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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.pesi.fauEu2Cdm;
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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.log4j.Logger;
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import eu.etaxonomy.cdm.api.application.CdmApplicationController;
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import eu.etaxonomy.cdm.api.application.ICdmRepository;
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import eu.etaxonomy.cdm.database.DbSchemaValidation;
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import eu.etaxonomy.cdm.io.common.CdmImportBase;
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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.ReferencedEntityBase;
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import eu.etaxonomy.cdm.model.common.RelationshipBase;
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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.State;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
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import eu.etaxonomy.cdm.model.description.TextData;
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import eu.etaxonomy.cdm.model.location.Country;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.media.ExternalLink;
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import eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity;
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import eu.etaxonomy.cdm.model.media.Media;
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import eu.etaxonomy.cdm.model.media.Rights;
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import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
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import eu.etaxonomy.cdm.model.name.HybridRelationship;
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import eu.etaxonomy.cdm.model.name.NameRelationship;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
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import eu.etaxonomy.cdm.model.name.Registration;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.name.TypeDesignationBase;
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import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
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import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
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import eu.etaxonomy.cdm.model.permission.User;
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import eu.etaxonomy.cdm.model.reference.OriginalSourceBase;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.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.TermVocabulary;
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import eu.etaxonomy.cdm.persistence.query.MatchMode;
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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 FauEu2CdmImportBase
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extends CdmImportBase<FauEu2CdmImportConfigurator, FauEu2CdmImportState> {
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private static final long serialVersionUID = 8917991155285743172L;
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private static final Logger logger = Logger.getLogger(FauEu2CdmImportBase.class);
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//quick and dirty
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private FauEu2CdmImportState state;
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//TODO move to state
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private Map<UUID, CdmBase> sessionCache = new HashMap<>();
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protected Set<CdmBase> toSave = new HashSet<>();
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protected ICdmRepository sourceRepo(FauEu2CdmImportState state){
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ICdmRepository repo = state.getSourceRepository();
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if (repo == null){
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System.out.println("start source repo");
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boolean omitTermLoading = true;
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repo = CdmApplicationController.NewInstance(state.getConfig().getSource(),
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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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}
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return repo;
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}
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protected Contact detache(Contact contact) 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);
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}
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}
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protected IIntextReferencable detache(IIntextReferencable cdmBase, boolean onlyForDefinedSignature) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
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return (IIntextReferencable)detache((CdmBase)cdmBase);
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}
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protected IIntextReferenceTarget detache(IIntextReferenceTarget cdmBase, boolean onlyForDefinedSignature) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
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return (IIntextReferenceTarget)detache((CdmBase)cdmBase);
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}
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protected <T extends CdmBase> T detache(T cdmBase) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
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return detache(cdmBase, false);
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}
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private Map<Class,Set<UUID>> existingObjects = new HashMap<>();
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protected <T extends CdmBase> T detache(T cdmBase, boolean notFromSource) 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)){
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return getCached(cdmBase);
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}else {
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if (existingObjects.get(cdmBase.getClass()) == null){
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loadExistingUuids(cdmBase.getClass());
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}
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boolean exists = existingObjects.get(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);
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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);
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}
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}
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/**
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* @param class1
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* @return
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*/
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private Set<UUID> loadExistingUuids(Class<? extends CdmBase> clazz) {
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List<UUID> list = getCommonService().listUuid(clazz);
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Set<UUID> result = new HashSet<>(list);
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existingObjects.put(clazz, result);
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return result;
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}
