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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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Andreas Müller
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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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4329e9eb
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Andreas Müller
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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){
|
| 241 |
8876144e
|
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|
return handlePersistedHomotypicalGroup((HomotypicalGroup)cdmBase, state);
|
| 242 |
77281e25
|
Andreas Müller
|
}else if(cdmBase instanceof TypeDesignationBase){
|
| 243 |
8876144e
|
Andreas Müller
|
return handlePersistedTypeDesignationBase((TypeDesignationBase)cdmBase, state);
|
| 244 |
77281e25
|
Andreas Müller
|
}else if(cdmBase instanceof TaxonDescription){
|
| 245 |
8876144e
|
Andreas Müller
|
return handlePersistedTaxonDescription((TaxonDescription)cdmBase, state);
|
| 246 |
77281e25
|
Andreas Müller
|
}else if(cdmBase instanceof NomenclaturalStatus){
|
| 247 |
8876144e
|
Andreas Müller
|
return handlePersistedNomenclaturalStatus((NomenclaturalStatus)cdmBase, state);
|
| 248 |
77281e25
|
Andreas Müller
|
}else if(cdmBase instanceof TaxonNameDescription){
|
| 249 |
8876144e
|
Andreas Müller
|
return handlePersistedTaxonNameDescription((TaxonNameDescription)cdmBase, state);
|
| 250 |
77281e25
|
Andreas Müller
|
}else if(cdmBase instanceof TaxonRelationship){
|
| 251 |
8876144e
|
Andreas Müller
|
return handlePersistedTaxonRelationship((TaxonRelationship)cdmBase, state);
|
| 252 |
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|
Andreas Müller
|
}else if(cdmBase instanceof HybridRelationship){
|
| 253 |
8876144e
|
Andreas Müller
|
return handlePersistedHybridRelationship((HybridRelationship)cdmBase, state);
|
| 254 |
77281e25
|
Andreas Müller
|
}else if(cdmBase instanceof NameRelationship){
|
| 255 |
8876144e
|
Andreas Müller
|
return handlePersistedNameRelationship((NameRelationship)cdmBase, state);
|
| 256 |
77281e25
|
Andreas Müller
|
}else if(cdmBase instanceof TaxonNodeAgentRelation){
|
| 257 |
8876144e
|
Andreas Müller
|
return handlePersistedTaxonNodeAgentRelation((TaxonNodeAgentRelation)cdmBase, state);
|
| 258 |
77281e25
|
Andreas Müller
|
}else if(cdmBase instanceof User){
|
| 259 |
8876144e
|
Andreas Müller
|
return handlePersistedUser((User)cdmBase, state);
|
| 260 |
77281e25
|
Andreas Müller
|
}else if(cdmBase instanceof Extension){
|
| 261 |
8876144e
|
Andreas Müller
|
return handlePersistedExtension((Extension)cdmBase, state);
|
| 262 |
77281e25
|
Andreas Müller
|
}else if(cdmBase instanceof Marker){
|
| 263 |
8876144e
|
Andreas Müller
|
return handlePersistedMarker((Marker)cdmBase, state);
|
| 264 |
77281e25
|
Andreas Müller
|
}else if(cdmBase instanceof Annotation){
|
| 265 |
8876144e
|
Andreas Müller
|
return handlePersistedAnnotation((Annotation)cdmBase, state);
|
| 266 |
77281e25
|
Andreas Müller
|
}else if(cdmBase instanceof LanguageString){
|
| 267 |
8876144e
|
Andreas Müller
|
return handlePersistedLanguageString((LanguageString)cdmBase, state);
|
| 268 |
77281e25
|
Andreas Müller
|
}else if(cdmBase instanceof TermVocabulary){
|
| 269 |
8876144e
|
Andreas Müller
|
return handlePersistedVocabulary((TermVocabulary<?>)cdmBase, state);
|
| 270 |
|
|
}else if(cdmBase instanceof TermTree){
|
| 271 |
|
|
return handlePersistedTermTree((TermTree<?>)cdmBase, state);
|
| 272 |
77281e25
|
Andreas Müller
|
}else if(cdmBase instanceof NamedArea){
|
| 273 |
8876144e
|
Andreas Müller
|
return handlePersistedNamedArea((NamedArea)cdmBase, state);
|
| 274 |
77281e25
|
Andreas Müller
|
}else if(cdmBase instanceof TermNode){
|
| 275 |
8876144e
|
Andreas Müller
|
return handlePersistedTermNode((TermNode)cdmBase, state);
|
| 276 |
77281e25
|
Andreas Müller
|
}else if(cdmBase instanceof Representation){
|
| 277 |
8876144e
|
Andreas Müller
|
return handlePersistedRepresentation((Representation)cdmBase, state);
|
| 278 |
77281e25
|
Andreas Müller
|
}else if(cdmBase instanceof InstitutionalMembership){
|
| 279 |
8876144e
|
Andreas Müller
|
return handlePersistedInstitutionalMembership((InstitutionalMembership)cdmBase, state);
|
| 280 |
77281e25
|
Andreas Müller
|
}else if(cdmBase instanceof Institution){
|
| 281 |
8876144e
|
Andreas Müller
|
return handlePersistedInstitution((Institution)cdmBase, state);
|
| 282 |
77281e25
|
Andreas Müller
|
}else if(cdmBase instanceof IntextReference){
|
| 283 |
8876144e
|
Andreas Müller
|
return handlePersistedIntextReference((IntextReference)cdmBase, state);
|
| 284 |
77281e25
|
Andreas Müller
|
}else if(cdmBase instanceof ExtensionType){
|
| 285 |
8876144e
|
Andreas Müller
|
return handlePersistedExtensionType((ExtensionType)cdmBase, state);
|
| 286 |
77281e25
|
Andreas Müller
|
}else if(cdmBase instanceof NomenclaturalStatusType){
|
| 287 |
8876144e
|
Andreas Müller
|
return handlePersistedNomenclaturalStatusType((NomenclaturalStatusType)cdmBase, state);
|
| 288 |
77281e25
|
Andreas Müller
|
}else if(cdmBase instanceof MarkerType){
|
| 289 |
8876144e
|
Andreas Müller
|
return handlePersistedMarkerType((MarkerType)cdmBase, state);
|
| 290 |
77281e25
|
Andreas Müller
|
}else if(cdmBase instanceof Rights){
|
| 291 |
8876144e
|
Andreas Müller
|
return handlePersistedRights((Rights)cdmBase, state);
|
| 292 |
77281e25
|
Andreas Müller
|
}else if(cdmBase instanceof DefinedTerm){
|
| 293 |
8876144e
|
Andreas Müller
|
return handlePersistedDefinedTerm((DefinedTerm)cdmBase, state);
|
| 294 |
77281e25
|
Andreas Müller
|
}else if(cdmBase instanceof DefinedTermBase){
|
| 295 |
8876144e
|
Andreas Müller
|
return handlePersistedTerm((DefinedTermBase<?>)cdmBase, state);
|
| 296 |
77281e25
|
Andreas Müller
|
}else {
|
| 297 |
|
|
throw new RuntimeException("Type not yet supported: " + cdmBase.getClass().getCanonicalName());
|
| 298 |
|
|
}
|
| 299 |
|
|
}
|
| 300 |
|
|
|
| 301 |
|
|
|
| 302 |
8876144e
