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/**
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* Copyright (C) 2019 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.io.cdm2cdm;
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import java.lang.reflect.Field;
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import java.lang.reflect.InvocationTargetException;
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import java.lang.reflect.Method;
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import java.util.ArrayList;
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import java.util.Collection;
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import java.util.HashMap;
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import java.util.HashSet;
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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.logging.log4j.LogManager;
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import org.apache.logging.log4j.Logger;
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import eu.etaxonomy.cdm.api.application.CdmApplicationController;
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import eu.etaxonomy.cdm.api.application.ICdmRepository;
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import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
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import eu.etaxonomy.cdm.database.DbSchemaValidation;
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import eu.etaxonomy.cdm.database.ICdmDataSource;
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import eu.etaxonomy.cdm.database.ICdmImportSource;
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import eu.etaxonomy.cdm.io.common.CdmImportBase;
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import eu.etaxonomy.cdm.io.common.ITaxonNodeOutStreamPartitioner;
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import eu.etaxonomy.cdm.io.common.TaxonNodeOutStreamPartitioner;
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import eu.etaxonomy.cdm.io.common.TaxonNodeOutStreamPartitionerConcurrent;
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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.AnnotatableEntity;
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import eu.etaxonomy.cdm.model.common.Annotation;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.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.IIntextReferencable;
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import eu.etaxonomy.cdm.model.common.IIntextReferenceTarget;
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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.IntextReference;
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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.Marker;
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import eu.etaxonomy.cdm.model.common.MarkerType;
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import eu.etaxonomy.cdm.model.common.RelationshipBase;
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import eu.etaxonomy.cdm.model.common.SingleSourcedEntityBase;
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import eu.etaxonomy.cdm.model.common.SourcedEntityBase;
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import eu.etaxonomy.cdm.model.common.VersionableEntity;
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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.DescriptionElementSource;
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import eu.etaxonomy.cdm.model.description.DescriptiveDataSet;
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import eu.etaxonomy.cdm.model.description.Distribution;
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import eu.etaxonomy.cdm.model.description.FeatureState;
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import eu.etaxonomy.cdm.model.description.SpecimenDescription;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
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import eu.etaxonomy.cdm.model.description.TextData;
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import eu.etaxonomy.cdm.model.location.Country;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.media.ExternalLink;
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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.name.HomotypicalGroup;
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import eu.etaxonomy.cdm.model.name.HybridRelationship;
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import eu.etaxonomy.cdm.model.name.NameRelationship;
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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.Registration;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.name.TypeDesignationBase;
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import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
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import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
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import eu.etaxonomy.cdm.model.permission.User;
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import eu.etaxonomy.cdm.model.reference.NamedSource;
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import eu.etaxonomy.cdm.model.reference.NamedSourceBase;
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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.SecundumSource;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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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.TaxonNodeAgentRelation;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
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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.Representation;
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import eu.etaxonomy.cdm.model.term.TermBase;
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import eu.etaxonomy.cdm.model.term.TermCollection;
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import eu.etaxonomy.cdm.model.term.TermNode;
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import eu.etaxonomy.cdm.model.term.TermRelationBase;
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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.persistence.query.MatchMode;
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/**
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* Base class for migrating data from one CDM instance to another.
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*
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* @author a.mueller
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* @since 17.08.2019
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*/
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public abstract class Cdm2CdmImportBase
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extends CdmImportBase<Cdm2CdmImportConfigurator, Cdm2CdmImportState> {
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private static final long serialVersionUID = 1344722304369624443L;
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private static final Logger logger = LogManager.getLogger();
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//quick and dirty
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private Cdm2CdmImportState stateX;
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protected ICdmRepository sourceRepo(Cdm2CdmImportState state){
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ICdmRepository repo = state.getSourceRepository();
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if (repo == null){
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ICdmImportSource source = state.getConfig().getSource();
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if (source instanceof ICdmRepository){
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repo = (ICdmRepository)source;
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}else if (source instanceof ICdmDataSource){
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System.out.println("start source repo");
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boolean omitTermLoading = true;
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repo = CdmApplicationController.NewInstance((ICdmDataSource)source,
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DbSchemaValidation.VALIDATE, omitTermLoading);
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state.setSourceRepository(repo);
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System.out.println("end source repo");
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}else{
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throw new IllegalStateException("Unsupported ICdmImportSource type");
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}
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}
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return repo;
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}
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protected Contact detach(Contact contact, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
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contact = CdmBase.deproxy(contact);
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if (contact == null){
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return contact;
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}else{
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return handlePersistedContact(contact, state);
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}
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}
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protected IIntextReferencable detach(IIntextReferencable cdmBase, boolean onlyForDefinedSignature, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
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return (IIntextReferencable)detach((CdmBase)cdmBase, state);
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}
