon.getUuid());
|
|
902
|
annotation = taxon.getAnnotations().iterator().next();
|
|
903
|
|
|
904
|
Assert.assertEquals("My annotation on <cdm:name cdmId='"+uuidPinusAlba+"' intextId='"+uuidIntextRefName+"'>Abies alba</cdm:name> and its habit.",
|
|
905
|
annotation.getText());
|
|
906
|
}
|
|
907
|
|
|
908
|
@Test
|
|
909
|
public void testReallocatePersonTeam() throws MergeException {
|
|
910
|
|
|
911
|
TaxonName name1 = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
912
|
name1.setTitleCache("BotanicalName1", true);
|
|
913
|
|
|
914
|
IBook book1 = ReferenceFactory.newBook();
|
|
915
|
|
|
916
|
Team team1 = Team.NewInstance();
|
|
917
|
Team team2 = Team.NewInstance();
|
|
918
|
team1.setTitleCache("team1", true);
|
|
919
|
team2.setTitleCache("team2", true);
|
|
920
|
|
|
921
|
Person person1 = Person.NewTitledInstance("person1");
|
|
922
|
Person person2 = Person.NewTitledInstance("person2");
|
|
923
|
|
|
924
|
team1.setNomenclaturalTitleCache("T.1", true);
|
|
925
|
String street1 = "Strasse1";
|
|
926
|
person1.setContact(Contact.NewInstance(street1, "12345", "Berlin", Country.ARGENTINAARGENTINEREPUBLIC(),"pobox" , "Region", "a@b.de", "f12345", "+49-30-123456", URI.create("www.abc.de"), Point.NewInstance(2.4, 3.2, ReferenceSystem.WGS84(), 3)));
|
|
927
|
team2.setContact(Contact.NewInstance("Street2", null, "London", null, null, null, null, "874599873", null, null, null));
|
|
928
|
String street3 = "Street3";
|
|
929
|
team2.addAddress(street3, null, null, null, null, null, Point.NewInstance(1.1, 2.2, null, 4));
|
|
930
|
String emailAddress1 = "Email1";
|
|
931
|
team1.addEmailAddress(emailAddress1);
|
|
932
|
|
|
933
|
//FIXME
|
|
934
|
// team2.addTeamMember(person1);
|
|
935
|
team2.addTeamMember(person2);
|
|
936
|
String emailAddress2 = "Email2";
|
|
937
|
team2.addEmailAddress(emailAddress2);
|
|
938
|
|
|
939
|
Credit credit1 = Credit.NewInstance(team2, "credit1");
|
|
940
|
book1.addCredit(credit1);
|
|
941
|
|
|
942
|
agentDao.save(team1);
|
|
943
|
agentDao.save(team2);
|
|
944
|
agentDao.save(person1);
|
|
945
|
agentDao.save(person2);
|
|
946
|
|
|
947
|
cdmGenericDao.save((Reference)book1);
|
|
948
|
|
|
949
|
//starting condition
|
|
950
|
name1.setCombinationAuthorship(person1);
|
|
951
|
Assert.assertEquals("Name1 should have person1 as combination author", person1, name1.getCombinationAuthorship());
|
|
952
|
|
|
953
|
DefaultMergeStrategy strategy = DefaultMergeStrategy.NewInstance(TeamOrPersonBase.class);
|
|
954
|
// strategy.setOnlyReallocateLinks(true);
|
|
955
|
|
|
956
|
FieldUnit fieldUnit1 = FieldUnit.NewInstance();
|
|
957
|
fieldUnit1.setPrimaryCollector(person1);
|
|
958
|
cdmGenericDao.save(fieldUnit1);
|
|
959
|
try {
|
|
960
|
cdmGenericDao.merge(team2, person1, strategy);
|
|
961
|
Assert.fail("We expect exception because fieldunit.primaryCollector is of type person");
|
|
962
|
} catch (MergeException e) {
|
|
963
|
if (! e.getMessage().contains("Object can not be merged into new object as it is referenced in a way that does not allow merging")){
|
|
964