|
Andreas Müller
|
protected TaxonNode handlePersistedTaxonNode(TaxonNode node, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 303 |
77281e25
|
Andreas Müller
|
|
| 304 |
8876144e
|
Andreas Müller
|
TaxonNode result = handlePersisted((AnnotatableEntity)node, state);
|
| 305 |
77281e25
|
Andreas Müller
|
if (result ==null){
|
| 306 |
|
|
return result;
|
| 307 |
|
|
}
|
| 308 |
|
|
//complete
|
| 309 |
8876144e
|
Andreas Müller
|
handleCollection(result, TaxonNode.class, "agentRelations", TaxonNodeAgentRelation.class, state);
|
| 310 |
a5f7d622
|
Andreas Müller
|
result.setTaxon(detach(result.getTaxon(), state));
|
| 311 |
|
|
result.setCitation(detach(node.getReference(), state));
|
| 312 |
|
|
result.setSynonymToBeUsed(detach(result.getSynonymToBeUsed(), state));
|
| 313 |
8876144e
|
Andreas Müller
|
handleMap(result, TaxonNode.class, "excludedNote", Language.class, LanguageString.class, state);
|
| 314 |
77281e25
|
Andreas Müller
|
//classification, parent, children
|
| 315 |
a5f7d622
|
Andreas Müller
|
this.setInvisible(node, "classification", detach(node.getClassification(), state));
|
| 316 |
8876144e
|
Andreas Müller
|
handleParentTaxonNode(result, state);
|
| 317 |
77281e25
|
Andreas Müller
|
setNewCollection(node, TaxonNode.class, "childNodes", TaxonNode.class);
|
| 318 |
|
|
return result;
|
| 319 |
|
|
}
|
| 320 |
|
|
|
| 321 |
8876144e
|
Andreas Müller
|
private void handleParentTaxonNode(TaxonNode childNode, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 322 |
a5f7d622
|
Andreas Müller
|
TaxonNode parent = detach(childNode.getParent(), true, state);
|
| 323 |
77281e25
|
Andreas Müller
|
//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 |
8876144e
|
Andreas Müller
|
protected Taxon handlePersistedTaxon(Taxon taxon, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 336 |
|
|
Taxon result = handlePersisted((TaxonBase)taxon, state);
|
| 337 |
77281e25
|
Andreas Müller
|
//complete
|
| 338 |
8876144e
|
Andreas Müller
|
handleCollection(result, Taxon.class, "synonyms", Synonym.class, state);
|
| 339 |
77281e25
|
Andreas Müller
|
// handleCollection(result, Taxon.class, "taxonNodes", TaxonNode.class);
|
| 340 |
|
|
setNewCollection(result, Taxon.class, "taxonNodes", TaxonNode.class);
|
| 341 |
8876144e
|
Andreas Müller
|
handleCollection(result, Taxon.class, "relationsFromThisTaxon", TaxonRelationship.class, state);
|
| 342 |
|
|
handleCollection(result, Taxon.class, "relationsToThisTaxon", TaxonRelationship.class, state);
|
| 343 |
77281e25
|
Andreas Müller
|
if (this.doDescriptions(state)){
|
| 344 |
8876144e
|
Andreas Müller
|
handleCollection(result, Taxon.class, "descriptions", TaxonDescription.class, state);
|
| 345 |
77281e25
|
Andreas Müller
|
}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 |
8876144e
|
Andreas Müller
|
protected Synonym handlePersistedSynonym(Synonym synonym, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 356 |
|
|
Synonym result = handlePersisted((TaxonBase)synonym, state);
|
| 357 |
77281e25
|
Andreas Müller
|
//complete
|
| 358 |
a5f7d622
|
Andreas Müller
|
setInvisible(result, "acceptedTaxon", detach(result.getAcceptedTaxon(), state));
|
| 359 |
|
|
result.setType(detach(result.getType(), state));
|
| 360 |
77281e25
|
Andreas Müller
|
return result;
|
| 361 |
|
|
}
|
| 362 |
|
|
|
| 363 |
8876144e
|
Andreas Müller
|
protected TaxonRelationship handlePersistedTaxonRelationship(TaxonRelationship taxRel, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 364 |
|
|
TaxonRelationship result = handlePersisted((RelationshipBase)taxRel, state);
|
| 365 |
77281e25
|
Andreas Müller
|
//complete
|
| 366 |
a5f7d622
|
Andreas Müller
|
result.setFromTaxon(detach(result.getFromTaxon(), state));
|
| 367 |
|
|
result.setToTaxon(detach(result.getToTaxon(), state));
|
| 368 |
|
|
result.setType(detach(result.getType(), state));
|
| 369 |
77281e25
|
Andreas Müller
|
return result;
|
| 370 |
|
|
}
|
| 371 |
|
|
|
| 372 |
8876144e
|
Andreas Müller
|
protected NameRelationship handlePersistedNameRelationship(NameRelationship rel, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 373 |
|
|
NameRelationship result = handlePersisted((RelationshipBase)rel, state);
|
| 374 |
77281e25
|
Andreas Müller
|
//complete
|
| 375 |
a5f7d622
|
Andreas Müller
|
setInvisible(result, "relatedFrom", detach(result.getFromName(), state));
|
| 376 |
|
|
setInvisible(result, "relatedTo", detach(result.getToName(), state));
|
| 377 |
8876144e
|
Andreas Müller
|
// result.setFromName(detache(result.getFromName(), state));
|
| 378 |
|
|
// result.setToName(detache(result.getToName(), state));
|
| 379 |
a5f7d622
|
Andreas Müller
|
result.setType(detach(result.getType(), state));
|
| 380 |
77281e25
|
Andreas Müller
|
return result;
|
| 381 |
|
|
}
|
| 382 |
|
|
|
| 383 |
8876144e
|
Andreas Müller
|
protected HybridRelationship handlePersistedHybridRelationship(HybridRelationship rel, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 384 |
|
|
HybridRelationship result = handlePersisted((RelationshipBase)rel, state);
|
| 385 |
77281e25
|
Andreas Müller
|
//complete
|
| 386 |
a5f7d622
|
Andreas Müller
|
setInvisible(result, "relatedFrom", detach(result.getParentName(), state));
|
| 387 |
|
|
setInvisible(result, "relatedTo", detach(result.getHybridName(), state));
|
| 388 |
77281e25
|
Andreas Müller
|
// result.setFromName(detache(result.getFromName()));
|
| 389 |
|
|
// result.setToName(detache(result.getToName()));
|
| 390 |
a5f7d622
|
Andreas Müller
|
result.setType(detach(result.getType(), state));
|
| 391 |
77281e25
|
Andreas Müller
|
return result;
|
| 392 |
|
|
}
|
| 393 |
|
|
|
| 394 |
8876144e
|
Andreas Müller
|
protected NomenclaturalStatus handlePersistedNomenclaturalStatus(NomenclaturalStatus status, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 395 |
|
|
NomenclaturalStatus result = handlePersisted((SingleSourcedEntityBase)status, state);
|
| 396 |
77281e25
|
Andreas Müller
|
//complete
|
| 397 |
a5f7d622
|
Andreas Müller
|
result.setType(detach(result.getType(), state));