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protected IIntextReferenceTarget detach(IIntextReferenceTarget cdmBase, boolean onlyForDefinedSignature, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
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return (IIntextReferenceTarget)detach((CdmBase)cdmBase, state);
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}
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protected <T extends CdmBase> T detach(T cdmBase, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
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return detach(cdmBase, false, state);
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}
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protected <T extends CdmBase> T detach(T cdmBase, boolean notFromSource, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
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cdmBase = CdmBase.deproxy(cdmBase);
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if (cdmBase == null ){
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return cdmBase;
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}else if(isInCache(cdmBase, state)){
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return getCached(cdmBase, state);
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}else {
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if (state.getExistingObjects(cdmBase.getClass()) == null){
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loadExistingUuids(cdmBase.getClass(), state);
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}
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boolean exists = state.getExistingObjects(cdmBase.getClass()).contains(cdmBase.getUuid());
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if (exists){
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Class<T> clazz = (Class<T>)cdmBase.getClass();
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T existingObj = getCommonService().find(clazz, cdmBase.getUuid());
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if (existingObj != null){
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cache(existingObj, state);
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return existingObj;
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}else{
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logger.warn("Object should exist already but does not exist in target. This should not happen: " + cdmBase.getClass().getSimpleName() + "/" + cdmBase.getUuid());
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}
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}
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}
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if ( !cdmBase.isPersited()){
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logger.warn("Non persisted object not in cache and not in target DB. This should not happen: " + cdmBase.getUuid());
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return cdmBase; //should not happen anymore; either in cache or in target or persisted in source
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}else{
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return notFromSource? null : (T)handlePersisted(cdmBase, state);
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}
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}
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private Set<UUID> loadExistingUuids(Class<? extends CdmBase> clazz, Cdm2CdmImportState state) {
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List<UUID> list = getCommonService().listUuid(clazz);
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Set<UUID> result = new HashSet<>(list);
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state.putExistingObjects(clazz, result);
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return result;
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}
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protected <A extends CdmBase> CdmBase handlePersisted(A cdmBase, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
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if(cdmBase instanceof TaxonNode){
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return handlePersistedTaxonNode((TaxonNode)cdmBase, state);
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}else if(cdmBase instanceof Taxon){
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return handlePersistedTaxon((Taxon)cdmBase, state);
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}else if(cdmBase instanceof Synonym){
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return handlePersistedSynonym((Synonym)cdmBase, state);
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}else if(cdmBase instanceof TaxonName){
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return handlePersistedTaxonName((TaxonName)cdmBase, state);
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}else if(cdmBase instanceof Team){
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return handlePersistedTeam((Team)cdmBase, state);
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}else if(cdmBase instanceof Person){
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return handlePersistedPerson((Person)cdmBase, state);
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}else if(cdmBase instanceof Classification){
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return handlePersistedClassification((Classification)cdmBase, state);
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}else if(cdmBase instanceof Reference){
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return handlePersistedReference((Reference)cdmBase, state);
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}else if(cdmBase instanceof SpecimenOrObservationBase){
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return handlePersistedSpecimenOrObservationBase((SpecimenOrObservationBase)cdmBase, state);
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}else if(cdmBase instanceof IdentifiableSource){
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return handlePersistedIdentifiableSource((IdentifiableSource)cdmBase, state);
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}else if(cdmBase instanceof DescriptionElementSource){
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return handlePersistedDescriptionElementSource((DescriptionElementSource)cdmBase, state);
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}else if(cdmBase instanceof CommonTaxonName){
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return handlePersistedCommonTaxonName((CommonTaxonName)cdmBase, state);
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}else if(cdmBase instanceof Distribution){
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return handlePersistedDistribution((Distribution)cdmBase, state);
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}else if(cdmBase instanceof TextData){
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return handlePersistedTextData((TextData)cdmBase, state);
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}else if(cdmBase instanceof HomotypicalGroup){
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return handlePersistedHomotypicalGroup((HomotypicalGroup)cdmBase, state);
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}else if(cdmBase instanceof TypeDesignationBase){
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return handlePersistedTypeDesignationBase((TypeDesignationBase)cdmBase, state);
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}else if(cdmBase instanceof TaxonDescription){
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return handlePersistedTaxonDescription((TaxonDescription)cdmBase, state);
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}else if(cdmBase instanceof NomenclaturalStatus){
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return handlePersistedNomenclaturalStatus((NomenclaturalStatus)cdmBase, state);
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}else if(cdmBase instanceof TaxonNameDescription){
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return handlePersistedTaxonNameDescription((TaxonNameDescription)cdmBase, state);
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}else if(cdmBase instanceof TaxonRelationship){
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return handlePersistedTaxonRelationship((TaxonRelationship)cdmBase, state);
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}else if(cdmBase instanceof HybridRelationship){
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return handlePersistedHybridRelationship((HybridRelationship)cdmBase, state);
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}else if(cdmBase instanceof NameRelationship){
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return handlePersistedNameRelationship((NameRelationship)cdmBase, state);
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}else if(cdmBase instanceof TaxonNodeAgentRelation){
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return handlePersistedTaxonNodeAgentRelation((TaxonNodeAgentRelation)cdmBase, state);
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}else if(cdmBase instanceof User){
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return handlePersistedUser((User)cdmBase, state);
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}else if(cdmBase instanceof Extension){
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return handlePersistedExtension((Extension)cdmBase, state);
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}else if(cdmBase instanceof Marker){
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return handlePersistedMarker((Marker)cdmBase, state);
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}else if(cdmBase instanceof Annotation){
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return handlePersistedAnnotation((Annotation)cdmBase, state);
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}else if(cdmBase instanceof LanguageString){
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return handlePersistedLanguageString((LanguageString)cdmBase, state);
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}else if(cdmBase instanceof TermVocabulary){