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protected <A extends CdmBase> CdmBase handlePersisted(A cdmBase) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
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if(cdmBase instanceof TaxonNode){
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return handlePersistedTaxonNode((TaxonNode)cdmBase);
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}else if(cdmBase instanceof Taxon){
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return handlePersistedTaxon((Taxon)cdmBase);
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}else if(cdmBase instanceof Synonym){
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return handlePersistedSynonym((Synonym)cdmBase);
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}else if(cdmBase instanceof TaxonName){
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return handlePersistedTaxonName((TaxonName)cdmBase);
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}else if(cdmBase instanceof Team){
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return handlePersistedTeam((Team)cdmBase);
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}else if(cdmBase instanceof Person){
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return handlePersistedPerson((Person)cdmBase);
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}else if(cdmBase instanceof Classification){
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return handlePersistedClassification((Classification)cdmBase);
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}else if(cdmBase instanceof Reference){
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return handlePersistedReference((Reference)cdmBase);
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}else if(cdmBase instanceof SpecimenOrObservationBase){
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return handlePersistedSpecimenOrObservationBase((SpecimenOrObservationBase)cdmBase);
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}else if(cdmBase instanceof IdentifiableSource){
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return handlePersistedIdentifiableSource((IdentifiableSource)cdmBase);
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}else if(cdmBase instanceof DescriptionElementSource){
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return handlePersistedDescriptionElementSource((DescriptionElementSource)cdmBase);
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}else if(cdmBase instanceof CommonTaxonName){
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return handlePersistedCommonTaxonName((CommonTaxonName)cdmBase);
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}else if(cdmBase instanceof Distribution){
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return handlePersistedDistribution((Distribution)cdmBase);
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}else if(cdmBase instanceof TextData){
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return handlePersistedTextData((TextData)cdmBase);
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}else if(cdmBase instanceof HomotypicalGroup){
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return handlePersistedHomotypicalGroup((HomotypicalGroup)cdmBase);
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}else if(cdmBase instanceof TypeDesignationBase){
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return handlePersistedTypeDesignationBase((TypeDesignationBase)cdmBase);
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}else if(cdmBase instanceof TaxonDescription){
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return handlePersistedTaxonDescription((TaxonDescription)cdmBase);
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}else if(cdmBase instanceof NomenclaturalStatus){
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return handlePersistedNomenclaturalStatus((NomenclaturalStatus)cdmBase);
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}else if(cdmBase instanceof TaxonNameDescription){
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return handlePersistedTaxonNameDescription((TaxonNameDescription)cdmBase);
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}else if(cdmBase instanceof TaxonRelationship){
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return handlePersistedTaxonRelationship((TaxonRelationship)cdmBase);
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}else if(cdmBase instanceof HybridRelationship){
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return handlePersistedHybridRelationship((HybridRelationship)cdmBase);
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}else if(cdmBase instanceof NameRelationship){
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return handlePersistedNameRelationship((NameRelationship)cdmBase);
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}else if(cdmBase instanceof TaxonNodeAgentRelation){
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return handlePersistedTaxonNodeAgentRelation((TaxonNodeAgentRelation)cdmBase);
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}else if(cdmBase instanceof User){
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return handlePersistedUser((User)cdmBase);
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}else if(cdmBase instanceof Extension){
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return handlePersistedExtension((Extension)cdmBase);
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}else if(cdmBase instanceof Marker){
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return handlePersistedMarker((Marker)cdmBase);
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}else if(cdmBase instanceof Annotation){
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return handlePersistedAnnotation((Annotation)cdmBase);
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}else if(cdmBase instanceof LanguageString){
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return handlePersistedLanguageString((LanguageString)cdmBase);
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}else if(cdmBase instanceof TermVocabulary){
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return handlePersistedVocabulary((TermVocabulary<?>)cdmBase);
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}else if(cdmBase instanceof NamedArea){
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return handlePersistedNamedArea((NamedArea)cdmBase);
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}else if(cdmBase instanceof TermNode){
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return handlePersistedTermNode((TermNode)cdmBase);
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}else if(cdmBase instanceof Representation){
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return handlePersistedRepresentation((Representation)cdmBase);
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}else if(cdmBase instanceof InstitutionalMembership){
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return handlePersistedInstitutionalMembership((InstitutionalMembership)cdmBase);
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}else if(cdmBase instanceof Institution){
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return handlePersistedInstitution((Institution)cdmBase);
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}else if(cdmBase instanceof IntextReference){
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return handlePersistedIntextReference((IntextReference)cdmBase);
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}else if(cdmBase instanceof ExtensionType){
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return handlePersistedExtensionType((ExtensionType)cdmBase);