|
Assert.fail("The exception should be the one thrown by DeduplicationHelper.reallocateByHolder(...)");
|
|
965
|
}
|
|
966
|
fieldUnit1.setPrimaryCollector(null); //clean up for next test
|
|
967
|
} catch (Exception e) {
|
|
968
|
Assert.fail("Unhandled exception during merge");
|
|
969
|
}
|
|
970
|
Assert.assertEquals("Name1 should still have person1 as combination author", person1, name1.getCombinationAuthorship());
|
|
971
|
|
|
972
|
//test collections
|
|
973
|
team1.addTeamMember(person1);
|
|
974
|
try {
|
|
975
|
cdmGenericDao.merge(team2, person1, strategy);
|
|
976
|
Assert.fail("We expect exception because fieldunit.primaryCollector is of type person");
|
|
977
|
} catch (MergeException e) {
|
|
978
|
if (! e.getMessage().contains("Object can not be merged into new object as it is referenced in a way that does not allow merging")){
|
|
979
|
Assert.fail("The exception should be the one thrown by DeduplicationHelper.reallocateByHolder(...)");
|
|
980
|
}
|
|
981
|
team1.removeTeamMember(person1); //clean up for next test
|
|
982
|
} catch (Exception e) {
|
|
983
|
Assert.fail("Unhandled exception during merge");
|
|
984
|
}
|
|
985
|
Assert.assertEquals("Name1 should still have person1 as combination author", person1, name1.getCombinationAuthorship());
|
|
986
|
|
|
987
|
//test successful merge
|
|
988
|
cdmGenericDao.save(name1);
|
|
989
|
cdmGenericDao.merge(team2, person1, strategy);
|
|
990
|
Assert.assertEquals("Name1 should have team2 as combination author now", team2, name1.getCombinationAuthorship());
|
|
991
|
}
|
|
992
|
|
|
993
|
private void testMergeExceptions(CdmBase name1, CdmBase name2, CdmBase taxon, ICdmBase zooName1) throws MergeException{
|
|
994
|
//
|
|
995
|
try {
|
|
996
|
cdmGenericDao.merge(name1, null, null);
|
|
997
|
Assert.fail("Merging of 2 objects one or both of them null must throw an exception");
|
|
998
|
} catch (NullPointerException e) {
|
|
999
|
Assert.assertTrue("Merging of 2 objects of different types must throw an exception", true);
|
|
1000
|
}
|
|
1001
|
//
|
|
1002
|
try {
|
|
1003
|
cdmGenericDao.merge(null, name1, null);
|
|
1004
|
Assert.fail("Merging of 2 objects one or both of them null must throw an exception");
|
|
1005
|
} catch (NullPointerException e) {
|
|
1006
|
Assert.assertTrue("Merging of 2 objects of different types must throw an exception", true);
|
|
1007
|
}
|
|
1008
|
//exceptions to be thrown
|
|
1009
|
try {
|
|
1010
|
cdmGenericDao.merge(name1, taxon, null);
|
|
1011
|
//this is not fully true anymore !! In certain cases merging of objects of different classes is allowed
|
|
1012
|
Assert.fail("Merging of 2 objects of different types must throw an exception");
|
|
1013
|
} catch (MergeException e) {
|
|
1014
|
Assert.assertTrue("Merging of 2 objects of different types must throw an exception", true);
|
|
1015
|
}
|
|
1016
|
//next exception
|
|
1017
|
//for names this is not the case anymore
|
|
1018
|
// try {
|
|
1019
|
// cdmGenericDao.merge(name1, zooName1, null);
|
|
1020
|
// Assert.fail("Merging of 2 objects of different types must throw an exception");