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return handlePersistedVocabulary((TermVocabulary<?>)cdmBase, state);
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}else if(cdmBase instanceof TermTree){
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return handlePersistedTermTree((TermTree<?>)cdmBase, state);
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}else if(cdmBase instanceof NamedArea){
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return handlePersistedNamedArea((NamedArea)cdmBase, state);
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}else if(cdmBase instanceof TermNode){
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return handlePersistedTermNode((TermNode)cdmBase, state);
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}else if(cdmBase instanceof Representation){
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return handlePersistedRepresentation((Representation)cdmBase, state);
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}else if(cdmBase instanceof InstitutionalMembership){
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return handlePersistedInstitutionalMembership((InstitutionalMembership)cdmBase, state);
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}else if(cdmBase instanceof Institution){
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return handlePersistedInstitution((Institution)cdmBase, state);
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}else if(cdmBase instanceof IntextReference){
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return handlePersistedIntextReference((IntextReference)cdmBase, state);
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}else if(cdmBase instanceof ExtensionType){
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return handlePersistedExtensionType((ExtensionType)cdmBase, state);
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}else if(cdmBase instanceof NomenclaturalStatusType){
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return handlePersistedNomenclaturalStatusType((NomenclaturalStatusType)cdmBase, state);
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}else if(cdmBase instanceof MarkerType){
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return handlePersistedMarkerType((MarkerType)cdmBase, state);
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}else if(cdmBase instanceof Rights){
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return handlePersistedRights((Rights)cdmBase, state);
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}else if(cdmBase instanceof DefinedTerm){
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293
|
return handlePersistedDefinedTerm((DefinedTerm)cdmBase, state);
|
|
294
|
}else if(cdmBase instanceof DefinedTermBase){
|
|
295
|
return handlePersistedTerm((DefinedTermBase<?>)cdmBase, state);
|
|
296
|
}else {
|
|
297
|
throw new RuntimeException("Type not yet supported: " + cdmBase.getClass().getCanonicalName());
|
|
298
|
}
|
|
299
|
}
|
|
300
|
|
|
301
|
|
|
302
|
protected TaxonNode handlePersistedTaxonNode(TaxonNode node, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
303
|
|
|
304
|
TaxonNode result = handlePersisted((AnnotatableEntity)node, state);
|
|
305
|
if (result ==null){
|
|
306
|
return result;
|
|
307
|
}
|
|
308
|
//complete
|
|
309
|
handleCollection(result, TaxonNode.class, "agentRelations", TaxonNodeAgentRelation.class, state);
|
|
310
|
result.setTaxon(detach(result.getTaxon(), state));
|
|
311
|
result.setCitation(detach(node.getReference(), state));
|
|
312
|
result.setSynonymToBeUsed(detach(result.getSynonymToBeUsed(), state));
|
|
313
|
handleMap(result, TaxonNode.class, "excludedNote", Language.class, LanguageString.class, state);
|
|
314
|
//classification, parent, children
|
|
315
|
this.setInvisible(node, "classification", detach(node.getClassification(), state));
|
|
316
|
handleParentTaxonNode(result, state);
|
|
317
|
setNewCollection(node, TaxonNode.class, "childNodes", TaxonNode.class);
|
|
318
|
return result;
|
|
319
|
}
|
|
320
|
|
|
321
|
private void handleParentTaxonNode(TaxonNode childNode, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
322
|
TaxonNode parent = detach(childNode.getParent(), true, state);
|
|
323
|
//TODO
|
|
324
|
String microReference = null;
|
|
325
|
Reference reference = null;
|
|
326
|
if (parent == null && childNode.getClassification().getRootNode().equals(childNode)){
|
|
327
|
//do nothing
|
|
328
|
}else if (parent == null ){
|
|
329
|
childNode.getClassification().addChildNode(childNode, reference, microReference) ;
|
|
330
|
}else{
|
|
331
|
parent.addChildNode(childNode, reference, microReference);
|
|
332
|
}
|
|
333
|
}
|
|
334
|
|
|
335
|
protected Taxon handlePersistedTaxon(Taxon taxon, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
336
|
Taxon result = handlePersisted((TaxonBase)taxon, state);
|
|
337
|
//complete
|
|
338
|
handleCollection(result, Taxon.class, "synonyms", Synonym.class, state);
|
|
339
|
// handleCollection(result, Taxon.class, "taxonNodes", TaxonNode.class);
|
|
340
|
setNewCollection(result, Taxon.class, "taxonNodes", TaxonNode.class);
|
|
341
|
handleCollection(result, Taxon.class, "relationsFromThisTaxon", TaxonRelationship.class, state);
|
|
342
|
handleCollection(result, Taxon.class, "relationsToThisTaxon", TaxonRelationship.class, state);
|
|
343
|
if (this.doDescriptions(state)){
|
|
344
|
handleCollection(result, Taxon.class, "descriptions", TaxonDescription.class, state);
|
|
345
|
}else{
|
|
346
|
setNewCollection(result, Taxon.class, "descriptions", TaxonDescription.class);
|
|
347
|
}
|
|
348
|
return result;
|
|
349
|
}
|
|
350
|
|
|
351
|
protected boolean doDescriptions(Cdm2CdmImportState state) {
|
|
352
|
return false;
|
|
353
|
}
|
|
354
|
|
|
355
|
protected Synonym handlePersistedSynonym(Synonym synonym, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
356
|
Synonym result = handlePersisted((TaxonBase)synonym, state);
|
|
357
|
//complete
|
|
358
|
setInvisible(result, "acceptedTaxon", detach(result.getAcceptedTaxon(), state));
|
|
359
|
result.setType(detach(result.getType(), state));
|
|
360
|
return result;
|
|
361
|
}
|
|
362
|
|
|
363
|
protected TaxonRelationship handlePersistedTaxonRelationship(TaxonRelationship taxRel, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
364
|
TaxonRelationship result = handlePersisted((RelationshipBase)taxRel, state);
|
|
365
|
//complete
|
|
366
|
result.setFromTaxon(detach(result.getFromTaxon(), state));
|
|
367
|
result.setToTaxon(detach(result.getToTaxon(), state));
|
|
368
|
result.setType(detach(result.getType(), state));
|
|
369
|
return result;
|
|
370
|
}
|
|
371
|
|
|
372
|
protected NameRelationship handlePersistedNameRelationship(NameRelationship rel, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
373
|
NameRelationship result = handlePersisted((RelationshipBase)rel, state);
|
|
374
|
//complete
|
|
375
|
setInvisible(result, "relatedFrom", detach(result.getFromName(), state));
|
|
376
|
setInvisible(result, "relatedTo", detach(result.getToName(), state));
|
|
377
|
// result.setFromName(detache(result.getFromName(), state));
|
|
378
|
// result.setToName(detache(result.getToName(), state));
|
|
379
|
result.setType(detach(result.getType(), state));
|
|
380
|
return result;
|
|
381
|
}
|
|
382
|
|
|
383
|
protected HybridRelationship handlePersistedHybridRelationship(HybridRelationship rel, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
384
|
HybridRelationship result = handlePersisted((RelationshipBase)rel, state);
|
|
385
|
//complete
|
|
386
|
setInvisible(result, "relatedFrom", detach(result.getParentName(), state));
|
|
387
|
setInvisible(result, "relatedTo", detach(result.getHybridName(), state));
|
|
388
|
// result.setFromName(detache(result.getFromName()));
|
|
389
|
// result.setToName(detache(result.getToName()));
|
|
390
|
result.setType(detach(result.getType(), state));
|
|
391
|
return result;
|
|
392
|
}
|
|
393
|
|
|
394
|
protected NomenclaturalStatus handlePersistedNomenclaturalStatus(NomenclaturalStatus status, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
395
|
NomenclaturalStatus result = handlePersisted((SingleSourcedEntityBase)status, state);
|
|
396
|
//complete
|
|
397
|
result.setType(detach(result.getType(), state));
|
|
398
|
return result;
|
|
399
|
}
|
|
400
|
|
|
401
|
protected TypeDesignationBase handlePersistedTypeDesignationBase(TypeDesignationBase<?> designation, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
402
|
TypeDesignationBase result = handlePersisted((SourcedEntityBase)designation, state);
|
|
403
|
//complete
|
|
404
|
result.setCitation(detach(result.getCitation(), state));
|
|
405
|
handleCollection(result, TypeDesignationBase.class, "registrations", Registration.class, state);
|
|
406
|
handleCollection(result, TypeDesignationBase.class, "typifiedNames", TaxonName.class, state);
|
|
407
|
result.setTypeStatus(detach(result.getTypeStatus(), state));
|
|
408
|
return result;
|
|
409
|
}
|
|
410
|
|
|
411
|
protected InstitutionalMembership handlePersistedInstitutionalMembership(InstitutionalMembership institutionalMembership, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
412
|
InstitutionalMembership result = handlePersisted((VersionableEntity)institutionalMembership, state);
|
|
413
|
//complete
|
|
414
|
// result.setPerson(detache(result.getPerson()));
|
|
415
|
setInvisible(result, "person", detach(result.getPerson(), state));
|
|
416
|
result.setInstitute(detach(result.getInstitute(), state));
|
|
417
|
return result;
|
|
418
|
}
|
|
419
|
|
|
420
|
protected Institution handlePersistedInstitution(Institution institution, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
421
|
Institution result = handlePersisted((AgentBase)institution, state);
|
|
422
|
//complete
|
|
423
|
result.setIsPartOf(detach(result.getIsPartOf(), state));
|
|
424
|
handleCollection(result, Institution.class, "types", DefinedTerm.class, state);
|
|
425
|
return result;
|
|
426
|
}
|
|
427
|
|
|
428
|
protected TaxonNodeAgentRelation handlePersistedTaxonNodeAgentRelation(TaxonNodeAgentRelation nodeAgentRel, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
429
|