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}else if(cdmBase instanceof NomenclaturalStatusType){
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return handlePersistedNomenclaturalStatusType((NomenclaturalStatusType)cdmBase);
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}else if(cdmBase instanceof MarkerType){
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return handlePersistedMarkerType((MarkerType)cdmBase);
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}else if(cdmBase instanceof DefinedTerm){
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return handlePersistedDefinedTerm((DefinedTerm)cdmBase);
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}else if(cdmBase instanceof DefinedTermBase){
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return handlePersistedTerm((DefinedTermBase<?>)cdmBase);
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}else {
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throw new RuntimeException("Type not yet supported: " + cdmBase.getClass().getCanonicalName());
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}
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}
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protected TaxonNode handlePersistedTaxonNode(TaxonNode node) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
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TaxonNode result = handlePersisted((AnnotatableEntity)node);
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if (result ==null){
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return result;
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}
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//complete
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handleCollection(result, TaxonNode.class, "agentRelations", TaxonNodeAgentRelation.class);
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result.setTaxon(detache(result.getTaxon()));
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result.setReference(detache(node.getReference()));
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result.setSynonymToBeUsed(detache(result.getSynonymToBeUsed()));
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handleMap(result, TaxonNode.class, "excludedNote", Language.class, LanguageString.class);
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//classification, parent, children
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this.setInvisible(node, "classification", detache(node.getClassification()));
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handleParentTaxonNode(result);
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303
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setNewCollection(node, TaxonNode.class, "childNodes", TaxonNode.class);
|
|
304
|
return result;
|
|
305
|
}
|
|
306
|
|
|
307
|
private void handleParentTaxonNode(TaxonNode childNode) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
308
|
TaxonNode parent = detache(childNode.getParent(), true);
|
|
309
|
//TODO
|
|
310
|
String microReference = null;
|
|
311
|
Reference reference = null;
|
|
312
|
if (parent == null && childNode.getClassification().getRootNode().equals(childNode)){
|
|
313
|
//do nothing
|
|
314
|
}else if (parent == null ){
|
|
315
|
childNode.getClassification().addChildNode(childNode, reference, microReference) ;
|
|
316
|
}else{
|
|
317
|
parent.addChildNode(childNode, reference, microReference);
|
|
318
|
}
|
|
319
|
}
|
|
320
|
|
|
321
|
protected Taxon handlePersistedTaxon(Taxon taxon) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
322
|
Taxon result = handlePersisted((TaxonBase)taxon);
|
|
323
|
//complete
|
|
324
|
handleCollection(result, Taxon.class, "synonyms", Synonym.class);
|
|
325
|
// handleCollection(result, Taxon.class, "taxonNodes", TaxonNode.class);
|
|
326
|
setNewCollection(result, Taxon.class, "taxonNodes", TaxonNode.class);
|
|
327
|
handleCollection(result, Taxon.class, "relationsFromThisTaxon", TaxonRelationship.class);
|
|
328
|
handleCollection(result, Taxon.class, "relationsToThisTaxon", TaxonRelationship.class);
|
|
329
|
if (this.doDescriptions(state)){
|
|
330
|
handleCollection(result, Taxon.class, "descriptions", TaxonDescription.class);
|
|
331
|
}else{
|
|
332
|
setNewCollection(result, Taxon.class, "descriptions", TaxonDescription.class);
|
|
333
|
}
|
|
334
|
return result;
|
|
335
|
}
|
|
336
|
|
|
337
|
protected boolean doDescriptions(FauEu2CdmImportState state) {
|
|
338
|
return false;
|
|
339
|
}
|
|
340
|
|
|
341
|
protected Synonym handlePersistedSynonym(Synonym synonym) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
342
|
Synonym result = handlePersisted((TaxonBase)synonym);
|
|
343
|
//complete
|
|
344
|
setInvisible(result, "acceptedTaxon", detache(result.getAcceptedTaxon()));
|
|
345
|
result.setType(detache(result.getType()));
|
|
346
|
return result;
|
|
347
|
}
|
|
348
|
|
|
349
|
protected TaxonRelationship handlePersistedTaxonRelationship(TaxonRelationship taxRel) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
350
|
TaxonRelationship result = handlePersisted((RelationshipBase)taxRel);
|
|
351
|
//complete
|
|
352
|
result.setFromTaxon(detache(result.getFromTaxon()));
|
|
353
|
result.setToTaxon(detache(result.getToTaxon()));
|
|
354
|
result.setType(detache(result.getType()));
|
|
355
|
return result;
|
|
356
|
}
|
|
357
|
|
|
358
|
protected NameRelationship handlePersistedNameRelationship(NameRelationship rel) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
359
|
NameRelationship result = handlePersisted((RelationshipBase)rel);
|
|
360
|
//complete
|
|
361
|
setInvisible(result, "relatedFrom", detache(result.getFromName()));
|
|
362
|
setInvisible(result, "relatedTo", detache(result.getToName()));
|
|
363
|
// result.setFromName(detache(result.getFromName()));
|
|
364
|
// result.setToName(detache(result.getToName()));
|
|
365
|
result.setType(detache(result.getType()));
|
|
366
|
return result;
|
|
367
|
}
|
|
368
|
|
|
369
|
protected HybridRelationship handlePersistedHybridRelationship(HybridRelationship rel) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
370
|
HybridRelationship result = handlePersisted((RelationshipBase)rel);
|
|
371
|
//complete
|
|
372
|
setInvisible(result, "relatedFrom", detache(result.getParentName()));
|
|
373
|
setInvisible(result, "relatedTo", detache(result.getHybridName()));
|
|
374
|
// result.setFromName(detache(result.getFromName()));
|
|
375
|
// result.setToName(detache(result.getToName()));
|
|
376
|
result.setType(detache(result.getType()));
|
|
377
|
return result;
|
|
378
|
}
|
|
379
|
|
|
380
|
protected NomenclaturalStatus handlePersistedNomenclaturalStatus(NomenclaturalStatus status) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
381
|
NomenclaturalStatus result = handlePersisted((ReferencedEntityBase)status);
|
|
382
|
//complete
|
|
383
|
result.setType(detache(result.getType()));
|
|
384
|
return result;
|
|
385
|
}
|
|
386
|
|
|
387
|
protected TypeDesignationBase handlePersistedTypeDesignationBase(TypeDesignationBase<?> designation) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
388
|
TypeDesignationBase result = handlePersisted((SourcedEntityBase)designation);
|
|
389
|
//complete
|
|
390
|
result.setCitation(detache(result.getCitation()));
|
|
391
|
handleCollection(result, TypeDesignationBase.class, "registrations", Registration.class);
|
|
392
|
handleCollection(result, TypeDesignationBase.class, "typifiedNames", TaxonName.class);
|
|
393
|
result.setTypeStatus(detache(result.getTypeStatus()));
|
|
394
|
return result;
|
|
395
|
}
|
|
396
|
|
|
397
|
protected InstitutionalMembership handlePersistedInstitutionalMembership(InstitutionalMembership institutionalMembership) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
398
|
InstitutionalMembership result = handlePersisted((VersionableEntity)institutionalMembership);