|
|
1021
|
// } catch (MergeException e) {
|
|
1022
|
// Assert.assertTrue("Merging of 2 objects of different types must throw an exception", true);
|
|
1023
|
// }
|
|
1024
|
}
|
|
1025
|
|
|
1026
|
@Test
|
|
1027
|
public void findMatching(){
|
|
1028
|
IBook book1 = ReferenceFactory.newBook();
|
|
1029
|
IBook book2 = ReferenceFactory.newBook();
|
|
1030
|
IBook book3 = ReferenceFactory.newBook();
|
|
1031
|
|
|
1032
|
String title1 = "title1";
|
|
1033
|
String title2 = "title2";
|
|
1034
|
book1.setTitle(title1);
|
|
1035
|
book2.setTitle(title2);
|
|
1036
|
book3.setTitle(title1);
|
|
1037
|
|
|
1038
|
cdmGenericDao.saveOrUpdate((Reference)book1);
|
|
1039
|
cdmGenericDao.saveOrUpdate((Reference)book2);
|
|
1040
|
cdmGenericDao.saveOrUpdate((Reference)book3);
|
|
1041
|
|
|
1042
|
IMatchStrategyEqual matchStrategy = DefaultMatchStrategy.NewInstance(Reference.class);
|
|
1043
|
|
|
1044
|
try {
|
|
1045
|
List<IBook> matchResult = cdmGenericDao.findMatching(book3, matchStrategy);
|
|
1046
|
Assert.assertNotNull("Resultlist must not be null", matchResult);
|
|
1047
|
Assert.assertEquals("Resultlist must have 1 entries", 1, matchResult.size());
|
|
1048
|
Assert.assertSame("Resultlist entry must be book 1", book1, matchResult.get(0));
|
|
1049
|
|
|
1050
|
book1.setDatePublished(VerbatimTimePeriod.NewVerbatimInstance(1999, 2002));
|
|
1051
|
matchResult = cdmGenericDao.findMatching(book3, matchStrategy);
|
|
1052
|
Assert.assertTrue("Resultlist must have no entries", matchResult.isEmpty());
|
|
1053
|
|
|
1054
|
book3.setDatePublished(VerbatimTimePeriod.NewVerbatimInstance(1999));
|
|
1055
|
matchResult = cdmGenericDao.findMatching(book3, matchStrategy);
|
|
1056
|
Assert.assertTrue("Resultlist must have no entries", matchResult.isEmpty());
|
|
1057
|
|
|
1058
|
book3.setDatePublished(VerbatimTimePeriod.NewVerbatimInstance(1999,2002));
|
|
1059
|
matchResult = cdmGenericDao.findMatching(book3, matchStrategy);
|
|
1060
|
Assert.assertEquals("Resultlist must have 1 entries", 1, matchResult.size());
|
|
1061
|
Assert.assertSame("Resultlist entry must be book 1", book1, matchResult.get(0));
|
|
1062
|
|
|
1063
|
//BookSection
|
|
1064
|
IBookSection section1 = ReferenceFactory.newBookSection();
|
|
1065
|
section1.setInBook(book1);
|
|
1066
|
section1.setTitle("SecTitle");
|
|
1067
|
section1.setPages("22-33");
|
|
1068
|
IBookSection section2 = ReferenceFactory.newBookSection();
|
|
1069
|
section2.setInBook(book2);
|
|
1070
|
section2.setTitle("SecTitle");
|
|
1071
|
section2.setPages("22-33");
|
|
1072
|
IBookSection section3 = ReferenceFactory.newBookSection();
|
|
1073
|
section3.setInBook(book1);
|
|
1074
|
section3.setTitle("SecTitle");
|
|
1075
|
section3.setPages("22-33");
|
|
1076
|
cdmGenericDao.saveOrUpdate((Reference)section1);
|
|
1077
|
cdmGenericDao.saveOrUpdate((Reference)section2);
|
|
1078
|
cdmGenericDao.saveOrUpdate((Reference)section3);
|
|
1079
|
|
|
1080
|
List<IBookSection> sectionResult = cdmGenericDao.findMatching(section3, null);
|
|
1081
|