TaxonNodeAgentRelation result = handlePersisted((AnnotatableEntity)nodeAgentRel, state);
|
|
430
|
//complete
|
|
431
|
result.setAgent(detach(result.getAgent(), state));
|
|
432
|
result.setType(detach(result.getType(), state));
|
|
433
|
setInvisible(result, "taxonNode", detach(result.getTaxonNode(), state));
|
|
434
|
return result;
|
|
435
|
}
|
|
436
|
|
|
437
|
|
|
438
|
protected TaxonName handlePersistedTaxonName(TaxonName taxonName, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
439
|
@SuppressWarnings("rawtypes")
|
|
440
|
TaxonName result = handlePersisted((IdentifiableEntity)taxonName, state);
|
|
441
|
//complete
|
|
442
|
result.setRank(detach(result.getRank(), state));
|
|
443
|
result.setCombinationAuthorship(detach(result.getCombinationAuthorship(), state));
|
|
444
|
result.setExCombinationAuthorship(detach(result.getExCombinationAuthorship(), state));
|
|
445
|
result.setBasionymAuthorship(detach(result.getBasionymAuthorship(), state));
|
|
446
|
result.setExBasionymAuthorship(detach(result.getExBasionymAuthorship(), state));
|
|
447
|
result.setInBasionymAuthorship(detach(result.getInBasionymAuthorship(), state));
|
|
448
|
result.setInCombinationAuthorship(detach(result.getInCombinationAuthorship(), state));
|
|
449
|
|
|
450
|
result.setNomenclaturalReference(detach(result.getNomenclaturalReference(), state));
|
|
451
|
result.setNomenclaturalSource(detach(result.getNomenclaturalSource(), state));
|
|
452
|
result.setHomotypicalGroup(detach(result.getHomotypicalGroup(), state));
|
|
453
|
handleCollection(result, TaxonName.class, "descriptions", TaxonNameDescription.class, state);
|
|
454
|
handleCollection(result, TaxonName.class, "hybridChildRelations", HybridRelationship.class, state);
|
|
455
|
handleCollection(result, TaxonName.class, "hybridParentRelations", HybridRelationship.class, state);
|
|
456
|
handleCollection(result, TaxonName.class, "relationsFromThisName", NameRelationship.class, state);
|
|
457
|
handleCollection(result, TaxonName.class, "relationsToThisName", NameRelationship.class, state);
|
|
458
|
handleCollection(result, TaxonName.class, "status", NomenclaturalStatus.class, state);
|
|
459
|
|
|
460
|
handleCollection(result, TaxonName.class, "registrations", Registration.class, state);
|
|
461
|
handleCollection(result, TaxonName.class, "typeDesignations", TypeDesignationBase.class, state);
|
|
462
|
|
|
463
|
handleCollection(result, TaxonName.class, "taxonBases", TaxonBase.class, state);
|
|
464
|
|
|
465
|
return result;
|
|
466
|
}
|
|
467
|
|
|
468
|
protected HomotypicalGroup handlePersistedHomotypicalGroup(HomotypicalGroup group, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
469
|
HomotypicalGroup result = handlePersisted((AnnotatableEntity)group, state);
|
|
470
|
//complete
|
|
471
|
handleCollection(result, HomotypicalGroup.class, "typifiedNames", TaxonName.class, state);
|
|
472
|
return result;
|
|
473
|
}
|
|
474
|
|
|
475
|
protected Annotation handlePersistedAnnotation(Annotation annotation, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
476
|
Annotation result = handlePersisted((AnnotatableEntity)annotation, state);
|
|
477
|
//complete
|
|
478
|
result.setAnnotationType(detach(annotation.getAnnotationType(), state));
|
|
479
|
result.setCommentator(detach(result.getCommentator(), state));
|
|
480
|
handleCollection(result, Annotation.class, "intextReferences", IntextReference.class, state);
|
|
481
|
return result;
|
|
482
|
}
|
|
483
|
|
|
484
|
protected Extension handlePersistedExtension(Extension extension, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
485
|
Extension result = handlePersisted((VersionableEntity)extension, state);
|
|
486
|
//complete
|
|
487
|
result.setType(detach(extension.getType(), state));
|
|
488
|
return result;
|
|
489
|
}
|
|
490
|
|
|
491
|
protected Marker handlePersistedMarker(Marker marker, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
492
|
Marker result = handlePersisted((VersionableEntity)marker, state);
|
|
493
|
//complete
|
|
494
|
result.setMarkerType(detach(marker.getMarkerType(), state));
|
|
495
|
return result;
|
|
496
|
}
|
|
497
|
|
|
498
|
protected Team handlePersistedTeam(Team team, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
499
|
Team result = handlePersisted((TeamOrPersonBase)team, state);
|
|
500
|
//complete
|
|
501
|
handleCollection(result, Team.class, "teamMembers", Person.class, state);
|
|
502
|
return result;
|
|
503
|
}
|
|
504
|
|
|
505
|
protected Contact handlePersistedContact(Contact contact, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
506
|
Contact result = contact; // getTarget(contact);
|
|
507
|
if (result ==null){
|
|
508
|
return result;
|
|
509
|
}
|
|
510
|
if (!contact.getAddresses().isEmpty() || !contact.getEmailAddresses().isEmpty()
|
|
511
|
|| !contact.getFaxNumbers().isEmpty() ||!contact.getPhoneNumbers().isEmpty()
|
|
512
|
||!contact.getUrls().isEmpty()){
|
|
513
|
logger.warn("Addresses not yet implemented");
|
|
514
|
}
|
|
515
|
setInvisible(result, "addresses", new HashSet<>());
|
|
516
|
// handleCollection(result, Contact.class, "", Address.class);
|
|
517
|
setInvisible(result, "faxNumbers", new ArrayList<>());
|
|
518
|
setInvisible(result, "phoneNumbers", new ArrayList<>());
|
|
519
|
setInvisible(result, "emailAddresses", new ArrayList<>());
|
|
520
|
setInvisible(result, "urls", new ArrayList<>());
|
|
521
|
return result;
|
|
522
|
}
|
|
523
|
|
|
524
|
protected Person handlePersistedPerson(Person person, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
525
|
Person result = handlePersisted((TeamOrPersonBase)person, state);
|
|
526
|
//complete
|
|
527
|
handleCollection(result, Person.class, "institutionalMemberships", InstitutionalMembership.class, state);
|
|
528
|
return result;
|
|
529
|
}
|
|
530
|
|
|
531
|
protected NamedArea handlePersistedNamedArea(NamedArea area, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
532
|
NamedArea result = handlePersisted((OrderedTermBase)area, state);
|
|
533
|
//complete
|
|
534
|
handleCollection(result, NamedArea.class, "countries", Country.class, state);
|
|
535
|
result.setLevel(detach(result.getLevel(), state));
|
|
536
|
result.setType(detach(result.getType(), state));
|
|
537
|
result.setShape(detach(result.getShape(), state));
|
|
538
|
return result;
|
|
539
|
}
|
|
540
|
|
|
541
|
protected Classification handlePersistedClassification(Classification classification, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
542
|
Classification result = handlePersisted((IdentifiableEntity)classification, state);
|
|
543
|
//complete
|
|
544
|
result.setName(detach(classification.getName(), state));
|
|
545
|
result.setReference(detach(classification.getReference(), state));
|
|
546
|
result.setRootNode(detach(classification.getRootNode(), state));
|
|
547
|
handleCollection(result, Classification.class, "geoScopes", NamedArea.class, state);
|
|
548
|
handleMap(result, Classification.class, "description", Language.class, LanguageString.class, state);
|
|
549
|
return result;
|
|
550
|
}
|
|
551
|
|
|
552
|
protected Reference handlePersistedReference(Reference reference, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
553
|
Reference result = handlePersisted((IdentifiableMediaEntity)reference, state);
|
|
554
|
result.setAuthorship(detach(result.getAuthorship(), state));
|
|
555
|
result.setInstitution(detach(result.getInstitution(), state));
|
|
556
|
result.setSchool(detach(result.getSchool(), state));
|
|
557
|
result.setInReference(detach(result.getInReference(), state));
|
|
558
|
return result;
|
|
559
|
}
|
|
560
|
|
|
561
|
protected SpecimenOrObservationBase<?> handlePersistedSpecimenOrObservationBase(SpecimenOrObservationBase specimen, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
562
|
//TODO implement for classes
|
|
563
|
SpecimenOrObservationBase<?> result = handlePersisted((IdentifiableEntity)specimen, state);
|
|
564
|
//complete
|
|
565
|
result.setSex(detach(result.getSex(), state));
|
|
566
|
result.setLifeStage(detach(result.getLifeStage(), state));
|
|
567
|
result.setKindOfUnit(detach(result.getKindOfUnit(), state));
|
|
568
|
handleCollection(result, SpecimenOrObservationBase.class, "determinations", DeterminationEvent.class, state);
|
|
569
|
handleCollection(result, SpecimenOrObservationBase.class, "descriptions", SpecimenDescription.class, state);
|
|
570
|
handleCollection(result, SpecimenOrObservationBase.class, "derivationEvents", DerivationEvent.class, state);
|
|
571
|
handleMap(result, SpecimenOrObservationBase.class, "definition", Language.class, LanguageString.class, state);
|
|
572
|
return result;
|
|
573
|
}
|
|
574
|
|
|
575
|
protected IdentifiableSource handlePersistedIdentifiableSource(IdentifiableSource source, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
576
|
IdentifiableSource result = handlePersisted((OriginalSourceBase)source, state);
|
|
577
|
//complete
|
|
578
|
return result;
|
|
579
|
}
|
|
580
|
|
|
581
|
protected <T extends NamedSourceBase> T handlePersisted(NamedSourceBase source, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
582
|
T result = handlePersisted((OriginalSourceBase)source, state);
|
|
583
|
//complete
|
|
584
|
result.setNameUsedInSource(detach(result.getNameUsedInSource(), state));
|
|
585
|
return result;
|
|
586
|
}
|
|
587
|
|
|
588
|
protected NamedSource handlePersistedNamedSource(NamedSource source, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
589
|
NamedSource result = handlePersisted((NamedSourceBase)source, state);
|
|
590
|
//complete
|
|
591
|
return result;
|
|
592
|
}
|
|
593
|
|
|
594
|
protected SecundumSource handlePersistedSecundumSource(DescriptionElementSource source, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
595
|
SecundumSource result = handlePersisted((NamedSourceBase)source, state);
|
|
596
|
//TODO correct?
|
|
597
|
result.setSourcedTaxon(detach(result.getSourcedTaxon(), state));
|
|
598
|
return result;
|
|
599
|
}
|
|
600
|
|
|
601
|
protected DescriptionElementSource handlePersistedDescriptionElementSource(DescriptionElementSource source, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
602
|
DescriptionElementSource result = handlePersisted((NamedSourceBase)source, state);
|
|
603
|
//TODO correct?