|
| 398 |
77281e25
|
Andreas Müller
|
return result;
|
| 399 |
|
|
}
|
| 400 |
|
|
|
| 401 |
8876144e
|
Andreas Müller
|
protected TypeDesignationBase handlePersistedTypeDesignationBase(TypeDesignationBase<?> designation, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 402 |
|
|
TypeDesignationBase result = handlePersisted((SourcedEntityBase)designation, state);
|
| 403 |
77281e25
|
Andreas Müller
|
//complete
|
| 404 |
a5f7d622
|
Andreas Müller
|
result.setCitation(detach(result.getCitation(), state));
|
| 405 |
8876144e
|
Andreas Müller
|
handleCollection(result, TypeDesignationBase.class, "registrations", Registration.class, state);
|
| 406 |
|
|
handleCollection(result, TypeDesignationBase.class, "typifiedNames", TaxonName.class, state);
|
| 407 |
a5f7d622
|
Andreas Müller
|
result.setTypeStatus(detach(result.getTypeStatus(), state));
|
| 408 |
77281e25
|
Andreas Müller
|
return result;
|
| 409 |
|
|
}
|
| 410 |
|
|
|
| 411 |
8876144e
|
Andreas Müller
|
protected InstitutionalMembership handlePersistedInstitutionalMembership(InstitutionalMembership institutionalMembership, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 412 |
|
|
InstitutionalMembership result = handlePersisted((VersionableEntity)institutionalMembership, state);
|
| 413 |
77281e25
|
Andreas Müller
|
//complete
|
| 414 |
|
|
// result.setPerson(detache(result.getPerson()));
|
| 415 |
a5f7d622
|
Andreas Müller
|
setInvisible(result, "person", detach(result.getPerson(), state));
|
| 416 |
|
|
result.setInstitute(detach(result.getInstitute(), state));
|
| 417 |
77281e25
|
Andreas Müller
|
return result;
|
| 418 |
|
|
}
|
| 419 |
|
|
|
| 420 |
8876144e
|
Andreas Müller
|
protected Institution handlePersistedInstitution(Institution institution, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 421 |
|
|
Institution result = handlePersisted((AgentBase)institution, state);
|
| 422 |
77281e25
|
Andreas Müller
|
//complete
|
| 423 |
a5f7d622
|
Andreas Müller
|
result.setIsPartOf(detach(result.getIsPartOf(), state));
|
| 424 |
8876144e
|
Andreas Müller
|
handleCollection(result, Institution.class, "types", DefinedTerm.class, state);
|
| 425 |
77281e25
|
Andreas Müller
|
return result;
|
| 426 |
|
|
}
|
| 427 |
|
|
|
| 428 |
8876144e
|
Andreas Müller
|
protected TaxonNodeAgentRelation handlePersistedTaxonNodeAgentRelation(TaxonNodeAgentRelation nodeAgentRel, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 429 |
|
|
TaxonNodeAgentRelation result = handlePersisted((AnnotatableEntity)nodeAgentRel, state);
|
| 430 |
77281e25
|
Andreas Müller
|
//complete
|
| 431 |
a5f7d622
|
Andreas Müller
|
result.setAgent(detach(result.getAgent(), state));
|
| 432 |
|
|
result.setType(detach(result.getType(), state));
|
| 433 |
|
|
setInvisible(result, "taxonNode", detach(result.getTaxonNode(), state));
|
| 434 |
77281e25
|
Andreas Müller
|
return result;
|
| 435 |
|
|
}
|
| 436 |
|
|
|
| 437 |
|
|
|
| 438 |
8876144e
|
Andreas Müller
|
protected TaxonName handlePersistedTaxonName(TaxonName taxonName, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 439 |
77281e25
|
Andreas Müller
|
@SuppressWarnings("rawtypes")
|
| 440 |
8876144e
|
Andreas Müller
|
TaxonName result = handlePersisted((IdentifiableEntity)taxonName, state);
|
| 441 |
77281e25
|
Andreas Müller
|
//complete
|
| 442 |
a5f7d622
|
Andreas Müller
|
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 |
8876144e
|
Andreas Müller
|
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 |
77281e25
|
Andreas Müller
|
|
| 460 |
8876144e
|
Andreas Müller
|
handleCollection(result, TaxonName.class, "registrations", Registration.class, state);
|
| 461 |
|
|
handleCollection(result, TaxonName.class, "typeDesignations", TypeDesignationBase.class, state);
|
| 462 |
77281e25
|
Andreas Müller
|
|
| 463 |
8876144e
|
Andreas Müller
|
handleCollection(result, TaxonName.class, "taxonBases", TaxonBase.class, state);
|
| 464 |
77281e25
|
Andreas Müller
|
|
| 465 |
|
|
return result;
|
| 466 |
|
|
}
|
| 467 |
|
|
|
| 468 |
8876144e
|
Andreas Müller
|
protected HomotypicalGroup handlePersistedHomotypicalGroup(HomotypicalGroup group, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 469 |
|
|
HomotypicalGroup result = handlePersisted((AnnotatableEntity)group, state);
|
| 470 |
77281e25
|
Andreas Müller
|
//complete
|
| 471 |
8876144e
|
Andreas Müller
|
handleCollection(result, HomotypicalGroup.class, "typifiedNames", TaxonName.class, state);
|
| 472 |
77281e25
|
Andreas Müller
|
return result;
|
| 473 |
|
|
}
|
| 474 |
|
|
|
| 475 |
8876144e
|
Andreas Müller
|
protected Annotation handlePersistedAnnotation(Annotation annotation, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 476 |
|
|
Annotation result = handlePersisted((AnnotatableEntity)annotation, state);
|
| 477 |
77281e25
|
Andreas Müller
|
//complete
|
| 478 |
a5f7d622
|
Andreas Müller
|
result.setAnnotationType(detach(annotation.getAnnotationType(), state));
|
| 479 |
|
|
result.setCommentator(detach(result.getCommentator(), state));
|
| 480 |
8876144e
|
Andreas Müller
|
handleCollection(result, Annotation.class, "intextReferences", IntextReference.class, state);
|
| 481 |
77281e25
|
Andreas Müller
|
return result;
|
| 482 |
|
|
}
|
| 483 |
|
|
|
| 484 |
8876144e
|
Andreas Müller
|
protected Extension handlePersistedExtension(Extension extension, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 485 |
|
|
Extension result = handlePersisted((VersionableEntity)extension, state);
|
| 486 |
77281e25
|
Andreas Müller
|
//complete
|
| 487 |
a5f7d622
|
Andreas Müller
|
result.setType(detach(extension.getType(), state));
|
| 488 |
77281e25
|
Andreas Müller
|
return result;
|
| 489 |
|
|
}
|
| 490 |
|
|
|
| 491 |
8876144e
|
Andreas Müller
|
protected Marker handlePersistedMarker(Marker marker, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 492 |
|
|
Marker result = handlePersisted((VersionableEntity)marker, state);
|
| 493 |
77281e25
|
Andreas Müller
|
//complete
|
| 494 |
a5f7d622
|
Andreas Müller
|
result.setMarkerType(detach(marker.getMarkerType(), state));