Assert.assertEquals("Resultlist must have 1 entries", 1, sectionResult.size());
|
|
1082
|
Assert.assertSame("Resultlist entry must be section1", section1, sectionResult.get(0));
|
|
1083
|
|
|
1084
|
section2.setInBook(book2 = (IBook)book1.clone());
|
|
1085
|
cdmGenericDao.saveOrUpdate((Reference)book2);
|
|
1086
|
cdmGenericDao.saveOrUpdate((Reference)book1);
|
|
1087
|
matchResult = cdmGenericDao.findMatching(book3, matchStrategy);
|
|
1088
|
Assert.assertEquals("Resultlist must have 2 entries", 2, matchResult.size());
|
|
1089
|
sectionResult = cdmGenericDao.findMatching(section3, null);
|
|
1090
|
Assert.assertEquals("Resultlist must have 1 entries", 2, sectionResult.size());
|
|
1091
|
|
|
1092
|
Person person1 = Person.NewTitledInstance("person");
|
|
1093
|
Person person2 = Person.NewTitledInstance("person");
|
|
1094
|
Person person3 = Person.NewTitledInstance("person");
|
|
1095
|
|
|
1096
|
person1.setPrefix("pre1");
|
|
1097
|
person2.setPrefix("pre2");
|
|
1098
|
person3.setPrefix("pre3");
|
|
1099
|
|
|
1100
|
// matchResult = cdmGenericDao.findMatching(book3, matchStrategy);
|
|
1101
|
// Assert.assertEquals("Resultlist must have 2 entries", 2, matchResult.size());
|
|
1102
|
|
|
1103
|
book1.setAuthorship(person1);
|
|
1104
|
book2.setAuthorship(person1);
|
|
1105
|
book3.setAuthorship(person1);
|
|
1106
|
|
|
1107
|
boolean m = matchStrategy.invoke(book1, book3).isSuccessful();
|
|
1108
|
boolean m2 = matchStrategy.invoke(book2, book3).isSuccessful();
|
|
1109
|
|
|
1110
|
matchResult = cdmGenericDao.findMatching(book3, matchStrategy);
|
|
1111
|
Assert.assertEquals("Resultlist must have 2 entries", 2, matchResult.size());
|
|
1112
|
|
|
1113
|
book2.setAuthorship(person2);
|
|
1114
|
book3.setAuthorship(person3);
|
|
1115
|
matchResult = cdmGenericDao.findMatching(book3, null);
|
|
1116
|
Assert.assertEquals("Resultlist must have no entries", 0, matchResult.size());
|
|
1117
|
|
|
1118
|
person3.setPrefix("pre1");
|
|
1119
|
matchResult = cdmGenericDao.findMatching(book3, null);
|
|
1120
|
Assert.assertEquals("Resultlist must have 1 entry", 1, matchResult.size());
|
|
1121
|
Assert.assertSame("Resultlist entry must be book 1", book1, matchResult.get(0));
|
|
1122
|
|
|
1123
|
} catch (MatchException e) {
|
|
1124
|
Assert.fail("Find match must not throw Exception: " + e.getMessage());
|
|
1125
|
e.printStackTrace();
|
|
1126
|
}
|
|
1127
|
}
|
|
1128
|
|
|
1129
|
@Test
|
|
1130
|
public void findMatchingCache(){
|
|
1131
|
IBook book1 = ReferenceFactory.newBook();
|
|
1132
|
Team team1 = Team.NewInstance();
|
|
1133
|
Team team2 = Team.NewInstance();
|
|
1134
|
team1.setTitleCache("Team1", true);
|
|
1135
|
team2.setTitleCache("Team1", true);
|
|
1136
|
|
|
1137
|
book1.setTitle("Title1");
|
|
1138
|
book1.setEdition("Edition1");
|
|
1139
|
book1.setAuthorship(team1);
|
|
1140
|
|
|
1141
|
|
|
1142
|
IBook book2 = ((Reference)book1).clone();
|
|
1143
|
IBook book3 = ((Reference)book1).clone();
|
|
1144
|
|
|
1145
|
// Assert.assertTrue("Cloned book should match", matchStrategy.invoke(book1, bookClone));