|
|
604
|
detach(result.getSourcedElement(), state).addSource(result);
|
|
605
|
return result;
|
|
606
|
}
|
|
607
|
|
|
608
|
protected <T extends CommonTaxonName> T handlePersistedCommonTaxonName(CommonTaxonName element, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
609
|
T result = handlePersisted((DescriptionElementBase)element, state);
|
|
610
|
//complete
|
|
611
|
result.setLanguage(detach(result.getLanguage(), state));
|
|
612
|
result.setArea(detach(result.getArea(), state));
|
|
613
|
return result;
|
|
614
|
}
|
|
615
|
|
|
616
|
protected <T extends TextData> T handlePersistedTextData(TextData element, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
617
|
T result = handlePersisted((DescriptionElementBase)element, state);
|
|
618
|
//complete
|
|
619
|
result.setFormat(detach(result.getFormat(), state));
|
|
620
|
handleMap(result, TextData.class, "multilanguageText", Language.class, LanguageString.class, state);
|
|
621
|
return result;
|
|
622
|
}
|
|
623
|
|
|
624
|
protected <T extends Distribution> T handlePersistedDistribution(Distribution element, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
625
|
T result = handlePersisted((DescriptionElementBase)element, state);
|
|
626
|
//complete
|
|
627
|
result.setArea(detach(result.getArea(), state));
|
|
628
|
result.setStatus(detach(result.getStatus(), state));
|
|
629
|
return result;
|
|
630
|
}
|
|
631
|
|
|
632
|
protected ExtensionType handlePersistedExtensionType(ExtensionType term, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
633
|
ExtensionType result = handlePersisted((DefinedTermBase)term, state);
|
|
634
|
//complete
|
|
635
|
return result;
|
|
636
|
}
|
|
637
|
|
|
638
|
protected MarkerType handlePersistedMarkerType(MarkerType term, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
639
|
MarkerType result = handlePersisted((DefinedTermBase)term, state);
|
|
640
|
//complete
|
|
641
|
return result;
|
|
642
|
}
|
|
643
|
|
|
644
|
protected NomenclaturalStatusType handlePersistedNomenclaturalStatusType(NomenclaturalStatusType term, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
645
|
NomenclaturalStatusType result = handlePersisted((OrderedTermBase)term, state);
|
|
646
|
//complete
|
|
647
|
return result;
|
|
648
|
}
|
|
649
|
|
|
650
|
protected DefinedTerm handlePersistedDefinedTerm(DefinedTerm term, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
651
|
DefinedTerm result = handlePersisted((DefinedTermBase)term, state);
|
|
652
|
//complete
|
|
653
|
return result;
|
|
654
|
}
|
|
655
|
|
|
656
|
//placeholder for not implemented methods for subclasses
|
|
657
|
protected DefinedTermBase<?> handlePersistedTerm(DefinedTermBase term, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
658
|
DefinedTermBase<?> result = handlePersisted(term, state);
|
|
659
|
logger.warn("Class not yet handled: " + term.getClass().getSimpleName());
|
|
660
|
return result;
|
|
661
|
}
|
|
662
|
|
|
663
|
protected TermVocabulary<?> handlePersistedVocabulary(TermVocabulary voc, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
664
|
TermVocabulary<?> result = (TermVocabulary<?>)handlePersisted((TermCollection)voc, state);
|
|
665
|
handleCollection(result, TermVocabulary.class, "terms", DefinedTermBase.class, state);
|
|
666
|
return result;
|
|
667
|
}
|
|
668
|
|
|
669
|
protected TermTree<?> handlePersistedTermTree(TermTree tree, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
670
|
//TODO TermGraphBase is still missing
|
|
671
|
TermTree<?> result = (TermTree<?>)handlePersisted((TermCollection)tree, state);
|
|
672
|
//complete
|
|
673
|
result.getRoot().setUuid(tree.getRoot().getUuid());
|
|
674
|
return result;
|
|
675
|
}
|
|
676
|
|
|
677
|
protected TermNode<?> handlePersistedTermNode(TermNode node, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
678
|
TermNode<?> result = (TermNode<?>)handlePersisted((TermRelationBase)node, state);
|
|
679
|
//complete
|
|
680
|
setInvisible(result, "parent", detach(result.getParent(), state));
|
|
681
|
handleCollection(result, TermNode.class, "inapplicableIf", FeatureState.class, state);
|
|
682
|
handleCollection(result, TermNode.class, "onlyApplicableIf", FeatureState.class, state);
|
|
683
|
handleCollection(result, TermNode.class, "children", TermNode.class, state);
|
|
684
|
|
|
685
|
return result;
|
|
686
|
}
|
|
687
|
|
|
688
|
protected Representation handlePersistedRepresentation(Representation representation, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
689
|
Representation result = (Representation)handlePersisted((LanguageStringBase)representation, state);
|
|
690
|
return result;
|
|
691
|
}
|
|
692
|
|
|
693
|
protected <T extends TermBase> T handlePersisted(TermBase termBase, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
694
|
T result = handlePersisted((IdentifiableEntity)termBase, state);
|
|
695
|
//complete
|
|
696
|
handleCollection(result, TermBase.class, "representations", Representation.class, state);
|
|
697
|
return result;
|
|
698
|
}
|
|
699
|
|
|
700
|
protected <T extends TermCollection> T handlePersisted(TermCollection termCollection, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
701
|
T result = handlePersisted((TermBase)termCollection, state);
|
|
702
|
//complete
|
|
703
|
handleCollection(result, TermCollection.class, "termRelations", TermRelationBase.class, state);
|
|
704
|
return result;
|
|
705
|
}
|
|
706
|
|
|
707
|
protected <T extends TermRelationBase> T handlePersisted(TermRelationBase termRelationBase, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
708
|
T result = handlePersisted((VersionableEntity)termRelationBase, state);
|
|
709
|
result.setTerm(detach(result.getTerm(), state));
|
|
710
|
setInvisible(result, TermRelationBase.class, "graph", detach(result.getGraph(), state));
|
|
711
|
return result;
|
|
712
|
}
|
|
713
|
|
|
714
|
protected User handlePersistedUser(User user, Cdm2CdmImportState state) throws NoSuchFieldException, SecurityException, IllegalArgumentException, IllegalAccessException, InvocationTargetException, NoSuchMethodException {
|
|
715
|
User result = (User)handlePersistedCdmBase(user, state);
|
|
716
|
if (result.getUsername().equals("admin")){
|
|
717
|
//TODO why only admin, is this not a problem for all duplicated usernames? Was this a preliminary decision?
|
|
718
|
result = getUserService().listByUsername("admin", MatchMode.EXACT, null, null, null, null, null).iterator().next();
|
|
719
|
state.putPermanent(user.getUuid(), result);
|
|
720
|
cache(result, state); //necessary?