|
| 495 |
77281e25
|
Andreas Müller
|
return result;
|
| 496 |
|
|
}
|
| 497 |
|
|
|
| 498 |
8876144e
|
Andreas Müller
|
protected Team handlePersistedTeam(Team team, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 499 |
|
|
Team result = handlePersisted((TeamOrPersonBase)team, state);
|
| 500 |
77281e25
|
Andreas Müller
|
//complete
|
| 501 |
8876144e
|
Andreas Müller
|
handleCollection(result, Team.class, "teamMembers", Person.class, state);
|
| 502 |
77281e25
|
Andreas Müller
|
return result;
|
| 503 |
|
|
}
|
| 504 |
|
|
|
| 505 |
8876144e
|
Andreas Müller
|
protected Contact handlePersistedContact(Contact contact, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 506 |
77281e25
|
Andreas Müller
|
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 |
8876144e
|
Andreas Müller
|
protected Person handlePersistedPerson(Person person, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 525 |
|
|
Person result = handlePersisted((TeamOrPersonBase)person, state);
|
| 526 |
77281e25
|
Andreas Müller
|
//complete
|
| 527 |
8876144e
|
Andreas Müller
|
handleCollection(result, Person.class, "institutionalMemberships", InstitutionalMembership.class, state);
|
| 528 |
77281e25
|
Andreas Müller
|
return result;
|
| 529 |
|
|
}
|
| 530 |
|
|
|
| 531 |
8876144e
|
Andreas Müller
|
protected NamedArea handlePersistedNamedArea(NamedArea area, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 532 |
|
|
NamedArea result = handlePersisted((OrderedTermBase)area, state);
|
| 533 |
77281e25
|
Andreas Müller
|
//complete
|
| 534 |
8876144e
|
Andreas Müller
|
handleCollection(result, NamedArea.class, "countries", Country.class, state);
|
| 535 |
a5f7d622
|
Andreas Müller
|
result.setLevel(detach(result.getLevel(), state));
|
| 536 |
|
|
result.setType(detach(result.getType(), state));
|
| 537 |
|
|
result.setShape(detach(result.getShape(), state));
|
| 538 |
77281e25
|
Andreas Müller
|
return result;
|
| 539 |
|
|
}
|
| 540 |
|
|
|
| 541 |
8876144e
|
Andreas Müller
|
protected Classification handlePersistedClassification(Classification classification, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 542 |
|
|
Classification result = handlePersisted((IdentifiableEntity)classification, state);
|
| 543 |
77281e25
|
Andreas Müller
|
//complete
|
| 544 |
a5f7d622
|
Andreas Müller
|
result.setName(detach(classification.getName(), state));
|
| 545 |
|
|
result.setReference(detach(classification.getReference(), state));
|
| 546 |
|
|
result.setRootNode(detach(classification.getRootNode(), state));
|
| 547 |
8876144e
|
Andreas Müller
|
handleCollection(result, Classification.class, "geoScopes", NamedArea.class, state);
|
| 548 |
|
|
handleMap(result, Classification.class, "description", Language.class, LanguageString.class, state);
|
| 549 |
77281e25
|
Andreas Müller
|
return result;
|
| 550 |
|
|
}
|
| 551 |
|
|
|
| 552 |
8876144e
|
Andreas Müller
|
protected Reference handlePersistedReference(Reference reference, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 553 |
|
|
Reference result = handlePersisted((IdentifiableMediaEntity)reference, state);
|
| 554 |
a5f7d622
|
Andreas Müller
|
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 |
77281e25
|
Andreas Müller
|
return result;
|
| 559 |
|
|
}
|
| 560 |
|
|
|
| 561 |
8876144e
|
Andreas Müller
|
protected SpecimenOrObservationBase<?> handlePersistedSpecimenOrObservationBase(SpecimenOrObservationBase specimen, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 562 |
77281e25
|
Andreas Müller
|
//TODO implement for classes
|
| 563 |
8876144e
|
Andreas Müller
|
SpecimenOrObservationBase<?> result = handlePersisted((IdentifiableEntity)specimen, state);
|
| 564 |
77281e25
|
Andreas Müller
|
//complete
|
| 565 |
a5f7d622
|
Andreas Müller
|
result.setSex(detach(result.getSex(), state));
|
| 566 |
|
|
result.setLifeStage(detach(result.getLifeStage(), state));
|
| 567 |
|
|
result.setKindOfUnit(detach(result.getKindOfUnit(), state));
|
| 568 |
8876144e
|
Andreas Müller
|
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 |
77281e25
|
Andreas Müller
|
return result;
|
| 573 |
|
|
}
|
| 574 |
|
|
|
| 575 |
8876144e
|
Andreas Müller
|
protected IdentifiableSource handlePersistedIdentifiableSource(IdentifiableSource source, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 576 |
|
|
IdentifiableSource result = handlePersisted((OriginalSourceBase)source, state);
|
| 577 |
77281e25
|
Andreas Müller
|
//complete
|
| 578 |
|
|
return result;
|
| 579 |
|
|
}
|
| 580 |
|
|
|
| 581 |
8876144e
|
Andreas Müller
|
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 |
77281e25
|
Andreas Müller
|
//complete
|
| 584 |
a5f7d622
|
Andreas Müller
|
result.setNameUsedInSource(detach(result.getNameUsedInSource(), state));
|
| 585 |
77281e25
|
Andreas Müller
|
return result;
|
| 586 |
|
|
}
|
| 587 |
|
|
|
| 588 |
8876144e
|
Andreas Müller
|
protected NamedSource handlePersistedNamedSource(NamedSource source, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 589 |
|
|
NamedSource result = handlePersisted((NamedSourceBase)source, state);
|
| 590 |
4329e9eb
|
Andreas Müller
|
//complete
|
| 591 |
|
|
return result;
|
| 592 |
|
|
}
|
| 593 |
|
|
|
| 594 |
8876144e
|
Andreas Müller
|
protected SecundumSource handlePersistedSecundumSource(DescriptionElementSource source, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 595 |
|
|
SecundumSource result = handlePersisted((NamedSourceBase)source, state);
|
| 596 |
4329e9eb
|
Andreas Müller
|
//TODO correct?
|
| 597 |
a5f7d622
|
Andreas Müller
|
result.setSourcedTaxon(detach(result.getSourcedTaxon(), state));
|
| 598 |
4329e9eb
|
Andreas Müller
|
return result;
|
| 599 |
|
|
}
|
| 600 |
|
|
|
| 601 |
8876144e
|
Andreas Müller
|
protected DescriptionElementSource handlePersistedDescriptionElementSource(DescriptionElementSource source, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 602 |
|
|
DescriptionElementSource result = handlePersisted((NamedSourceBase)source, state);
|
| 603 |
4329e9eb
|
Andreas Müller
|
//TODO correct?