|
|
1146
|
// book1.setTitleCache("cache1");
|
|
1147
|
// Assert.assertFalse("Cached book should not match", matchStrategy.invoke(book1, bookClone));
|
|
1148
|
//
|
|
1149
|
// bookClone.setTitleCache("cache1");
|
|
1150
|
// Assert.assertTrue("Cached book with same cache should match", matchStrategy.invoke(book1, bookClone));
|
|
1151
|
//
|
|
1152
|
// bookClone.setTitleCache("cache2");
|
|
1153
|
// Assert.assertFalse("Cached book with differings caches should not match", matchStrategy.invoke(book1, bookClone));
|
|
1154
|
// bookClone.setTitleCache("cache1"); //restore
|
|
1155
|
//
|
|
1156
|
// bookClone.setEdition(null);
|
|
1157
|
// Assert.assertTrue("Cached book with a defined and a null edition should match", matchStrategy.invoke(book1, bookClone));
|
|
1158
|
|
|
1159
|
cdmGenericDao.saveOrUpdate((Reference)book1);
|
|
1160
|
cdmGenericDao.saveOrUpdate((Reference)book2);
|
|
1161
|
cdmGenericDao.saveOrUpdate((Reference)book3);
|
|
1162
|
cdmGenericDao.saveOrUpdate(team1);
|
|
1163
|
cdmGenericDao.saveOrUpdate(team2);
|
|
1164
|
|
|
1165
|
IMatchStrategyEqual matchStrategy = DefaultMatchStrategy.NewInstance(Reference.class);
|
|
1166
|
|
|
1167
|
try {
|
|
1168
|
List<IBook> matchResult = cdmGenericDao.findMatching(book3, matchStrategy);
|
|
1169
|
Assert.assertNotNull("Resultlist must not be null", matchResult);
|
|
1170
|
Assert.assertEquals("Resultlist must have 2 entries", 2, matchResult.size());
|
|
1171
|
Assert.assertTrue("Resultlist must contain book 1", matchResult.contains(book1));
|
|
1172
|
Assert.assertTrue("Resultlist must contain book 2", matchResult.contains(book2));
|
|
1173
|
|
|
1174
|
book1.setTitleCache("cache1", true);
|
|
1175
|
matchResult = cdmGenericDao.findMatching(book3, matchStrategy);
|
|
1176
|
Assert.assertEquals("Resultlist must have 1 entries", 1, matchResult.size());
|
|
1177
|
Assert.assertTrue("Resultlist must contain book 2", matchResult.contains(book2));
|
|
1178
|
|
|
1179
|
book2.setTitleCache("cache2", false);
|
|
1180
|
matchResult = cdmGenericDao.findMatching(book3, matchStrategy);
|
|
1181
|
Assert.assertEquals("Resultlist must have 1 entries", 1, matchResult.size());
|
|
1182
|
Assert.assertTrue("Resultlist must contain book 2", matchResult.contains(book2));
|
|
1183
|
|
|
1184
|
book2.setEdition(null);
|
|
1185
|
matchResult = cdmGenericDao.findMatching(book3, matchStrategy);
|
|
1186
|
Assert.assertEquals("Resultlist must have 0 entries", 0, matchResult.size());
|
|
1187
|
|
|
1188
|
book3.setTitleCache("cache1", true);
|
|
1189
|
matchResult = cdmGenericDao.findMatching(book3, matchStrategy);
|
|
1190
|
Assert.assertEquals("Resultlist must have 1 entries", 1, matchResult.size());
|
|
1191
|
Assert.assertTrue("Resultlist must contain book 1", matchResult.contains(book1));
|
|
1192
|
|
|
1193
|
IMatchStrategyEqual teamMatcher = DefaultMatchStrategy.NewInstance(Team.class);
|
|
1194
|
boolean teamsMatch = teamMatcher.invoke(team1, team2).isSuccessful();
|
|
1195
|
Assert.assertTrue("Team1 and team2 should match" ,teamsMatch);
|
|
1196
|