|
|
721
|
state.addToSave(result);
|
|
722
|
state.removeToSave(user);
|
|
723
|
}
|
|
724
|
if (!result.isPersited()){
|
|
725
|
result.setAuthorities(new HashSet<>());
|
|
726
|
result.setGrantedAuthorities(new HashSet<>());
|
|
727
|
setInvisible(result, "groups", new HashSet<>());
|
|
728
|
}
|
|
729
|
result.setPerson(detach(user.getPerson(), state));
|
|
730
|
return result;
|
|
731
|
}
|
|
732
|
|
|
733
|
|
|
734
|
protected LanguageString handlePersistedLanguageString(LanguageString languageString, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
735
|
LanguageString result = handlePersisted((LanguageStringBase)languageString, state);
|
|
736
|
//complete
|
|
737
|
handleCollection(result, LanguageString.class, "intextReferences", IntextReference.class, state);
|
|
738
|
return result;
|
|
739
|
}
|
|
740
|
|
|
741
|
protected Rights handlePersistedRights(Rights rights, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
742
|
Rights result = handlePersisted((LanguageStringBase)rights, state);
|
|
743
|
result.setAgent(detach(rights.getAgent(), state));
|
|
744
|
result.setType(detach(rights.getType(), state));
|
|
745
|
//complete
|
|
746
|
return result;
|
|
747
|
}
|
|
748
|
|
|
749
|
protected IntextReference handlePersistedIntextReference(IntextReference intextReference, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
750
|
IntextReference result = handlePersisted((VersionableEntity)intextReference, state);
|
|
751
|
result.setReferencedEntity(detach(result.getReferencedEntity(), false, state));
|
|
752
|
Method targetMethod = IntextReference.class.getDeclaredMethod("setTarget", IIntextReferenceTarget.class);
|
|
753
|
targetMethod.setAccessible(true);
|
|
754
|
targetMethod.invoke(result, detach(result.getTarget(), false, state));
|
|
755
|
return result;
|
|
756
|
}
|
|
757
|
|
|
758
|
protected <T extends TaxonDescription> T handlePersistedTaxonDescription(TaxonDescription taxDescription, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
759
|
T result = handlePersisted((DescriptionBase)taxDescription, state);
|
|
760
|
//complete
|
|
761
|
setInvisible(taxDescription, "taxon", detach(taxDescription.getTaxon(), state));
|
|
762
|
handleCollection(taxDescription, TaxonDescription.class, "geoScopes", NamedArea.class, state);
|
|
763
|
handleCollection(taxDescription, TaxonDescription.class, "scopes", DefinedTerm.class, state);
|
|
764
|
return result;
|
|
765
|
}
|
|
766
|
|
|
767
|
protected <T extends TaxonDescription> T handlePersistedTaxonNameDescription(TaxonNameDescription nameDescription, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
768
|
T result = handlePersisted((DescriptionBase)nameDescription, state);
|
|
769
|
//complete
|
|
770
|
setInvisible(nameDescription, "taxonName", detach(nameDescription.getTaxonName(), state));
|
|
771
|
return result;
|
|
772
|
}
|
|
773
|
|
|
774
|
|
|
775
|
// ***************************** BASE CLASSES ********************************************/
|
|
776
|
|
|
777
|
protected <T extends CdmBase> T handlePersistedCdmBase(CdmBase cdmBase, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
778
|
T result = (T)getTarget(cdmBase, state);
|
|
779
|
//complete
|
|
780
|
cdmBase.setCreatedBy(makeCreatedUpdatedBy(cdmBase.getCreatedBy(), state, false));
|
|
781
|
return result;
|
|
782
|
}
|
|
783
|
|
|
784
|
protected <T extends VersionableEntity> T handlePersisted(VersionableEntity entity, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
785
|
T result = (T)handlePersistedCdmBase((CdmBase)entity, state);
|
|
786
|
//complete
|
|
787
|
entity.setUpdatedBy(makeCreatedUpdatedBy(entity.getUpdatedBy(), state, true));
|
|
788
|
return result;
|
|
789
|
}
|
|
790
|
|
|
791
|
protected <T extends AnnotatableEntity> T handlePersisted(AnnotatableEntity entity, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
792
|
T result = handlePersisted((VersionableEntity)entity, state);
|
|
793
|
//complete
|
|
794
|
handleCollection(result, AnnotatableEntity.class, "annotations", Annotation.class, state);
|
|
795
|
handleCollection(result, AnnotatableEntity.class, "markers", Marker.class, state);
|
|
796
|
return result;
|
|
797
|
}
|
|
798
|
|
|
799
|
protected <T extends SourcedEntityBase<?>> T handlePersisted(SourcedEntityBase sourcedEntity,
|
|
800
|
Cdm2CdmImportState state)
|
|
801
|
throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
802
|
int originalId = sourcedEntity.getId();
|
|
803
|
T result = handlePersisted((AnnotatableEntity)sourcedEntity, state);
|
|
804
|
//complete
|
|
805
|
handleCollection(result, SourcedEntityBase.class, "sources", OriginalSourceBase.class, state);
|
|
806
|
if (!result.isPersited()){
|
|
807
|
if(state.getConfig().isRemoveImportSources()){
|
|
808
|
filterImportSources(result.getSources());
|
|
809
|
}
|
|
810
|
if (state.getConfig().isAddSources()){
|
|
811
|
Reference sourceRef = getSourceReference(state);
|
|
812
|
OriginalSourceBase newSource = result.addImportSource(String.valueOf(originalId), sourcedEntity.getClass().getSimpleName(),
|
|
813
|
sourceRef, null);
|
|
814
|
getCommonService().save(newSource);
|
|
815
|
addExistingObject(newSource, state);
|
|
816
|
}
|
|
817
|
}
|
|
818
|
return result;
|
|
819
|
}
|
|
820
|
|
|
821
|
/**
|
|
822
|
* @param sources
|
|
823
|
*/
|
|
824
|
private void filterImportSources(Set<? extends OriginalSourceBase> sources) {
|
|
825
|
Set<OriginalSourceBase> toDelete = new HashSet<>();
|
|
826
|
for (OriginalSourceBase osb: sources){
|
|
827
|
if (osb.getType() == OriginalSourceType.Import){
|
|
828
|
toDelete.add(osb);
|
|
829
|
}
|
|
830
|
}
|
|
831
|
for (OriginalSourceBase osb: toDelete){
|
|
832
|
sources.remove(osb);
|
|
833
|
}
|
|
834
|
}
|
|
835
|
|
|
836
|
protected <T extends IdentifiableEntity> T handlePersisted(IdentifiableEntity identifiableEntity, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
837
|
T result = handlePersisted((SourcedEntityBase)identifiableEntity, state);
|
|
838
|
//complete
|
|
839
|
handleCollection(result, IdentifiableEntity.class, "credits", Credit.class, state);
|
|
840
|
handleCollection(result, IdentifiableEntity.class, "extensions", Extension.class, state);
|
|
841
|
handleCollection(result, IdentifiableEntity.class, "identifiers", Identifier.class, state);
|
|
842
|
handleCollection(result, IdentifiableEntity.class, "rights", Rights.class, state);
|
|
843
|
handleCollection(result, IdentifiableEntity.class, "links", ExternalLink.class, state);
|
|
844
|
|
|
845
|
return result;
|
|
846
|
}
|
|
847
|
|
|
848
|
protected <T extends DefinedTermBase> T handlePersisted(DefinedTermBase definedTermBase, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
849
|
T result = handlePersisted((TermBase)definedTermBase, state);
|
|
850
|
//complete
|
|
851
|
handleCollection(result, DefinedTermBase.class, "media", Media.class, state);
|
|
852
|
handleCollection(result, DefinedTermBase.class, "generalizationOf", DefinedTermBase.class, state);
|
|
853
|
handleCollection(result, DefinedTermBase.class, "includes", DefinedTermBase.class, state);
|
|
854
|
result.setKindOf(detach(result.getKindOf(), state));
|
|
855
|
result.setPartOf(detach(result.getPartOf(), state));
|
|
856
|
setInvisible(result, DefinedTermBase.class, "vocabulary", detach(result.getVocabulary(), state));
|
|
857
|
|
|
858
|
return result;
|
|
859
|
}
|
|
860
|
|
|
861
|
