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// $Id$
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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.database.update.v36_40;
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import java.lang.reflect.Modifier;
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import java.sql.SQLException;
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import java.util.HashMap;
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import java.util.Map;
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import org.apache.log4j.Logger;
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import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
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import eu.etaxonomy.cdm.database.ICdmDataSource;
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import eu.etaxonomy.cdm.database.update.CaseType;
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import eu.etaxonomy.cdm.database.update.ITermUpdaterStep;
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import eu.etaxonomy.cdm.database.update.SchemaUpdaterStepBase;
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import eu.etaxonomy.cdm.model.agent.AgentBase;
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import eu.etaxonomy.cdm.model.agent.Institution;
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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.AnnotatableEntity;
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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.Credit;
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import eu.etaxonomy.cdm.model.common.DefinedTermBase;
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import eu.etaxonomy.cdm.model.common.EventBase;
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import eu.etaxonomy.cdm.model.common.ExtensionType;
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
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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.Language;
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import eu.etaxonomy.cdm.model.common.LanguageString;
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import eu.etaxonomy.cdm.model.common.LanguageStringBase;
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import eu.etaxonomy.cdm.model.common.MarkerType;
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import eu.etaxonomy.cdm.model.common.OrderedTerm;
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import eu.etaxonomy.cdm.model.common.OrderedTermBase;
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import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;
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import eu.etaxonomy.cdm.model.common.ReferencedEntityBase;
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import eu.etaxonomy.cdm.model.common.RelationshipBase;
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import eu.etaxonomy.cdm.model.common.RelationshipTermBase;
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import eu.etaxonomy.cdm.model.common.Representation;
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import eu.etaxonomy.cdm.model.common.TermVocabulary;
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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.DescriptionElementSource;
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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.FeatureTree;
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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.MultiAccessKey;
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import eu.etaxonomy.cdm.model.description.NaturalLanguageTerm;
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import eu.etaxonomy.cdm.model.description.PolytomousKey;
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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.StatisticalMeasure;
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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.description.WorkingSet;
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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.ReferenceSystem;
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import eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity;
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import eu.etaxonomy.cdm.model.media.Media;
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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.molecular.Amplification;
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import eu.etaxonomy.cdm.model.molecular.AmplificationResult;
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import eu.etaxonomy.cdm.model.molecular.Cloning;
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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.name.BacterialName;
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import eu.etaxonomy.cdm.model.name.BotanicalName;
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import eu.etaxonomy.cdm.model.name.CultivarPlantName;
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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.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.NonViralName;
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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.TypeDesignationStatusBase;
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import eu.etaxonomy.cdm.model.name.ViralName;
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import eu.etaxonomy.cdm.model.name.ZoologicalName;
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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.MaterialOrMethodEvent;
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import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen;
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import eu.etaxonomy.cdm.model.occurrence.PreservationMethod;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.SynonymRelationship;
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import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.model.taxon.TaxonNodeAgentRelation;
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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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/**
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* Updates the xxxObj_type field in Annotations, Markers, Extensions, Identifiers.