|
|
399
|
//complete
|
|
400
|
// result.setPerson(detache(result.getPerson()));
|
|
401
|
setInvisible(result, "person", detache(result.getPerson()));
|
|
402
|
result.setInstitute(detache(result.getInstitute()));
|
|
403
|
return result;
|
|
404
|
}
|
|
405
|
|
|
406
|
protected Institution handlePersistedInstitution(Institution institution) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
407
|
Institution result = handlePersisted((AgentBase)institution);
|
|
408
|
//complete
|
|
409
|
result.setIsPartOf(detache(result.getIsPartOf()));
|
|
410
|
handleCollection(result, Institution.class, "types", DefinedTerm.class);
|
|
411
|
return result;
|
|
412
|
}
|
|
413
|
|
|
414
|
protected TaxonNodeAgentRelation handlePersistedTaxonNodeAgentRelation(TaxonNodeAgentRelation nodeAgentRel) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
415
|
TaxonNodeAgentRelation result = handlePersisted((AnnotatableEntity)nodeAgentRel);
|
|
416
|
//complete
|
|
417
|
result.setAgent(detache(result.getAgent()));
|
|
418
|
result.setType(detache(result.getType()));
|
|
419
|
setInvisible(result, "taxonNode", detache(result.getTaxonNode()));
|
|
420
|
return result;
|
|
421
|
}
|
|
422
|
|
|
423
|
|
|
424
|
protected TaxonName handlePersistedTaxonName(TaxonName taxonName) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
425
|
@SuppressWarnings("rawtypes")
|
|
426
|
TaxonName result = handlePersisted((IdentifiableEntity)taxonName);
|
|
427
|
//complete
|
|
428
|
result.setRank(detache(result.getRank()));
|
|
429
|
result.setCombinationAuthorship(detache(result.getCombinationAuthorship()));
|
|
430
|
result.setExCombinationAuthorship(detache(result.getExCombinationAuthorship()));
|
|
431
|
result.setBasionymAuthorship(detache(result.getBasionymAuthorship()));
|
|
432
|
result.setExBasionymAuthorship(detache(result.getExBasionymAuthorship()));
|
|
433
|
result.setInBasionymAuthorship(detache(result.getInBasionymAuthorship()));
|
|
434
|
result.setInCombinationAuthorship(detache(result.getInCombinationAuthorship()));
|
|
435
|
|
|
436
|
result.setNomenclaturalReference(detache(result.getNomenclaturalReference()));
|
|
437
|
result.setNomenclaturalSource(detache(result.getNomenclaturalSource()));
|
|
438
|
result.setHomotypicalGroup(detache(result.getHomotypicalGroup()));
|
|
439
|
handleCollection(result, TaxonName.class, "descriptions", TaxonNameDescription.class);
|
|
440
|
handleCollection(result, TaxonName.class, "hybridChildRelations", HybridRelationship.class);
|
|
441
|
handleCollection(result, TaxonName.class, "hybridParentRelations", HybridRelationship.class);
|
|
442
|
handleCollection(result, TaxonName.class, "relationsFromThisName", NameRelationship.class);
|
|
443
|
handleCollection(result, TaxonName.class, "relationsToThisName", NameRelationship.class);
|
|
444
|
handleCollection(result, TaxonName.class, "status", NomenclaturalStatus.class);
|
|
445
|
|
|
446
|
handleCollection(result, TaxonName.class, "registrations", Registration.class);
|
|
447
|
handleCollection(result, TaxonName.class, "typeDesignations", TypeDesignationBase.class);
|
|
448
|
|
|
449
|
handleCollection(result, TaxonName.class, "taxonBases", TaxonBase.class);
|
|
450
|
|
|
451
|
return result;
|
|
452
|
}
|
|
453
|
|
|
454
|
protected HomotypicalGroup handlePersistedHomotypicalGroup(HomotypicalGroup group) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
455
|
HomotypicalGroup result = handlePersisted((AnnotatableEntity)group);
|
|
456
|
//complete
|
|
457
|
handleCollection(result, HomotypicalGroup.class, "typifiedNames", TaxonName.class);
|
|
458
|
return result;
|
|
459
|
}
|
|
460
|
|
|
461
|
protected Annotation handlePersistedAnnotation(Annotation annotation) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
462
|
Annotation result = handlePersisted((AnnotatableEntity)annotation);
|
|
463
|
//complete
|
|
464
|
result.setAnnotationType(detache(annotation.getAnnotationType()));
|
|
465
|
result.setCommentator(detache(result.getCommentator()));
|
|
466
|
handleCollection(result, Annotation.class, "intextReferences", IntextReference.class);
|
|
467
|
return result;
|
|
468
|
}
|
|
469
|
|
|
470
|
protected Extension handlePersistedExtension(Extension extension) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
471
|
Extension result = handlePersisted((VersionableEntity)extension);
|
|
472
|
//complete
|
|
473
|
result.setType(detache(extension.getType()));
|
|
474
|
return result;
|
|
475
|
}
|
|
476
|
|
|
477
|
protected Marker handlePersistedMarker(Marker marker) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
478
|
Marker result = handlePersisted((VersionableEntity)marker);
|
|
479
|
//complete
|
|
480
|
result.setMarkerType(detache(marker.getMarkerType()));
|
|
481
|
return result;
|
|
482
|
}
|
|
483
|
|
|
484
|
protected Team handlePersistedTeam(Team team) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
485
|
Team result = handlePersisted((TeamOrPersonBase)team);
|
|
486
|
//complete
|
|
487
|
handleCollection(result, Team.class, "teamMembers", Person.class);
|
|
488
|
return result;
|
|
489
|
}
|
|
490
|
|
|
491
|
protected Contact handlePersistedContact(Contact contact) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
492
|
Contact result = contact; // getTarget(contact);
|
|
493
|
if (result ==null){
|
|
494
|
return result;
|
|
495
|
}
|
|
496
|
if (!contact.getAddresses().isEmpty() || !contact.getEmailAddresses().isEmpty()
|
|
497
|
|| !contact.getFaxNumbers().isEmpty() ||!contact.getPhoneNumbers().isEmpty()
|
|
498
|
||!contact.getUrls().isEmpty()){
|
|
499
|
logger.warn("Addresses not yet implemented");
|
|
500
|
}
|
|
501
|
setInvisible(result, "addresses", new HashSet<>());
|
|
502
|
// handleCollection(result, Contact.class, "", Address.class);
|
|
503
|
setInvisible(result, "faxNumbers", new ArrayList<>());
|
|
504
|
setInvisible(result, "phoneNumbers", new ArrayList<>());
|
|
505
|
setInvisible(result, "emailAddresses", new ArrayList<>());
|
|
506
|
setInvisible(result, "urls", new ArrayList<>());
|
|
507
|
return result;
|
|
508
|
}
|
|
509
|
|
|
510
|
protected Person handlePersistedPerson(Person person) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
511
|
Person result = handlePersisted((TeamOrPersonBase)person);
|
|
512
|
//complete
|
|
513
|
handleCollection(result, Person.class, "institutionalMemberships", InstitutionalMembership.class);
|
|
514
|
return result;
|
|
515
|
}
|
|
516
|
|
|
517
|
protected NamedArea handlePersistedNamedArea(NamedArea area) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
518
|
NamedArea result = handlePersisted((OrderedTermBase)area);
|
|
519
|
//complete
|
|
520
|
handleCollection(result, NamedArea.class, "countries", Country.class);
|
|
521
|
result.setLevel(detache(result.getLevel()));
|
|
522
|
result.setType(detache(result.getType()));
|
|
523
|
result.setShape(detache(result.getShape()));
|
|
524
|
return result;
|
|
525
|
}
|
|
526
|
|
|
527
|
protected Classification handlePersistedClassification(Classification classification) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
528
|
Classification result = handlePersisted((IdentifiableEntity)classification);
|
|
529
|
//complete
|
|
530
|
result.setName(detache(classification.getName()));
|
|
531
|
result.setReference(detache(classification.getReference()));
|
|
532
|
result.setRootNode(detache(classification.getRootNode()));
|
|
533
|
handleCollection(result, Classification.class, "geoScopes", NamedArea.class);
|
|
534
|
handleMap(result, Classification.class, "description", Language.class, LanguageString.class);
|
|
535
|
return result;
|
|
536
|
}
|
|
537
|
|
|
538
|
protected Reference handlePersistedReference(Reference reference) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
539
|
Reference result = handlePersisted((IdentifiableMediaEntity)reference);
|
|
540
|