protected <T extends OriginalSourceBase> T handlePersisted(OriginalSourceBase source, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
862
|
T result = handlePersisted((AnnotatableEntity)source, state);
|
|
863
|
//complete
|
|
864
|
result.setCitation(detach(result.getCitation(), state));
|
|
865
|
handleCollection(result, OriginalSourceBase.class, "links", ExternalLink.class, state);
|
|
866
|
return result;
|
|
867
|
}
|
|
868
|
|
|
869
|
protected <T extends LanguageStringBase> T handlePersisted(LanguageStringBase lsBase, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
870
|
T result = handlePersisted((AnnotatableEntity)lsBase, state);
|
|
871
|
//complete
|
|
872
|
result.setLanguage(detach(lsBase.getLanguage(), state));
|
|
873
|
return result;
|
|
874
|
}
|
|
875
|
|
|
876
|
protected <T extends TeamOrPersonBase> T handlePersisted(TeamOrPersonBase teamOrPerson, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
877
|
T result = handlePersisted((AgentBase)teamOrPerson, state);
|
|
878
|
//complete
|
|
879
|
return result;
|
|
880
|
}
|
|
881
|
|
|
882
|
protected <T extends AgentBase> T handlePersisted(AgentBase agent, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
883
|
T result = handlePersisted((IdentifiableMediaEntity)agent, state);
|
|
884
|
result.setContact(detach(result.getContact(), state));
|
|
885
|
//complete
|
|
886
|
return result;
|
|
887
|
}
|
|
888
|
|
|
889
|
protected <T extends TaxonBase> T handlePersisted(TaxonBase taxonBase, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
890
|
T result = handlePersisted((IdentifiableEntity)taxonBase, state);
|
|
891
|
//complete
|
|
892
|
result.setName(detach(taxonBase.getName(), state));
|
|
893
|
result.setSec(detach(taxonBase.getSec(), state));
|
|
894
|
return result;
|
|
895
|
}
|
|
896
|
|
|
897
|
protected <T extends IdentifiableMediaEntity> T handlePersisted(IdentifiableMediaEntity mediaEntity, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
898
|
T result = handlePersisted((IdentifiableEntity)mediaEntity, state);
|
|
899
|
//complete
|
|
900
|
handleCollection(result, IdentifiableMediaEntity.class, "media", Media.class, state);
|
|
901
|
return result;
|
|
902
|
}
|
|
903
|
|
|
904
|
protected <T extends SingleSourcedEntityBase> T handlePersisted(SingleSourcedEntityBase referencedEntity, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
905
|
T result = handlePersisted((AnnotatableEntity)referencedEntity, state);
|
|
906
|
//complete
|
|
907
|
result.setCitation(detach(result.getCitation(), state));
|
|
908
|
return result;
|
|
909
|
}
|
|
910
|
|
|
911
|
protected <T extends DescriptionBase> T handlePersisted(DescriptionBase descriptionBase, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
912
|
T result = handlePersisted((IdentifiableEntity)descriptionBase, state);
|
|
913
|
//complete
|
|
914
|
handleCollection(result, DescriptionBase.class, "descriptionElements", DescriptionElementBase.class, state);
|
|
915
|
handleCollection(result, DescriptionBase.class, "descriptiveDataSets", DescriptiveDataSet.class, state);
|
|
916
|
handleCollection(result, DescriptionBase.class, "descriptionSources", Reference.class, state);
|
|
917
|
result.setDescribedSpecimenOrObservation(detach(descriptionBase.getDescribedSpecimenOrObservation(), state));
|
|
918
|
return result;
|
|
919
|
}
|
|
920
|
|
|
921
|
protected <T extends DescriptionElementBase> T handlePersisted(DescriptionElementBase element, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
922
|
T result = handlePersisted((AnnotatableEntity)element, state);
|
|
923
|
//complete
|
|
924
|
result.setFeature(detach(result.getFeature(), state));
|
|
925
|
setInvisible(result, DescriptionElementBase.class, "inDescription", detach(result.getInDescription(), state));
|
|
926
|
handleCollection(result, DescriptionElementBase.class, "sources", DescriptionElementSource.class, state);
|
|
927
|
handleCollection(result, DescriptionElementBase.class, "media", Media.class, state);
|
|
928
|
handleCollection(result, DescriptionElementBase.class, "modifiers", DefinedTerm.class, state);
|
|
929
|
handleMap(result, DescriptionElementBase.class, "modifyingText", Language.class, LanguageString.class, state);
|
|
930
|
|
|
931
|
return result;
|
|
932
|
}
|
|
933
|
|
|
934
|
protected <T extends RelationshipBase> T handlePersisted(RelationshipBase relBase, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
935
|
T result = handlePersisted((SingleSourcedEntityBase)relBase, state);
|
|
936
|
return result;
|
|
937
|
}
|
|
938
|
|
|
939
|
|
|
940
|
//************************** COLLECTIONS / MAPS ****************************************/
|
|
941
|
|
|
942
|
protected <HOLDER extends CdmBase, ITEM extends CdmBase> void handleCollection(
|
|
943
|
HOLDER holder, Class<? super HOLDER> declaringClass, String parameter, Class<ITEM> itemClass,
|
|
944
|
Cdm2CdmImportState state)
|
|
945
|
throws NoSuchFieldException, IllegalAccessException, InvocationTargetException, NoSuchMethodException {
|
|
946
|
|
|
947
|
Collection<ITEM> oldCollection = setNewCollection(holder, declaringClass, parameter, itemClass);
|
|
948
|
Collection<ITEM> newCollection = getTargetCollection(itemClass, oldCollection, state);
|
|
949
|
Field field = declaringClass.getDeclaredField(parameter);
|
|
950
|
field.setAccessible(true);
|
|
951
|
field.set(holder, newCollection);
|
|
952
|
}
|
|
953
|
|
|
954
|
protected <HOLDER extends CdmBase, KEY extends CdmBase, ITEM extends CdmBase>
|
|
955
|
void handleMap(
|
|
956
|
HOLDER holder, Class<? super HOLDER> declaringClass, String parameter,
|
|
957
|
Class<KEY> keyClass, Class<ITEM> itemClass, Cdm2CdmImportState state)
|
|
958
|
throws NoSuchFieldException, IllegalAccessException, InvocationTargetException, NoSuchMethodException {
|
|
959
|
|
|
960
|
//TODO we do not need to set the new map 2x
|
|
961
|
Map<KEY,ITEM> oldMap = setNewMap(holder, declaringClass, parameter, keyClass, itemClass);
|
|
962
|
Map<KEY,ITEM> newMap = getTargetMap(oldMap, state);
|
|
963
|
Field field = declaringClass.getDeclaredField(parameter);
|
|
964
|
field.setAccessible(true);
|
|
965
|
field.set(holder, newMap);
|
|
966
|
}
|
|
967
|
|
|
968
|
protected <T extends CdmBase> Collection<T> setNewCollection(CdmBase obj, Class<?> holderClass,
|
|
969
|
String parameter, Class<T> entityClass) throws NoSuchFieldException, SecurityException, IllegalArgumentException, IllegalAccessException {
|
|
970
|
Field field = holderClass.getDeclaredField(parameter);
|
|
971
|
field.setAccessible(true);
|
|
972
|
Collection<T> oldValue = (Collection<T>)field.get(obj);
|
|
973
|
Collection<T> newValue = null;
|
|
974
|
if (Set.class.isAssignableFrom(field.getType())){
|
|
975
|
newValue = new HashSet<>();
|
|
976
|
}else if (List.class.isAssignableFrom(field.getType())){
|
|
977
|
newValue = new ArrayList<>();
|
|
978
|
}else{
|
|
979
|
throw new RuntimeException("Unsupported collection type: " + field.getType().getCanonicalName());
|
|
980
|
}
|
|
981
|
field.set(obj, newValue);
|
|
982
|
return oldValue;
|
|
983
|
}
|
|
984
|
|
|
985
|
protected <KEY extends CdmBase, ITEM extends CdmBase> Map<KEY,ITEM> setNewMap(CdmBase obj, Class<?> holderClass,
|
|
986
|
String parameter, Class<KEY> keyClass, Class<ITEM> itemClass) throws NoSuchFieldException, SecurityException, IllegalArgumentException, IllegalAccessException {
|
|
987
|