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* Not needed anymore as long as we gave up bidirectionality #5743
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*
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* @author a.mueller
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* @date 25.04.2016
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*/
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public class ReferencedObjTypeUpdater extends SchemaUpdaterStepBase<ReferencedObjTypeUpdater> implements ITermUpdaterStep{
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private static final Logger logger = Logger.getLogger(ReferencedObjTypeUpdater.class);
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private static final String stepName = "Update referenced obj_type";
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// **************************** STATIC METHODS ********************************/
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public static final ReferencedObjTypeUpdater NewInstance(){
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return new ReferencedObjTypeUpdater(stepName);
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}
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protected ReferencedObjTypeUpdater(String stepName) {
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super(stepName);
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}
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@Override
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public Integer invoke(ICdmDataSource datasource, IProgressMonitor monitor, CaseType caseType) throws SQLException {
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//TODO should better be read from eu.etaxonomy.cdm.model.common.package-info @AnyMetaDef
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try {
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Class<AnnotatableEntity>[] annotatableClasses = new Class[]{
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Institution.class,
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Person.class,
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Team.class,
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CategoricalData.class,
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CommonTaxonName.class,
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DescriptionElementSource.class,
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Distribution.class,
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Feature.class,
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FeatureTree.class,
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IndividualsAssociation.class,
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MeasurementUnit.class,
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MediaKey.class,
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MultiAccessKey.class,
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NaturalLanguageTerm.class,
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PolytomousKey.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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StatisticalMeasure.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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WorkingSet.class,
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Country.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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Media.class,
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Rights.class,
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RightsType.class,
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Amplification.class,
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AmplificationResult.class,
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Cloning.class,
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DnaSample.class,
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PhylogeneticTree.class,
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Primer.class,
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Sequence.class,
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SingleRead.class,
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BacterialName.class,
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BotanicalName.class,
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CultivarPlantName.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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NameTypeDesignationStatus.class,
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NameTypeDesignation.class,
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NomenclaturalStatus.class,
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NomenclaturalStatusType.class,
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NonViralName.class,
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Rank.class,
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SpecimenTypeDesignationStatus.class,
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SpecimenTypeDesignation.class,
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ViralName.class,
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ZoologicalName.class,
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Collection.class,
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DerivationEvent.class,
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DerivationEventType.class,
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DerivedUnit.class,
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DeterminationEvent.class,
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FieldUnit.class,
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GatheringEvent.class,
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MaterialOrMethodEvent.class,
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MediaSpecimen.class,
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PreservationMethod.class,
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Reference.class,
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Classification.class,
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Synonym.class,
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SynonymRelationship.class,
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SynonymRelationshipType.class,
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Taxon.class,
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TaxonNode.class,
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TaxonNodeAgentRelation.class,
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TaxonRelationship.class,
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TaxonRelationshipType.class,
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TermVocabulary.class,
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OrderedTermVocabulary.class,
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AnnotationType.class,
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DefinedTermBase.class,
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ExtensionType.class,
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Language.class,
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MarkerType.class,
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OrderedTerm.class,
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Annotation.class,
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Identifier.class,
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Credit.class,
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LanguageString.class,
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Representation.class,
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IdentifiableSource.class
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};
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for (Class<AnnotatableEntity> annotatableClass : annotatableClasses){
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updateSingleClass(datasource, monitor, caseType, annotatableClass);
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}
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return 0;
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} catch (Exception e) {
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monitor.warning(e.getMessage(), e);
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logger.warn(e.getMessage());
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return null;
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}
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}
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/**
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* @param datasource
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* @param monitor
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* @param caseType
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* @param annotatableClass2
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* @throws SQLException
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*/
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private void updateSingleClass(ICdmDataSource datasource, IProgressMonitor monitor,
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CaseType caseType, Class<? extends AnnotatableEntity> annotatableClass) throws SQLException {
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if (IdentifiableEntity.class.isAssignableFrom(annotatableClass)){