result.setAuthorship(detache(result.getAuthorship()));
|
|
541
|
result.setInstitution(detache(result.getInstitution()));
|
|
542
|
result.setSchool(detache(result.getSchool()));
|
|
543
|
result.setInReference(detache(result.getInReference()));
|
|
544
|
return result;
|
|
545
|
}
|
|
546
|
|
|
547
|
protected SpecimenOrObservationBase<?> handlePersistedSpecimenOrObservationBase(SpecimenOrObservationBase specimen) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
548
|
//TODO implement for classes
|
|
549
|
SpecimenOrObservationBase<?> result = handlePersisted((IdentifiableEntity)specimen);
|
|
550
|
//complete
|
|
551
|
result.setSex(detache(result.getSex()));
|
|
552
|
result.setLifeStage(detache(result.getLifeStage()));
|
|
553
|
result.setKindOfUnit(detache(result.getKindOfUnit()));
|
|
554
|
handleCollection(result, SpecimenOrObservationBase.class, "determinations", DeterminationEvent.class);
|
|
555
|
handleCollection(result, SpecimenOrObservationBase.class, "descriptions", SpecimenDescription.class);
|
|
556
|
handleCollection(result, SpecimenOrObservationBase.class, "derivationEvents", DerivationEvent.class);
|
|
557
|
handleMap(result, SpecimenOrObservationBase.class, "definition", Language.class, LanguageString.class);
|
|
558
|
return result;
|
|
559
|
}
|
|
560
|
|
|
561
|
protected IdentifiableSource handlePersistedIdentifiableSource(IdentifiableSource source) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
562
|
IdentifiableSource result = handlePersisted((OriginalSourceBase)source);
|
|
563
|
//complete
|
|
564
|
return result;
|
|
565
|
}
|
|
566
|
|
|
567
|
protected DescriptionElementSource handlePersistedDescriptionElementSource(DescriptionElementSource source) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
568
|
DescriptionElementSource result = handlePersisted((OriginalSourceBase)source);
|
|
569
|
//complete
|
|
570
|
result.setNameUsedInSource(detache(result.getNameUsedInSource()));
|
|
571
|
return result;
|
|
572
|
}
|
|
573
|
|
|
574
|
protected <T extends CommonTaxonName> T handlePersistedCommonTaxonName(CommonTaxonName element) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
575
|
T result = handlePersisted((DescriptionElementBase)element);
|
|
576
|
//complete
|
|
577
|
result.setLanguage(detache(result.getLanguage()));
|
|
578
|
result.setArea(detache(result.getArea()));
|
|
579
|
return result;
|
|
580
|
}
|
|
581
|
|
|
582
|
protected <T extends TextData> T handlePersistedTextData(TextData element) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
583
|
T result = handlePersisted((DescriptionElementBase)element);
|
|
584
|
//complete
|
|
585
|
result.setFormat(detache(result.getFormat()));
|
|
586
|
handleMap(result, TextData.class, "multilanguageText", Language.class, LanguageString.class);
|
|
587
|
return result;
|
|
588
|
}
|
|
589
|
|
|
590
|
protected <T extends Distribution> T handlePersistedDistribution(Distribution element) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
591
|
T result = handlePersisted((DescriptionElementBase)element);
|
|
592
|
//complete
|
|
593
|
result.setArea(detache(result.getArea()));
|
|
594
|
result.setStatus(detache(result.getStatus()));
|
|
595
|
return result;
|
|
596
|
}
|
|
597
|
|
|
598
|
protected ExtensionType handlePersistedExtensionType(ExtensionType term) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
599
|
ExtensionType result = handlePersisted((DefinedTermBase)term);
|
|
600
|
//complete
|
|
601
|
return result;
|
|
602
|
}
|
|
603
|
|
|
604
|
protected MarkerType handlePersistedMarkerType(MarkerType term) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
605
|
MarkerType result = handlePersisted((DefinedTermBase)term);
|
|
606
|
//complete
|
|
607
|
return result;
|
|
608
|
}
|
|
609
|
|
|
610
|
protected NomenclaturalStatusType handlePersistedNomenclaturalStatusType(NomenclaturalStatusType term) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
611
|
NomenclaturalStatusType result = handlePersisted((OrderedTermBase)term);
|
|
612
|
//complete
|
|
613
|
return result;
|
|
614
|
}
|
|
615
|
|
|
616
|
protected DefinedTerm handlePersistedDefinedTerm(DefinedTerm term) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
617
|
DefinedTerm result = handlePersisted((DefinedTermBase)term);
|
|
618
|
//complete
|
|
619
|
return result;
|
|
620
|
}
|
|
621
|
|
|
622
|
//placeholder for not implemented methods for subclasses
|
|
623
|
protected DefinedTermBase<?> handlePersistedTerm(DefinedTermBase term) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
624
|
DefinedTermBase<?> result = handlePersisted(term);
|
|
625
|
logger.warn("Class not yet handled: " + term.getClass().getSimpleName());
|
|
626
|
return result;
|
|
627
|
}
|
|
628
|
|
|
629
|
protected TermVocabulary<?> handlePersistedVocabulary(TermVocabulary voc) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
630
|
TermVocabulary<?> result = (TermVocabulary<?>)handlePersisted((TermCollection)voc);
|
|
631
|
handleCollection(result, TermVocabulary.class, "terms", DefinedTermBase.class);
|
|
632
|
return result;
|
|
633
|
}
|
|
634
|
|
|
635
|
protected TermNode<?> handlePersistedTermNode(TermNode node) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
636
|
TermNode<?> result = (TermNode<?>)handlePersisted((TermRelationBase)node);
|
|
637
|
//complete
|
|
638
|
setInvisible(result, "parent", detache(result.getParent()));
|
|
639
|
handleCollection(result, TermNode.class, "inapplicableIf", FeatureState.class);
|
|
640
|
handleCollection(result, TermNode.class, "onlyApplicableIf", FeatureState.class);
|
|
641
|
handleCollection(result, TermNode.class, "inapplicableIf_old", State.class);
|
|
642
|
handleCollection(result, TermNode.class, "onlyApplicableIf_old", State.class);
|
|
643
|
handleCollection(result, TermNode.class, "children", TermNode.class);
|
|
644
|
|
|
645
|
return result;
|
|
646
|
}
|
|
647
|
|
|
648
|
protected Representation handlePersistedRepresentation(Representation representation) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
649
|
Representation result = (Representation)handlePersisted((LanguageStringBase)representation);
|
|
650
|
return result;
|
|
651
|
}
|
|
652
|
|
|
653
|
protected <T extends TermBase> T handlePersisted(TermBase termBase) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
654
|
T result = handlePersisted((IdentifiableEntity)termBase);
|
|
655
|
//complete
|
|
656
|
handleCollection(result, TermBase.class, "representations", Representation.class);
|
|
657
|
return result;
|
|
658
|
}
|
|
659
|
|
|
660
|
protected <T extends TermCollection> T handlePersisted(TermCollection termCollection) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
661
|
T result = handlePersisted((TermBase)termCollection);
|
|
662
|
//complete
|
|
663
|
handleCollection(result, TermCollection.class, "termRelations", TermRelationBase.class);
|
|
664
|
return result;
|
|
665
|
}
|
|
666
|
|
|
667
|
protected <T extends TermRelationBase> T handlePersisted(TermRelationBase termRelationBase) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
668
|
T result = handlePersisted((VersionableEntity)termRelationBase);
|
|
669
|
result.setTerm(detache(result.getTerm()));
|
|
670
|
setInvisible(result, TermRelationBase.class, "graph", detache(result.getGraph()));
|
|
671
|
return result;
|
|
672
|
}
|
|
673
|
|
|
674
|
protected User handlePersistedUser(User user) throws NoSuchFieldException, SecurityException, IllegalArgumentException, IllegalAccessException, InvocationTargetException, NoSuchMethodException {
|
|
675
|
User result = (User)handlePersistedCdmBase(user);
|
|
676
|
if (result.getUsername().equals("admin")){
|
|
677
|
result = getUserService().listByUsername("admin", MatchMode.EXACT, null, null, null, null, null).iterator().next();
|
|
678
|
getState().putPermanent(user.getUuid(), result);
|
|
679
|
cache(result); //necessary?