|
| 604 |
a5f7d622
|
Andreas Müller
|
detach(result.getSourcedElement(), state).addSource(result);
|
| 605 |
4329e9eb
|
Andreas Müller
|
return result;
|
| 606 |
|
|
}
|
| 607 |
|
|
|
| 608 |
8876144e
|
Andreas Müller
|
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 |
77281e25
|
Andreas Müller
|
//complete
|
| 611 |
a5f7d622
|
Andreas Müller
|
result.setLanguage(detach(result.getLanguage(), state));
|
| 612 |
|
|
result.setArea(detach(result.getArea(), state));
|
| 613 |
77281e25
|
Andreas Müller
|
return result;
|
| 614 |
|
|
}
|
| 615 |
|
|
|
| 616 |
8876144e
|
Andreas Müller
|
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 |
77281e25
|
Andreas Müller
|
//complete
|
| 619 |
a5f7d622
|
Andreas Müller
|
result.setFormat(detach(result.getFormat(), state));
|
| 620 |
8876144e
|
Andreas Müller
|
handleMap(result, TextData.class, "multilanguageText", Language.class, LanguageString.class, state);
|
| 621 |
77281e25
|
Andreas Müller
|
return result;
|
| 622 |
|
|
}
|
| 623 |
|
|
|
| 624 |
8876144e
|
Andreas Müller
|
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 |
77281e25
|
Andreas Müller
|
//complete
|
| 627 |
a5f7d622
|
Andreas Müller
|
result.setArea(detach(result.getArea(), state));
|
| 628 |
|
|
result.setStatus(detach(result.getStatus(), state));
|
| 629 |
77281e25
|
Andreas Müller
|
return result;
|
| 630 |
|
|
}
|
| 631 |
|
|
|
| 632 |
8876144e
|
Andreas Müller
|
protected ExtensionType handlePersistedExtensionType(ExtensionType term, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 633 |
|
|
ExtensionType result = handlePersisted((DefinedTermBase)term, state);
|
| 634 |
77281e25
|
Andreas Müller
|
//complete
|
| 635 |
|
|
return result;
|
| 636 |
|
|
}
|
| 637 |
|
|
|
| 638 |
8876144e
|
Andreas Müller
|
protected MarkerType handlePersistedMarkerType(MarkerType term, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 639 |
|
|
MarkerType result = handlePersisted((DefinedTermBase)term, state);
|
| 640 |
77281e25
|
Andreas Müller
|
//complete
|
| 641 |
|
|
return result;
|
| 642 |
|
|
}
|
| 643 |
|
|
|
| 644 |
8876144e
|
Andreas Müller
|
protected NomenclaturalStatusType handlePersistedNomenclaturalStatusType(NomenclaturalStatusType term, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 645 |
|
|
NomenclaturalStatusType result = handlePersisted((OrderedTermBase)term, state);
|
| 646 |
77281e25
|
Andreas Müller
|
//complete
|
| 647 |
|
|
return result;
|
| 648 |
|
|
}
|
| 649 |
|
|
|
| 650 |
8876144e
|
Andreas Müller
|
protected DefinedTerm handlePersistedDefinedTerm(DefinedTerm term, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 651 |
|
|
DefinedTerm result = handlePersisted((DefinedTermBase)term, state);
|
| 652 |
77281e25
|
Andreas Müller
|
//complete
|
| 653 |
|
|
return result;
|
| 654 |
|
|
}
|
| 655 |
|
|
|
| 656 |
|
|
//placeholder for not implemented methods for subclasses
|
| 657 |
8876144e
|
Andreas Müller
|
protected DefinedTermBase<?> handlePersistedTerm(DefinedTermBase term, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 658 |
|
|
DefinedTermBase<?> result = handlePersisted(term, state);
|
| 659 |
77281e25
|
Andreas Müller
|
logger.warn("Class not yet handled: " + term.getClass().getSimpleName());
|
| 660 |
|
|
return result;
|
| 661 |
|
|
}
|
| 662 |
|
|
|
| 663 |
8876144e
|
Andreas Müller
|
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 |
77281e25
|
Andreas Müller
|
return result;
|
| 675 |
|
|
}
|
| 676 |
|
|
|
| 677 |
8876144e
|
Andreas Müller
|
protected TermNode<?> handlePersistedTermNode(TermNode node, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 678 |
|
|
TermNode<?> result = (TermNode<?>)handlePersisted((TermRelationBase)node, state);
|
| 679 |
77281e25
|
Andreas Müller
|
//complete
|
| 680 |
a5f7d622
|
Andreas Müller
|
setInvisible(result, "parent", detach(result.getParent(), state));
|
| 681 |
8876144e
|
Andreas Müller
|
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 |
77281e25
|
Andreas Müller
|
|
| 685 |
|
|
return result;
|
| 686 |
|
|
}
|
| 687 |
|
|
|
| 688 |
8876144e
|
Andreas Müller
|
protected Representation handlePersistedRepresentation(Representation representation, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 689 |
|
|
Representation result = (Representation)handlePersisted((LanguageStringBase)representation, state);
|
| 690 |
77281e25
|
Andreas Müller
|
return result;
|
| 691 |
|
|
}
|
| 692 |
|
|
|
| 693 |
8876144e
|
Andreas Müller
|
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 |
77281e25
|
Andreas Müller
|
//complete
|
| 696 |
8876144e
|
Andreas Müller
|
handleCollection(result, TermBase.class, "representations", Representation.class, state);
|
| 697 |
77281e25
|
Andreas Müller
|
return result;
|
| 698 |
|
|
}
|
| 699 |
|
|
|
| 700 |
8876144e
|
Andreas Müller
|
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 |
77281e25
|
Andreas Müller
|
//complete
|
| 703 |
8876144e
|
Andreas Müller
|
handleCollection(result, TermCollection.class, "termRelations", TermRelationBase.class, state);
|
| 704 |
77281e25
|
Andreas Müller
|
return result;
|
| 705 |
|
|
}
|
| 706 |
|
|
|
| 707 |
8876144e
|
Andreas Müller
|
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 |
a5f7d622
|
Andreas Müller
|
result.setTerm(detach(result.getTerm(), state));
|
| 710 |
|
|
setInvisible(result, TermRelationBase.class, "graph", detach(result.getGraph(), state));
|
| 711 |
77281e25
|
Andreas Müller
|
return result;
|
| 712 |
|
|
}
|
| 713 |
|
|
|
| 714 |
8876144e
|
Andreas Müller
|
protected User handlePersistedUser(User user, Cdm2CdmImportState state) throws NoSuchFieldException, SecurityException, IllegalArgumentException, IllegalAccessException, InvocationTargetException, NoSuchMethodException {
|
| 715 |
|
|
User result = (User)handlePersistedCdmBase(user, state);
|
| 716 |
77281e25
|
Andreas Müller
|
if (result.getUsername().equals("admin")){
|
| 717 |
aae87424
|
Andreas Müller
|
//TODO why only admin, is this not a problem for all duplicated usernames? Was this a preliminary decision?
|
| 718 |
77281e25
|
Andreas Müller
|
result = getUserService().listByUsername("admin", MatchMode.EXACT, null, null, null, null, null).iterator().next();
|
| 719 |
8876144e
|
Andreas Müller
|
state.putPermanent(user.getUuid(), result);
|
| 720 |
|
|
cache(result, state); //necessary?