|
|
1197
|
book3.setAuthorship(team2);
|
|
1198
|
matchResult = cdmGenericDao.findMatching(book3, matchStrategy);
|
|
1199
|
Assert.assertEquals("Resultlist must have 1 entries", 1, matchResult.size());
|
|
1200
|
Assert.assertTrue("Resultlist must contain book 1", matchResult.contains(book1));
|
|
1201
|
|
|
1202
|
book3.setAuthorship(null);
|
|
1203
|
matchResult = cdmGenericDao.findMatching(book3, matchStrategy);
|
|
1204
|
Assert.assertEquals("Resultlist must have 1 entries", 1, matchResult.size());
|
|
1205
|
Assert.assertTrue("Resultlist must contain book 1", matchResult.contains(book1));
|
|
1206
|
|
|
1207
|
book2.setTitleCache(book3.getTitleCache(), true);
|
|
1208
|
matchResult = cdmGenericDao.findMatching(book3, matchStrategy);
|
|
1209
|
Assert.assertEquals("Resultlist must have 2 entries", 2, matchResult.size());
|
|
1210
|
Assert.assertTrue("Resultlist must contain book 1", matchResult.contains(book1));
|
|
1211
|
Assert.assertTrue("Resultlist must contain book 2", matchResult.contains(book2));
|
|
1212
|
|
|
1213
|
team2.setTitleCache("team2", true);
|
|
1214
|
teamsMatch = teamMatcher.invoke(team1, team2).isSuccessful();
|
|
1215
|
Assert.assertFalse("Team1 and team2 should not match" ,teamsMatch);
|
|
1216
|
|
|
1217
|
book3.setAuthorship(team1);
|
|
1218
|
book2.setAuthorship(team2);
|
|
1219
|
matchResult = cdmGenericDao.findMatching(book3, matchStrategy);
|
|
1220
|
Assert.assertEquals("Resultlist must have 1 entries", 1, matchResult.size());
|
|
1221
|
Assert.assertTrue("Resultlist must contain book 1", matchResult.contains(book1));
|
|
1222
|
|
|
1223
|
} catch (MatchException e) {
|
|
1224
|
Assert.fail("Find match must not throw Exception: " + e.getMessage());
|
|
1225
|
e.printStackTrace();
|
|
1226
|
}
|
|
1227
|
}
|
|
1228
|
|
|
1229
|
//from original testing within class, can be removed if not needed anymore
|
|
1230
|
private void test() {
|
|
1231
|
SessionFactoryImpl factory = (SessionFactoryImpl)((CdmGenericDaoImpl)cdmGenericDao).getSession().getSessionFactory();
|
|
1232
|
Type propType = factory.getReferencedPropertyType(TaxonName.class.getCanonicalName(), "titleCache");
|
|
1233
|
Map<?,?> collMetadata = factory.getAllCollectionMetadata();
|
|
1234
|
Object roles = factory.getCollectionRolesByEntityParticipant("eu.etaxonomy.cdm.model.name.BotanicalName");
|
|
1235
|
CollectionPersister collPersister;
|
|
1236
|
try {
|
|
1237
|
collPersister = factory.getCollectionPersister(TaxonName.class.getCanonicalName()+".annotations");
|
|
1238
|
} catch (MappingException e) {
|
|
1239
|
// TODO Auto-generated catch block
|
|
1240
|
e.printStackTrace();
|
|
1241
|
}
|
|
1242
|
Statistics statistics = factory.getStatistics();
|
|
1243
|
Map<?,?> allClassMetadata = factory.getAllClassMetadata();
|
|
1244
|
logger.debug("");
|
|
1245
|
}
|
|
1246
|
|
|
1247
|
@Test
|
|
1248
|
public void testGetHqlResult() {
|
|
1249
|
logger.warn("Not yet implemented");
|
|
1250
|
}
|
|
1251
|
|
|
1252
|
@Override
|
|
1253
|
public void createTestDataSet() throws FileNotFoundException {}
|
|
1254
|
}
|