|
|
680
|
toSave.add(result);
|
|
681
|
toSave.remove(user);
|
|
682
|
}
|
|
683
|
if (!result.isPersited()){
|
|
684
|
result.setAuthorities(new HashSet<>());
|
|
685
|
result.setGrantedAuthorities(new HashSet<>());
|
|
686
|
setInvisible(result, "groups", new HashSet<>());
|
|
687
|
}
|
|
688
|
return result;
|
|
689
|
}
|
|
690
|
|
|
691
|
|
|
692
|
protected LanguageString handlePersistedLanguageString(LanguageString languageString) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
693
|
LanguageString result = handlePersisted((LanguageStringBase)languageString);
|
|
694
|
//complete
|
|
695
|
handleCollection(result, LanguageString.class, "intextReferences", IntextReference.class);
|
|
696
|
return result;
|
|
697
|
}
|
|
698
|
|
|
699
|
protected IntextReference handlePersistedIntextReference(IntextReference intextReference) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
700
|
IntextReference result = handlePersisted((VersionableEntity)intextReference);
|
|
701
|
result.setReferencedEntity(detache(result.getReferencedEntity(), false));
|
|
702
|
Method targetMethod = IntextReference.class.getDeclaredMethod("setTarget", IIntextReferenceTarget.class);
|
|
703
|
targetMethod.setAccessible(true);
|
|
704
|
targetMethod.invoke(result, detache(result.getTarget(), false));
|
|
705
|
return result;
|
|
706
|
}
|
|
707
|
|
|
708
|
protected <T extends TaxonDescription> T handlePersistedTaxonDescription(TaxonDescription taxDescription) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
709
|
T result = handlePersisted((DescriptionBase)taxDescription);
|
|
710
|
//complete
|
|
711
|
setInvisible(taxDescription, "taxon", detache(taxDescription.getTaxon()));
|
|
712
|
handleCollection(taxDescription, TaxonDescription.class, "geoScopes", NamedArea.class);
|
|
713
|
handleCollection(taxDescription, TaxonDescription.class, "scopes", DefinedTerm.class);
|
|
714
|
return result;
|
|
715
|
}
|
|
716
|
|
|
717
|
protected <T extends TaxonDescription> T handlePersistedTaxonNameDescription(TaxonNameDescription nameDescription) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
718
|
T result = handlePersisted((DescriptionBase)nameDescription);
|
|
719
|
//complete
|
|
720
|
setInvisible(nameDescription, "taxonName", detache(nameDescription.getTaxonName()));
|
|
721
|
return result;
|
|
722
|
}
|
|
723
|
|
|
724
|
|
|
725
|
// ***************************** BASE CLASSES ********************************************/
|
|
726
|
|
|
727
|
protected <T extends CdmBase> T handlePersistedCdmBase(CdmBase cdmBase) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
728
|
T result = (T)getTarget(cdmBase);
|
|
729
|
//complete
|
|
730
|
cdmBase.setCreatedBy(detache(cdmBase.getCreatedBy()));
|
|
731
|
return result;
|
|
732
|
}
|
|
733
|
|
|
734
|
protected <T extends VersionableEntity> T handlePersisted(VersionableEntity entity) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
735
|
T result = (T)handlePersistedCdmBase((CdmBase)entity);
|
|
736
|
//complete
|
|
737
|
entity.setUpdatedBy(detache(entity.getUpdatedBy()));
|
|
738
|
return result;
|
|
739
|
}
|
|
740
|
|
|
741
|
protected <T extends AnnotatableEntity> T handlePersisted(AnnotatableEntity entity) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
742
|
T result = handlePersisted((VersionableEntity)entity);
|
|
743
|
//complete
|
|
744
|
handleCollection(result, AnnotatableEntity.class, "annotations", Annotation.class);
|
|
745
|
handleCollection(result, AnnotatableEntity.class, "markers", Marker.class);
|
|
746
|
return result;
|
|
747
|
}
|
|
748
|
|
|
749
|
protected <T extends SourcedEntityBase> T handlePersisted(SourcedEntityBase sourcedEntity) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
750
|
T result = handlePersisted((AnnotatableEntity)sourcedEntity);
|
|
751
|
//complete
|
|
752
|
handleCollection(result, SourcedEntityBase.class, "sources", OriginalSourceBase.class);
|
|
753
|
return result;
|
|
754
|
}
|
|
755
|
|
|
756
|
protected <T extends IdentifiableEntity> T handlePersisted(IdentifiableEntity identifiableEntity) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
757
|
T result = handlePersisted((SourcedEntityBase)identifiableEntity);
|
|
758
|
//complete
|
|
759
|
handleCollection(result, IdentifiableEntity.class, "credits", Credit.class);
|
|
760
|
handleCollection(result, IdentifiableEntity.class, "extensions", Extension.class);
|
|
761
|
handleCollection(result, IdentifiableEntity.class, "identifiers", Identifier.class);
|
|
762
|
handleCollection(result, IdentifiableEntity.class, "rights", Rights.class);
|
|
763
|
return result;
|
|
764
|
}
|
|
765
|
|
|
766
|
protected <T extends DefinedTermBase> T handlePersisted(DefinedTermBase definedTermBase) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
767
|
T result = handlePersisted((TermBase)definedTermBase);
|
|
768
|
//complete
|
|
769
|
handleCollection(result, DefinedTermBase.class, "media", Media.class);
|
|
770
|
handleCollection(result, DefinedTermBase.class, "generalizationOf", DefinedTermBase.class);
|
|
771
|
handleCollection(result, DefinedTermBase.class, "includes", DefinedTermBase.class);
|
|
772
|
result.setKindOf(detache(result.getKindOf()));
|
|
773
|
result.setPartOf(detache(result.getPartOf()));
|
|
774
|
setInvisible(result, DefinedTermBase.class, "vocabulary", detache(result.getVocabulary()));
|
|
775
|
|
|
776
|
return result;
|
|
777
|
}
|
|
778
|
|
|
779
|
protected <T extends OriginalSourceBase> T handlePersisted(OriginalSourceBase source) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
780
|
T result = handlePersisted((ReferencedEntityBase)source);
|
|
781
|
//complete
|
|
782
|
handleCollection(result, OriginalSourceBase.class, "links", ExternalLink.class);