|
| 721 |
|
|
state.addToSave(result);
|
| 722 |
|
|
state.removeToSave(user);
|
| 723 |
77281e25
|
Andreas Müller
|
}
|
| 724 |
|
|
if (!result.isPersited()){
|
| 725 |
|
|
result.setAuthorities(new HashSet<>());
|
| 726 |
|
|
result.setGrantedAuthorities(new HashSet<>());
|
| 727 |
|
|
setInvisible(result, "groups", new HashSet<>());
|
| 728 |
|
|
}
|
| 729 |
a5f7d622
|
Andreas Müller
|
result.setPerson(detach(user.getPerson(), state));
|
| 730 |
77281e25
|
Andreas Müller
|
return result;
|
| 731 |
|
|
}
|
| 732 |
|
|
|
| 733 |
|
|
|
| 734 |
8876144e
|
Andreas Müller
|
protected LanguageString handlePersistedLanguageString(LanguageString languageString, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 735 |
|
|
LanguageString result = handlePersisted((LanguageStringBase)languageString, state);
|
| 736 |
77281e25
|
Andreas Müller
|
//complete
|
| 737 |
8876144e
|
Andreas Müller
|
handleCollection(result, LanguageString.class, "intextReferences", IntextReference.class, state);
|
| 738 |
77281e25
|
Andreas Müller
|
return result;
|
| 739 |
|
|
}
|
| 740 |
|
|
|
| 741 |
8876144e
|
Andreas Müller
|
protected Rights handlePersistedRights(Rights rights, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 742 |
|
|
Rights result = handlePersisted((LanguageStringBase)rights, state);
|
| 743 |
a5f7d622
|
Andreas Müller
|
result.setAgent(detach(rights.getAgent(), state));
|
| 744 |
|
|
result.setType(detach(rights.getType(), state));
|
| 745 |
77281e25
|
Andreas Müller
|
//complete
|
| 746 |
|
|
return result;
|
| 747 |
|
|
}
|
| 748 |
|
|
|
| 749 |
8876144e
|
Andreas Müller
|
protected IntextReference handlePersistedIntextReference(IntextReference intextReference, Cdm2CdmImportState state) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 750 |
|
|
IntextReference result = handlePersisted((VersionableEntity)intextReference, state);
|
| 751 |
a5f7d622
|
Andreas Müller
|
result.setReferencedEntity(detach(result.getReferencedEntity(), false, state));
|
| 752 |
77281e25
|
Andreas Müller
|
Method targetMethod = IntextReference.class.getDeclaredMethod("setTarget", IIntextReferenceTarget.class);
|
| 753 |
|
|
targetMethod.setAccessible(true);
|
| 754 |
a5f7d622
|
Andreas Müller
|
targetMethod.invoke(result, detach(result.getTarget(), false, state));
|
| 755 |
77281e25
|
Andreas Müller
|
return result;
|
| 756 |
|
|
}
|
| 757 |
|
|
|
| 758 |
8876144e
|
Andreas Müller
|
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 |
77281e25
|
Andreas Müller
|
//complete
|
| 761 |
a5f7d622
|
Andreas Müller
|
setInvisible(taxDescription, "taxon", detach(taxDescription.getTaxon(), state));
|
| 762 |
8876144e
|
Andreas Müller
|
handleCollection(taxDescription, TaxonDescription.class, "geoScopes", NamedArea.class, state);
|
| 763 |
|
|
handleCollection(taxDescription, TaxonDescription.class, "scopes", DefinedTerm.class, state);
|
| 764 |
77281e25
|
Andreas Müller
|
return result;
|
| 765 |
|
|
}
|
| 766 |
|
|
|
| 767 |
8876144e
|
Andreas Müller
|
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 |
77281e25
|
Andreas Müller
|
//complete
|
| 770 |
a5f7d622
|
Andreas Müller
|
setInvisible(nameDescription, "taxonName", detach(nameDescription.getTaxonName(), state));
|
| 771 |
77281e25
|
Andreas Müller
|
return result;
|
| 772 |
|
|
}
|
| 773 |
|
|
|
| 774 |
|
|
|
| 775 |
|
|
// ***************************** BASE CLASSES ********************************************/
|
| 776 |
|
|
|
| 777 |
8876144e
|
Andreas Müller
|
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 |
77281e25
|
Andreas Müller
|
//complete
|
| 780 |
aae87424
|
Andreas Müller
|
cdmBase.setCreatedBy(makeCreatedUpdatedBy(cdmBase.getCreatedBy(), state, false));
|
| 781 |
77281e25
|
Andreas Müller
|
return result;
|
| 782 |
|
|
}
|
| 783 |
|
|
|
| 784 |
8876144e
|
Andreas Müller
|
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 |
77281e25
|
Andreas Müller
|
//complete
|
| 787 |
aae87424
|
Andreas Müller
|
entity.setUpdatedBy(makeCreatedUpdatedBy(entity.getUpdatedBy(), state, true));
|
| 788 |
77281e25
|
Andreas Müller
|
return result;
|
| 789 |
|
|
}
|
| 790 |
|
|
|
| 791 |
8876144e
|
Andreas Müller
|
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 |
77281e25
|
Andreas Müller
|
//complete
|
| 794 |
8876144e
|
Andreas Müller
|
handleCollection(result, AnnotatableEntity.class, "annotations", Annotation.class, state);
|
| 795 |
|
|
handleCollection(result, AnnotatableEntity.class, "markers", Marker.class, state);
|
| 796 |
77281e25
|
Andreas Müller
|
return result;
|
| 797 |
|
|
}
|
| 798 |
|
|
|
| 799 |
8876144e
|
Andreas Müller
|
protected <T extends SourcedEntityBase<?>> T handlePersisted(SourcedEntityBase sourcedEntity,
|
| 800 |
|
|
Cdm2CdmImportState state)
|
| 801 |
|
|
throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
| 802 |
77281e25
|
Andreas Müller
|
int originalId = sourcedEntity.getId();
|
| 803 |
8876144e
|
Andreas Müller
|
T result = handlePersisted((AnnotatableEntity)sourcedEntity, state);
|
| 804 |
77281e25
|
Andreas Müller
|
//complete
|
| 805 |
8876144e
|
Andreas Müller
|
handleCollection(result, SourcedEntityBase.class, "sources", OriginalSourceBase.class, state);
|
| 806 |
daf61d74
|
Andreas Müller
|
if (!result.isPersited()){
|
| 807 |
8876144e
|
Andreas Müller
|
if(state.getConfig().isRemoveImportSources()){
|
| 808 |
daf61d74
|
Andreas Müller
|
filterImportSources(result.getSources());
|
| 809 |
|
|
}
|
| 810 |
8876144e
|
Andreas Müller
|
if (state.getConfig().isAddSources()){
|
| 811 |
|
|
Reference sourceRef = getSourceReference(state);
|
| 812 |
bf4426c2
|
Andreas Müller
|
OriginalSourceBase newSource = result.addImportSource(String.valueOf(originalId), sourcedEntity.getClass().getSimpleName(),
|
| 813 |
daf61d74
|
Andreas Müller
|
sourceRef, null);
|
| 814 |
|
|
getCommonService().save(newSource);
|
| 815 |
8876144e
|
Andreas Müller
|
addExistingObject(newSource, state);
|
| 816 |
daf61d74
|
Andreas Müller
|
}
|
| 817 |
|
|
}
|
| 818 |
77281e25
|
Andreas Müller
|
return result;