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updateIdentifableEntitiy(datasource, monitor, caseType, (Class<IdentifiableEntity>)annotatableClass);
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}
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updateAnnotatableEntitiy(datasource, monitor, caseType, annotatableClass);
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}
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/**
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* @param datasource
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* @param monitor
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* @param caseType
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* @param annotatableClass
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* @throws SQLException
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*/
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private void updateAnnotatableEntitiy(ICdmDataSource datasource, IProgressMonitor monitor, CaseType caseType,
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Class<? extends AnnotatableEntity> annotatableClass) throws SQLException {
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String sql, table;
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table = "Annotation";
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sql = "UPDATE @table SET annotatedObj_type = '@simpleClassName' WHERE id IN (SELECT annotations_id FROM @MnTable)";
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sql = setParameters(caseType, sql, table, annotatableClass);
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datasource.executeUpdate(sql);
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replaceAndExecute(datasource, caseType, annotatableClass, sql, table);
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table = "Marker";
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sql = "UPDATE @table SET markedObj_type = '@simpleClassName' WHERE id IN (SELECT markers_id FROM @MnTable)";
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sql = setParameters(caseType, sql, table, annotatableClass);
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datasource.executeUpdate(sql);
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}
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/**
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* @param caseType
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* @param sql
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* @param table
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* @param identifiableClass
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* @param isAudit
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* @return
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*/
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private String setParameters(CaseType caseType, String sql, String table, Class<?> identifiableClass) {
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String simpleName = identifiableClass.getSimpleName();
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Class<?> tableClass = getTable(identifiableClass);
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String tableName = tableClass.getSimpleName();
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if (tableName.equals("Rights")){
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tableName = "RightsInfo";
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}
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String casedTable = caseType.transformTo(table);
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String mnTable = caseType.transformTo(tableName + "_" + table);
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return sql.replace("@table", casedTable)
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.replace("@simpleClassName", simpleName)
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.replace("@MnTable", mnTable);
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}
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/**
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* @param datasource
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* @param monitor
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* @param caseType
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* @param annotatableClass
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* @throws SQLException
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*/
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private void updateIdentifableEntitiy(ICdmDataSource datasource, IProgressMonitor monitor, CaseType caseType,
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Class<? extends IdentifiableEntity> identifiableClass) throws SQLException {
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String sql, table;
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//credits, rights => do not have xxxObj_type field
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//, extensions, identifiers, sources
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//Extensions
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table = "Extension";
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sql = "UPDATE @table SET extendedObj_type = '@simpleClassName' WHERE id IN (SELECT extensions_id FROM @MnTable)";
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replaceAndExecute(datasource, caseType, identifiableClass, sql, table);
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//Identifier
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table = "Identifier";
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sql = "UPDATE @table SET identifiedObj_type = '@simpleClassName' WHERE id IN (SELECT identifiers_id FROM @MnTable)";
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replaceAndExecute(datasource, caseType, identifiableClass, sql, table);
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//OriginalSourceBase
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table = "OriginalSourceBase";
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sql = "UPDATE @table SET sourcedObj_type = '@simpleClassName' WHERE id IN (SELECT sources_id FROM @MnTable)";
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replaceAndExecute(datasource, caseType, identifiableClass, sql, table);
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}
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/**
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* @param datasource
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* @param caseType
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* @param annotatableClass
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* @param sql
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* @param table
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* @throws SQLException
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*/
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private void replaceAndExecute(ICdmDataSource datasource, CaseType caseType,
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Class<? extends AnnotatableEntity> annotatableClass, String sql, String table) throws SQLException {
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sql = setParameters(caseType, sql, table, annotatableClass);
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datasource.executeUpdate(sql);
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}
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/**
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* @param identifiableClass
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*/
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private Class<?> getTable(Class<?> clazz) {
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Class<?> spezificClass = specificClasses.get(clazz);
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if (spezificClass != null){
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return spezificClass;
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}else{
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boolean isAbstract = Modifier.isAbstract(clazz.getModifiers());
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if (isAbstract){
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return clazz;
|
389
|
}else{
|
390
|
Class<?> superClass = clazz.getSuperclass();
|
391
|
//MappedSuperClasses
|
392
|
if (superClass == EventBase.class
|
393
|
|| superClass == AnnotatableEntity.class
|
394
|
|| superClass == IdentifiableEntity.class
|
395
|
|| superClass == RelationshipBase.class
|
396
|
|| superClass == ReferencedEntityBase.class
|
397
|
|| superClass == IdentifiableMediaEntity.class
|
398
|
|| superClass == LanguageStringBase.class
|
399
|
) {
|
400
|
return clazz;
|
401
|
}
|
402
|
return getTable(superClass);
|
403
|
}
|
404
|
}
|
405
|
}
|
406
|
|
407
|
private static Map<Class, Class> specificClasses = new HashMap<Class, Class>();
|
408
|
static{
|
409
|
specificClasses.put(TeamOrPersonBase.class, AgentBase.class);
|
410
|
specificClasses.put(TermVocabulary.class, TermVocabulary.class);
|
411
|
specificClasses.put(TypeDesignationStatusBase.class, DefinedTermBase.class);
|
412
|
specificClasses.put(OrderedTermBase.class, DefinedTermBase.class);
|
413
|
specificClasses.put(OrderedTermVocabulary.class, TermVocabulary.class);
|
414
|
specificClasses.put(Rights.class, Rights.class);
|
415
|
specificClasses.put(RelationshipTermBase.class, DefinedTermBase.class);
|
416
|
|
417
|
|
418
|
|
419
|
|
420
|
}
|
421
|
|
422
|
}
|