|
|
783
|
return result;
|
|
784
|
}
|
|
785
|
|
|
786
|
protected <T extends LanguageStringBase> T handlePersisted(LanguageStringBase lsBase) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
787
|
T result = handlePersisted((AnnotatableEntity)lsBase);
|
|
788
|
//complete
|
|
789
|
result.setLanguage(detache(lsBase.getLanguage()));
|
|
790
|
return result;
|
|
791
|
}
|
|
792
|
|
|
793
|
protected <T extends TeamOrPersonBase> T handlePersisted(TeamOrPersonBase teamOrPerson) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
794
|
T result = handlePersisted((AgentBase)teamOrPerson);
|
|
795
|
//complete
|
|
796
|
return result;
|
|
797
|
}
|
|
798
|
|
|
799
|
protected <T extends AgentBase> T handlePersisted(AgentBase agent) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
800
|
T result = handlePersisted((IdentifiableMediaEntity)agent);
|
|
801
|
result.setContact(detache(result.getContact()));
|
|
802
|
//complete
|
|
803
|
return result;
|
|
804
|
}
|
|
805
|
|
|
806
|
protected <T extends TaxonBase> T handlePersisted(TaxonBase taxonBase) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
807
|
T result = handlePersisted((IdentifiableEntity)taxonBase);
|
|
808
|
//complete
|
|
809
|
result.setName(detache(taxonBase.getName()));
|
|
810
|
result.setSec(detache(taxonBase.getSec()));
|
|
811
|
return result;
|
|
812
|
}
|
|
813
|
|
|
814
|
protected <T extends IdentifiableMediaEntity> T handlePersisted(IdentifiableMediaEntity mediaEntity) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
815
|
T result = handlePersisted((IdentifiableEntity)mediaEntity);
|
|
816
|
//complete
|
|
817
|
handleCollection(result, IdentifiableMediaEntity.class, "media", Media.class);
|
|
818
|
return result;
|
|
819
|
}
|
|
820
|
|
|
821
|
protected <T extends ReferencedEntityBase> T handlePersisted(ReferencedEntityBase referencedEntity) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
822
|
T result = handlePersisted((AnnotatableEntity)referencedEntity);
|
|
823
|
//complete
|
|
824
|
result.setCitation(detache(result.getCitation()));
|
|
825
|
return result;
|
|
826
|
}
|
|
827
|
|
|
828
|
protected <T extends DescriptionBase> T handlePersisted(DescriptionBase descriptionBase) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
829
|
T result = handlePersisted((IdentifiableEntity)descriptionBase);
|
|
830
|
//complete
|
|
831
|
handleCollection(result, DescriptionBase.class, "descriptionElements", DescriptionElementBase.class);
|
|
832
|
handleCollection(result, DescriptionBase.class, "descriptiveDataSets", DescriptiveDataSet.class);
|
|
833
|
handleCollection(result, DescriptionBase.class, "descriptionSources", Reference.class);
|
|
834
|
result.setDescribedSpecimenOrObservation(detache(descriptionBase.getDescribedSpecimenOrObservation()));
|
|
835
|
return result;
|
|
836
|
}
|
|
837
|
|
|
838
|
protected <T extends DescriptionElementBase> T handlePersisted(DescriptionElementBase element) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
839
|
T result = handlePersisted((AnnotatableEntity)element);
|
|
840
|
//complete
|
|
841
|
result.setFeature(detache(result.getFeature()));
|
|
842
|
setInvisible(result, DescriptionElementBase.class, "inDescription", detache(result.getInDescription()));
|
|
843
|
handleCollection(result, DescriptionElementBase.class, "sources", DescriptionElementSource.class);
|
|
844
|
handleCollection(result, DescriptionElementBase.class, "media", Media.class);
|
|
845
|
handleCollection(result, DescriptionElementBase.class, "modifiers", DefinedTerm.class);
|
|
846
|
handleMap(result, DescriptionElementBase.class, "modifyingText", Language.class, LanguageString.class);
|
|
847
|
|
|
848
|
return result;
|
|
849
|
}
|
|
850
|
|
|
851
|
protected <T extends RelationshipBase> T handlePersisted(RelationshipBase relBase) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
852
|
T result = handlePersisted((ReferencedEntityBase)relBase);
|
|
853
|
return result;
|
|
854
|
}
|
|
855
|
|
|
856
|
|
|
857
|
//************************** COLLECTIONS / MAPS ****************************************/
|
|
858
|
|
|
859
|
protected <HOLDER extends CdmBase, ITEM extends CdmBase> void handleCollection(
|
|
860
|
HOLDER holder, Class<? super HOLDER> declaringClass, String parameter, Class<ITEM> itemClass)
|
|
861
|
throws NoSuchFieldException, IllegalAccessException, InvocationTargetException, NoSuchMethodException {
|
|
862
|
|
|
863
|
Collection<ITEM> oldCollection = setNewCollection(holder, declaringClass, parameter, itemClass);
|
|
864
|
Collection<ITEM> newCollection = getTargetCollection(itemClass, oldCollection);
|
|
865
|
Field field = declaringClass.getDeclaredField(parameter);
|
|
866
|
field.setAccessible(true);
|
|
867
|
field.set(holder, newCollection);
|
|
868
|
}
|
|
869
|
|
|
870
|
protected <HOLDER extends CdmBase, KEY extends CdmBase, ITEM extends CdmBase>
|
|
871
|
void handleMap(
|
|
872
|
HOLDER holder, Class<? super HOLDER> declaringClass, String parameter,
|
|
873
|
Class<KEY> keyClass, Class<ITEM> itemClass)
|
|
874
|
throws NoSuchFieldException, IllegalAccessException, InvocationTargetException, NoSuchMethodException {
|
|
875
|
|
|
876
|
//TODO we do not need to set the new map 2x
|
|
877
|
Map<KEY,ITEM> oldMap = setNewMap(holder, declaringClass, parameter, keyClass, itemClass);
|
|
878
|
Map<KEY,ITEM> newMap = getTargetMap(oldMap);
|
|
879
|
Field field = declaringClass.getDeclaredField(parameter);
|
|
880
|
field.setAccessible(true);
|
|
881
|
field.set(holder, newMap);
|
|
882
|
}
|
|
883
|
|
|
884
|
protected <T extends CdmBase> Collection<T> setNewCollection(CdmBase obj, Class<?> holderClass,
|
|
885
|