|
| 819 |
|
|
}
|
| 820 |
|
|
|
| 821 |
daf61d74
|
Andreas Müller
|
/**
|
| 822 |
|
|
* @param sources
|
| 823 |
|
|
*/
|
| 824 |
b6eee3e3
|
Andreas Müller
|
private void filterImportSources(Set<? extends OriginalSourceBase> sources) {
|
| 825 |
bf4426c2
|
Andreas Müller
|
Set<OriginalSourceBase> toDelete = new HashSet<>();
|
| 826 |
|
|
for (OriginalSourceBase osb: sources){
|
| 827 |
daf61d74
|
Andreas Müller
|
if (osb.getType() == OriginalSourceType.Import){
|
| 828 |
|
|
toDelete.add(osb);
|
| 829 |
|
|
}
|
| 830 |
|
|
}
|
| 831 |
bf4426c2
|
Andreas Müller
|
for (OriginalSourceBase osb: toDelete){
|
| 832 |
daf61d74
|
Andreas Müller
|
sources.remove(osb);
|
| 833 |
|
|
}
|
| 834 |
|
|
}
|
| 835 |
|
|
|
| 836 |
8876144e
|
Andreas Müller
|
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 |
77281e25
|
Andreas Müller
|
//complete
|
| 839 |
8876144e
|
Andreas Müller
|
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 |
77281e25
|
Andreas Müller
|
return result;
|
| 846 |
|
|
}
|
| 847 |
|
|
|
| 848 |
8876144e
|
Andreas Müller
|
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 |
77281e25
|
Andreas Müller
|
//complete
|
| 851 |
8876144e
|
Andreas Müller
|
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 |
a5f7d622
|
Andreas Müller
|
result.setKindOf(detach(result.getKindOf(), state));
|
| 855 |
|
|
result.setPartOf(detach(result.getPartOf(), state));
|
| 856 |
|
|
setInvisible(result, DefinedTermBase.class, "vocabulary", detach(result.getVocabulary(), state));
|
| 857 |
77281e25
|
Andreas Müller
|
|
| 858 |
|
|
return result;
|
| 859 |
|
|
}
|
| 860 |
|
|
|
| 861 |
8876144e
|
Andreas Müller
|
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 |
77281e25
|
Andreas Müller
|
//complete
|
| 864 |
a5f7d622
|
Andreas Müller
|
result.setCitation(detach(result.getCitation(), state));
|
| 865 |
8876144e
|
Andreas Müller
|
handleCollection(result, OriginalSourceBase.class, "links", ExternalLink.class, state);
|
| 866 |
77281e25
|
Andreas Müller
|
return result;
|
| 867 |
|
|
}
|
| 868 |
|
|
|
| 869 |
8876144e
|
Andreas Müller
|
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 |
77281e25
|
Andreas Müller
|
//complete
|
| 872 |
a5f7d622
|
Andreas Müller
|
result.setLanguage(detach(lsBase.getLanguage(), state));
|
| 873 |
77281e25
|
Andreas Müller
|
return result;
|
| 874 |
|
|
}
|
| 875 |
|
|
|
| 876 |
8876144e
|
Andreas Müller
|
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 |
77281e25
|
Andreas Müller
|
//complete
|
| 879 |
|
|
return result;
|
| 880 |
|
|
}
|
| 881 |
|
|
|
| 882 |
8876144e
|
Andreas Müller
|
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 |
a5f7d622
|
Andreas Müller
|
result.setContact(detach(result.getContact(), state));
|
| 885 |
77281e25
|
Andreas Müller
|
//complete
|
| 886 |
|
|
return result;
|
| 887 |
|
|
}
|
| 888 |
|
|
|
| 889 |
8876144e
|
Andreas Müller
|
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 |
77281e25
|
Andreas Müller
|
//complete
|
| 892 |
a5f7d622
|
Andreas Müller
|
result.setName(detach(taxonBase.getName(), state));
|
| 893 |
|
|
result.setSec(detach(taxonBase.getSec(), state));
|
| 894 |
77281e25
|
Andreas Müller
|
return result;
|
| 895 |
|
|
}
|
| 896 |
|
|
|
| 897 |
8876144e
|
Andreas Müller
|
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 |
77281e25
|
Andreas Müller
|
//complete
|
| 900 |
8876144e
|
Andreas Müller
|
handleCollection(result, IdentifiableMediaEntity.class, "media", Media.class, state);
|
| 901 |
77281e25
|
Andreas Müller
|
return result;
|
| 902 |
|
|
}
|
| 903 |
|
|
|
| 904 |
8876144e
|
Andreas Müller
|
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 |
03e4c253
|
Andreas Müller
|
//complete
|
| 907 |
a5f7d622
|
Andreas Müller
|
result.setCitation(detach(result.getCitation(), state));
|
| 908 |
03e4c253
|
Andreas Müller
|
return result;
|
| 909 |
|
|
}
|
| 910 |
|
|
|
| 911 |
8876144e
|
Andreas Müller
|
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 |
77281e25
|
Andreas Müller
|
//complete
|
| 914 |
8876144e
|
Andreas Müller
|
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 |
a5f7d622
|
Andreas Müller
|
result.setDescribedSpecimenOrObservation(detach(descriptionBase.getDescribedSpecimenOrObservation(), state));
|
| 918 |
77281e25
|
Andreas Müller
|
return result;
|
| 919 |
|
|
}
|
| 920 |
|
|
|
| 921 |
8876144e
|
Andreas Müller
|
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 |
77281e25
|
Andreas Müller
|
//complete
|
| 924 |
a5f7d622
|
Andreas Müller
|
result.setFeature(detach(result.getFeature(), state));
|
| 925 |
|
|
setInvisible(result, DescriptionElementBase.class, "inDescription", detach(result.getInDescription(), state));
|
| 926 |
8876144e
|
Andreas Müller
|
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 |
77281e25
|
Andreas Müller
|
|
| 931 |
|
|
return result;
|
| 932 |
|
|
}
|
| 933 |
|
|
|
| 934 |
8876144e
|
Andreas Müller
|
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 |
77281e25
|
Andreas Müller
|
return result;
|
| 937 |
|
|
}
|
| 938 |
|
|
|
| 939 |
|
|
|
| 940 |
|
|
//************************** COLLECTIONS / MAPS ****************************************/
|
| 941 |
|
|
|
| 942 |
|
|
protected <HOLDER extends CdmBase, ITEM extends CdmBase> void handleCollection(
|
| 943 |
8876144e
|
Andreas Müller
|
HOLDER holder, Class<? super HOLDER> declaringClass, String parameter, Class<ITEM> itemClass,
|
| 944 |
|
|
Cdm2CdmImportState state)
|
| 945 |
77281e25
|
Andreas Müller
|
throws NoSuchFieldException, IllegalAccessException, InvocationTargetException, NoSuchMethodException {
|
| 946 |
|
|
|
| 947 |
|
|
Collection<ITEM> oldCollection = setNewCollection(holder, declaringClass, parameter, itemClass);
|
| 948 |
8876144e
|
Andreas Müller
|
Collection<ITEM> newCollection = getTargetCollection(itemClass, oldCollection, state);
|
| 949 |
77281e25
|
Andreas Müller
|
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 |
8876144e
|
Andreas Müller
|
Class<KEY> keyClass, Class<ITEM> itemClass, Cdm2CdmImportState state)
|