Field field = holderClass.getDeclaredField(parameter);
|
|
988
|
field.setAccessible(true);
|
|
989
|
Map<KEY,ITEM> oldValue = (Map<KEY,ITEM>)field.get(obj);
|
|
990
|
Map<KEY,ITEM> newValue = null;
|
|
991
|
if (Map.class.isAssignableFrom(field.getType())){
|
|
992
|
newValue = new HashMap<>();
|
|
993
|
}else{
|
|
994
|
throw new RuntimeException("Unsupported map type: " + field.getType().getCanonicalName());
|
|
995
|
}
|
|
996
|
field.set(obj, newValue);
|
|
997
|
return oldValue;
|
|
998
|
}
|
|
999
|
|
|
1000
|
|
|
1001
|
private <T extends Collection<S>, S extends CdmBase> Collection<S> getTargetCollection(
|
|
1002
|
Class<S> clazz, T sourceCollection, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
1003
|
Collection<S> result = new ArrayList<>();
|
|
1004
|
if (Set.class.isAssignableFrom(sourceCollection.getClass())){
|
|
1005
|
result = new HashSet<>();
|
|
1006
|
}
|
|
1007
|
for (S entity : sourceCollection){
|
|
1008
|
S target = detach(entity, state);
|
|
1009
|
result.add(target);
|
|
1010
|
}
|
|
1011
|
return result;
|
|
1012
|
}
|
|
1013
|
|
|
1014
|
private <K extends CdmBase, V extends CdmBase> Map<K,V> getTargetMap(Map<K,V> sourceMap, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
1015
|
Map<K,V> result = new HashMap<>();
|
|
1016
|
for (K key : sourceMap.keySet()){
|
|
1017
|
K targetKey = detach(key, state);
|
|
1018
|
V targetValue = detach(sourceMap.get(key), state);
|
|
1019
|
result.put(targetKey, targetValue);
|
|
1020
|
}
|
|
1021
|
return result;
|
|
1022
|
}
|
|
1023
|
|
|
1024
|
// ****************************** USER HANDLING
|
|
1025
|
|
|
1026
|
private User makeCreatedUpdatedBy(User createdByOriginal, Cdm2CdmImportState state, boolean isUpdatedBy) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
1027
|
UserImportMode mode = isUpdatedBy? state.getConfig().getUpdatedByMode() : state.getConfig().getCreatedByMode();
|
|
1028
|
|
|
1029
|
switch (mode) {
|
|
1030
|
case NONE:
|
|
1031
|
return null;
|
|
1032
|
case ORIGINAL:
|
|
1033
|
return detach(createdByOriginal, state);
|
|
1034
|
default:
|
|
1035
|
logger.warn("Mode not yet supported: " + mode);
|
|
1036
|
return null;
|
|
1037
|
}
|
|
1038
|
}
|
|
1039
|
|
|
1040
|
|
|
1041
|
// ****************************** INVISIBLE **************************************/
|
|
1042
|
|
|
1043
|
protected void setInvisible(Object holder, String fieldName, Object value) throws NoSuchFieldException, SecurityException, IllegalArgumentException, IllegalAccessException {
|
|
1044
|
setInvisible(holder, holder.getClass(), fieldName, value);
|
|
1045
|
}
|
|
1046
|
protected void setInvisible(Object holder, Class<?> holderClazz, String fieldName, Object value) throws NoSuchFieldException, SecurityException, IllegalArgumentException, IllegalAccessException {
|
|
1047
|
Field field = holderClazz.getDeclaredField(fieldName);
|
|
1048
|
field.setAccessible(true);
|
|
1049
|
field.set(holder, value);
|
|
1050
|
}
|
|
1051
|
|
|
1052
|
// ************************* GET TARGET ******************************************/
|
|
1053
|
|
|
1054
|
|
|
1055
|
//TODO this should be cached for partition
|
|
1056
|
private <T extends CdmBase> T getTarget(T source, Cdm2CdmImportState state) {
|
|
1057
|
if (source == null){
|
|
1058
|
return null;
|
|
1059
|
}
|
|
1060
|
T result = getCached(source, state);
|
|
1061
|
// if (result == null){
|
|
1062
|
// Class<T> clazz = (Class<T>)source.getClass();
|
|
1063
|
// result = getCommonService().find(clazz, source.getUuid());
|
|
1064
|
// }
|
|
1065
|
if (result == null){
|
|
1066
|
//Alternative: clone?
|
|
1067
|
result = CdmBase.deproxy(source);
|
|
1068
|
result.setId(0);
|
|
1069
|
cache(result, state);
|
|
1070
|
state.addToSave(result);
|
|
1071
|
}
|
|
1072
|
return result;
|
|
1073
|
}
|
|
1074
|
|
|
1075
|
// ******************* CACHE *******************************************************/
|
|
1076
|
|
|
1077
|
protected void cache(CdmBase cdmBase, Cdm2CdmImportState state) {
|
|
1078
|
if (cdmBase instanceof User || cdmBase instanceof DefinedTermBase){
|
|
1079
|
state.putPermanent(cdmBase.getUuid(), cdmBase);
|
|
1080
|
}else{
|
|
1081
|
state.putToSessionCache(cdmBase);
|
|
1082
|
}
|
|
1083
|
addExistingObject(cdmBase, state);
|
|
1084
|
}
|
|
1085
|
|
|
1086
|
private void addExistingObject(CdmBase cdmBase, Cdm2CdmImportState state) {
|
|
1087
|
cdmBase = CdmBase.deproxy(cdmBase);
|
|
1088
|
Set<UUID> set = state.getExistingObjects(cdmBase.getClass());
|
|
1089
|
if (set == null){
|
|
1090
|
set = loadExistingUuids(cdmBase.getClass(), state);
|
|
1091
|
// set = new HashSet<>();
|
|
1092
|
// existingObjects.put(cdmBase.getClass(), set);
|
|
1093
|
}
|
|
1094
|
set.add(cdmBase.getUuid());
|
|
1095
|
}
|
|
1096
|
|
|
1097
|
protected boolean isInCache(CdmBase cdmBase, Cdm2CdmImportState state) {
|
|
1098
|
return getCached(cdmBase, state) != null;
|
|
1099
|
}
|
|
1100
|
|
|
1101
|
protected <T extends CdmBase> T getCached(T cdmBase, Cdm2CdmImportState state) {
|
|
1102
|
T result = (T)state.getFromSessionCache(cdmBase.getUuid());
|
|
1103
|
if (result == null){
|
|
1104
|
result = (T)state.getPermanent(cdmBase.getUuid());
|
|
1105
|
}
|
|
1106
|
return result;
|
|
1107
|
}
|
|
1108
|
|
|
1109
|
protected void clearCache(Cdm2CdmImportState state) {
|
|
1110
|
state.clearSessionCache();
|
|
1111
|
}
|
|
1112
|
|
|
1113
|
private Reference getSourceReference(Cdm2CdmImportState state) {
|
|
1114
|
UUID uuid = state.getConfig().getSourceRefUuid();
|
|
1115
|
if (uuid == null && state.getConfig().getSourceReference() != null){
|
|
1116
|
uuid = state.getConfig().getSourceReference().getUuid();
|
|
1117
|
state.getConfig().setSourceRefUuid(uuid);
|
|
1118
|
}
|
|
1119
|
Reference result = (Reference)state.getFromSessionCache(uuid);
|
|
1120
|
if (result == null){
|
|
1121
|
result = (Reference)state.getPermanent(uuid);
|
|
1122
|
}
|
|
1123
|
if (result == null){
|
|
1124
|
result = getReferenceService().find(uuid);
|
|
1125
|
}
|
|
1126
|
|
|
1127
|
if (result == null){
|
|
1128
|
result = state.getConfig().getSourceReference();
|
|
1129
|
if (result == null){
|
|
1130
|
result = ReferenceFactory.newDatabase();
|
|
1131
|
//TODO
|
|
1132
|
result.setTitle("Cdm2Cdm Import");
|
|
1133
|
}
|
|
1134
|
getReferenceService().save(result);
|
|
1135
|
state.putToSessionCache(result);
|
|
1136
|
}
|
|
1137
|
return result;
|
|
1138
|
}
|
|
1139
|
|
|
1140
|
|
|
1141
|
protected ITaxonNodeOutStreamPartitioner getTaxonNodePartitioner(Cdm2CdmImportState state, IProgressMonitor monitor,
|
|
1142
|
Cdm2CdmImportConfigurator config) {
|
|
1143
|
ITaxonNodeOutStreamPartitioner partitioner = config.getPartitioner();
|
|
1144
|
if (partitioner == null){
|
|
1145
|
if(!config.isConcurrent()){
|
|
1146
|
partitioner = TaxonNodeOutStreamPartitioner.NewInstance(sourceRepo(state), state,
|
|
1147
|
state.getConfig().getTaxonNodeFilter(), 100,
|
|
1148
|
monitor, 1, TaxonNodeOutStreamPartitioner.fullPropertyPaths);
|
|
1149
|
((TaxonNodeOutStreamPartitioner)partitioner).setLastCommitManually(true);
|
|
1150
|
}else{
|
|
1151
|
partitioner = TaxonNodeOutStreamPartitionerConcurrent
|
|
1152
|
.NewInstance(state.getConfig().getSource(), state.getConfig().getTaxonNodeFilter(),
|
|
1153
|
1000, monitor, 1, TaxonNodeOutStreamPartitioner.fullPropertyPaths);
|
|
1154
|
}
|
|
1155
|
}
|
|
1156
|
return partitioner;
|
|
1157
|
}
|
|
1158
|
|
|
1159
|
}
|