String parameter, Class<T> entityClass) throws NoSuchFieldException, SecurityException, IllegalArgumentException, IllegalAccessException {
|
|
886
|
Field field = holderClass.getDeclaredField(parameter);
|
|
887
|
field.setAccessible(true);
|
|
888
|
Collection<T> oldValue = (Collection<T>)field.get(obj);
|
|
889
|
Collection<T> newValue = null;
|
|
890
|
if (Set.class.isAssignableFrom(field.getType())){
|
|
891
|
newValue = new HashSet<>();
|
|
892
|
}else if (List.class.isAssignableFrom(field.getType())){
|
|
893
|
newValue = new ArrayList<>();
|
|
894
|
}else{
|
|
895
|
throw new RuntimeException("Unsupported collection type: " + field.getType().getCanonicalName());
|
|
896
|
}
|
|
897
|
field.set(obj, newValue);
|
|
898
|
return oldValue;
|
|
899
|
}
|
|
900
|
|
|
901
|
protected <KEY extends CdmBase, ITEM extends CdmBase> Map<KEY,ITEM> setNewMap(CdmBase obj, Class<?> holderClass,
|
|
902
|
String parameter, Class<KEY> keyClass, Class<ITEM> itemClass) throws NoSuchFieldException, SecurityException, IllegalArgumentException, IllegalAccessException {
|
|
903
|
Field field = holderClass.getDeclaredField(parameter);
|
|
904
|
field.setAccessible(true);
|
|
905
|
Map<KEY,ITEM> oldValue = (Map<KEY,ITEM>)field.get(obj);
|
|
906
|
Map<KEY,ITEM> newValue = null;
|
|
907
|
if (Map.class.isAssignableFrom(field.getType())){
|
|
908
|
newValue = new HashMap<>();
|
|
909
|
}else{
|
|
910
|
throw new RuntimeException("Unsupported map type: " + field.getType().getCanonicalName());
|
|
911
|
}
|
|
912
|
field.set(obj, newValue);
|
|
913
|
return oldValue;
|
|
914
|
}
|
|
915
|
|
|
916
|
|
|
917
|
private <T extends Collection<S>, S extends CdmBase> Collection<S> getTargetCollection(Class<S> clazz, T sourceCollection) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
918
|
Collection<S> result = new ArrayList<>();
|
|
919
|
if (Set.class.isAssignableFrom(sourceCollection.getClass())){
|
|
920
|
result = new HashSet<>();
|
|
921
|
}
|
|
922
|
for (S entity : sourceCollection){
|
|
923
|
S target = detache(entity);
|
|
924
|
result.add(target);
|
|
925
|
}
|
|
926
|
return result;
|
|
927
|
}
|
|
928
|
|
|
929
|
private <K extends CdmBase, V extends CdmBase> Map<K,V> getTargetMap(Map<K,V> sourceMap) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
|
|
930
|
Map<K,V> result = new HashMap<>();
|
|
931
|
for (K key : sourceMap.keySet()){
|
|
932
|
K targetKey = detache(key);
|
|
933
|
V targetValue = detache(sourceMap.get(key));
|
|
934
|
result.put(targetKey, targetValue);
|
|
935
|
}
|
|
936
|
return result;
|
|
937
|
}
|
|
938
|
|
|
939
|
// ****************************** INVISIBLE **************************************/
|
|
940
|
|
|
941
|
protected void setInvisible(Object holder, String fieldName, Object value) throws NoSuchFieldException, SecurityException, IllegalArgumentException, IllegalAccessException {
|
|
942
|
setInvisible(holder, holder.getClass(), fieldName, value);
|
|
943
|
}
|
|
944
|
protected void setInvisible(Object holder, Class<?> holderClazz, String fieldName, Object value) throws NoSuchFieldException, SecurityException, IllegalArgumentException, IllegalAccessException {
|
|
945
|
Field field = holderClazz.getDeclaredField(fieldName);
|
|
946
|
field.setAccessible(true);
|
|
947
|
field.set(holder, value);
|
|
948
|
}
|
|
949
|
|
|
950
|
// ************************* GET TARGET ******************************************/
|
|
951
|
|
|
952
|
|
|
953
|
//TODO this should be cached for partition
|
|
954
|
private <T extends CdmBase> T getTarget(T source) {
|
|
955
|
if (source == null){
|
|
956
|
return null;
|
|
957
|
}
|
|
958
|
T result = getCached(source);
|
|
959
|
// if (result == null){
|
|
960
|
// Class<T> clazz = (Class<T>)source.getClass();
|
|
961
|
// result = getCommonService().find(clazz, source.getUuid());
|
|
962
|
// }
|
|
963
|
if (result == null){
|
|
964
|
//Alternative: clone?
|
|
965
|
result = CdmBase.deproxy(source);
|
|
966
|
result.setId(0);
|
|
967
|
cache(result);
|
|
968
|
toSave.add(result);
|
|
969
|
}
|
|
970
|
return result;
|
|
971
|
}
|
|
972
|
|
|
973
|
// ******************* CACHE *******************************************************/
|
|
974
|
|
|
975
|
|
|
976
|
protected void cache(CdmBase cdmBase) {
|
|
977
|
if (cdmBase instanceof User || cdmBase instanceof DefinedTermBase){
|
|
978
|
getState().putPermanent(cdmBase.getUuid(), cdmBase);
|
|
979
|
}else{
|
|
980
|
sessionCache.put(cdmBase.getUuid(), cdmBase);
|
|
981
|
}
|
|
982
|
addExistingObject(cdmBase);
|
|
983
|
|
|
984
|
}
|
|
985
|
|
|
986
|
private void addExistingObject(CdmBase cdmBase) {
|
|
987
|
cdmBase = CdmBase.deproxy(cdmBase);
|
|
988
|
Set<UUID> set = existingObjects.get(cdmBase.getClass());
|
|
989
|
if (set == null){
|
|
990
|
set = loadExistingUuids(cdmBase.getClass());
|
|
991
|
// set = new HashSet<>();
|
|
992
|
// existingObjects.put(cdmBase.getClass(), set);
|
|
993
|
}
|
|
994
|
set.add(cdmBase.getUuid());
|
|
995
|
}
|
|
996
|
|
|
997
|
protected boolean isInCache(CdmBase cdmBase) {
|
|
998
|
return getCached(cdmBase) != null;
|
|
999
|
}
|
|
1000
|
|
|
1001
|
protected <T extends CdmBase> T getCached(T cdmBase) {
|
|
1002
|
T result = (T)sessionCache.get(cdmBase.getUuid());
|
|
1003
|
if (result == null){
|
|
1004
|
result = (T)getState().getPermanent(cdmBase.getUuid());
|
|
1005
|
}
|
|
1006
|
return result;
|
|
1007
|
}
|
|
1008
|
|
|
1009
|
protected void clearCache() {
|
|
1010
|
sessionCache.clear();
|
|
1011
|
}
|
|
1012
|
|
|
1013
|
public FauEu2CdmImportState getState() {
|
|
1014
|
return state;
|
|
1015
|
}
|
|
1016
|
|
|
1017
|
public void setState(FauEu2CdmImportState state) {
|
|
1018
|
this.state = state;
|
|
1019
|
}
|
|
1020
|
|
|
1021
|
}
|