| 958 |
77281e25
|
Andreas Müller
|
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 |
8876144e
|
Andreas Müller
|
Map<KEY,ITEM> newMap = getTargetMap(oldMap, state);
|
| 963 |
77281e25
|
Andreas Müller
|
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 |
8876144e
|
Andreas Müller
|
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 |
77281e25
|
Andreas Müller
|
Collection<S> result = new ArrayList<>();
|
| 1004 |
|
|
if (Set.class.isAssignableFrom(sourceCollection.getClass())){
|
| 1005 |
|
|
result = new HashSet<>();
|
| 1006 |
|
|
}
|
| 1007 |
|
|
for (S entity : sourceCollection){
|
| 1008 |
a5f7d622
|
Andreas Müller
|
S target = detach(entity, state);
|
| 1009 |
77281e25
|
Andreas Müller
|
result.add(target);
|
| 1010 |
|
|
}
|
| 1011 |
|
|
return result;
|
| 1012 |
|
|
}
|
| 1013 |
|
|
|
| 1014 |
8876144e
|
Andreas Müller
|
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 |
77281e25
|
Andreas Müller
|
Map<K,V> result = new HashMap<>();
|
| 1016 |
|
|
for (K key : sourceMap.keySet()){
|
| 1017 |
a5f7d622
|
Andreas Müller
|
K targetKey = detach(key, state);
|
| 1018 |
|
|
V targetValue = detach(sourceMap.get(key), state);
|
| 1019 |
77281e25
|
Andreas Müller
|
result.put(targetKey, targetValue);
|
| 1020 |
|
|
}
|
| 1021 |
|
|
return result;
|
| 1022 |
|
|
}
|
| 1023 |
|
|
|
| 1024 |
aae87424
|
Andreas Müller
|
// ****************************** 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 |
77281e25
|
Andreas Müller
|
// ****************************** 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 |
8876144e
|
Andreas Müller
|
private <T extends CdmBase> T getTarget(T source, Cdm2CdmImportState state) {
|
| 1057 |
77281e25
|
Andreas Müller
|
if (source == null){
|
| 1058 |
|
|
return null;
|
| 1059 |
|
|
}
|
| 1060 |
8876144e
|
Andreas Müller
|
T result = getCached(source, state);
|
| 1061 |
77281e25
|
Andreas Müller
|
// 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 |
8876144e
|
Andreas Müller
|
cache(result, state);
|
| 1070 |
|
|
state.addToSave(result);
|
| 1071 |
77281e25
|
Andreas Müller
|
}
|
| 1072 |
|
|
return result;
|
| 1073 |
|
|
}
|
| 1074 |
|
|
|
| 1075 |
|
|
// ******************* CACHE *******************************************************/
|
| 1076 |
|
|
|
| 1077 |
8876144e
|
Andreas Müller
|
protected void cache(CdmBase cdmBase, Cdm2CdmImportState state) {
|
| 1078 |
77281e25
|
Andreas Müller
|
if (cdmBase instanceof User || cdmBase instanceof DefinedTermBase){
|
| 1079 |
8876144e
|
Andreas Müller
|
state.putPermanent(cdmBase.getUuid(), cdmBase);
|
| 1080 |
77281e25
|
Andreas Müller
|
}else{
|
| 1081 |
8876144e
|
Andreas Müller
|
state.putToSessionCache(cdmBase);
|
| 1082 |
77281e25
|
Andreas Müller
|
}
|
| 1083 |
8876144e
|
Andreas Müller
|
addExistingObject(cdmBase, state);
|
| 1084 |
77281e25
|
Andreas Müller
|
}
|
| 1085 |
|
|
|
| 1086 |
8876144e
|
Andreas Müller
|
private void addExistingObject(CdmBase cdmBase, Cdm2CdmImportState state) {
|
| 1087 |
77281e25
|
Andreas Müller
|
cdmBase = CdmBase.deproxy(cdmBase);
|
| 1088 |
8876144e
|
Andreas Müller
|
Set<UUID> set = state.getExistingObjects(cdmBase.getClass());
|
| 1089 |
77281e25
|
Andreas Müller
|
if (set == null){
|
| 1090 |
8876144e
|
Andreas Müller
|
set = loadExistingUuids(cdmBase.getClass(), state);
|
| 1091 |
77281e25
|
Andreas Müller
|
// set = new HashSet<>();
|
| 1092 |
|
|
// existingObjects.put(cdmBase.getClass(), set);
|
| 1093 |
|
|
}
|
| 1094 |
|
|
set.add(cdmBase.getUuid());
|
| 1095 |
|
|
}
|
| 1096 |
|
|
|
| 1097 |
8876144e
|
Andreas Müller
|
protected boolean isInCache(CdmBase cdmBase, Cdm2CdmImportState state) {
|
| 1098 |
|
|
return getCached(cdmBase, state) != null;
|
| 1099 |
77281e25
|
Andreas Müller
|
}
|
| 1100 |
|
|
|
| 1101 |
8876144e
|
Andreas Müller
|
protected <T extends CdmBase> T getCached(T cdmBase, Cdm2CdmImportState state) {
|
| 1102 |
|
|
T result = (T)state.getFromSessionCache(cdmBase.getUuid());
|
| 1103 |
77281e25
|
Andreas Müller
|
if (result == null){
|
| 1104 |
8876144e
|
Andreas Müller
|
result = (T)state.getPermanent(cdmBase.getUuid());
|
| 1105 |
77281e25
|
Andreas Müller
|
}
|
| 1106 |
|
|
return result;
|
| 1107 |
|
|
}
|
| 1108 |
|
|
|
| 1109 |
8876144e
|
Andreas Müller
|
protected void clearCache(Cdm2CdmImportState state) {
|
| 1110 |
|
|
state.clearSessionCache();
|
| 1111 |
77281e25
|
Andreas Müller
|
}
|
| 1112 |
|
|
|
| 1113 |
|
|
private Reference getSourceReference(Cdm2CdmImportState state) {
|
| 1114 |
|
|
UUID uuid = state.getConfig().getSourceRefUuid();
|
| 1115 |
8876144e
|
Andreas Müller
|
if (uuid == null && state.getConfig().getSourceReference() != null){
|
| 1116 |
77281e25
|
Andreas Müller
|
uuid = state.getConfig().getSourceReference().getUuid();
|
| 1117 |
|
|
state.getConfig().setSourceRefUuid(uuid);
|
| 1118 |
|
|
}
|
| 1119 |
8876144e
|
Andreas Müller
|
Reference result = (Reference)state.getFromSessionCache(uuid);
|
| 1120 |
77281e25
|
Andreas Müller
|
if (result == null){
|
| 1121 |
8876144e
|
Andreas Müller
|
result = (Reference)state.getPermanent(uuid);
|
| 1122 |
77281e25
|
Andreas Müller
|
}
|
| 1123 |
|
|
if (result == null){
|
| 1124 |
|
|
result = getReferenceService().find(uuid);
|
| 1125 |
|
|
}
|
| 1126 |
8876144e
|
Andreas Müller
|
|
| 1127 |
77281e25
|
Andreas Müller
|
if (result == null){
|
| 1128 |
|
|
result = state.getConfig().getSourceReference();
|
| 1129 |
8876144e
|
Andreas Müller
|
if (result == null){
|
| 1130 |
|
|
result = ReferenceFactory.newDatabase();
|
| 1131 |
|
|
//TODO
|
| 1132 |
|
|
result.setTitle("Cdm2Cdm Import");
|
| 1133 |
|
|
}
|
| 1134 |
77281e25
|
Andreas Müller
|
getReferenceService().save(result);
|
| 1135 |
8876144e
|
Andreas Müller
|
state.putToSessionCache(result);
|
| 1136 |
77281e25
|
Andreas Müller
|
}
|
| 1137 |
|
|
return result;
|
| 1138 |
|
|
}
|
| 1139 |
|
|
|
| 1140 |
|
|
|
| 1141 |
8876144e
|
Andreas Müller
|
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 |
77281e25
|
Andreas Müller
|
}
|
| 1158 |
|
|
|
| 1159 |
|
|
}
|