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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.taxeditor.editor.e4;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Map;
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import java.util.Map.Entry;
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import java.util.Set;
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import java.util.UUID;
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import org.eclipse.core.commands.ExecutionException;
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import org.eclipse.core.commands.operations.IOperationHistory;
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import org.eclipse.core.runtime.IAdaptable;
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import org.eclipse.core.runtime.IStatus;
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import org.eclipse.core.runtime.NullProgressMonitor;
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import org.eclipse.core.runtime.Status;
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import org.eclipse.e4.ui.di.UISynchronize;
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import org.eclipse.ui.ide.undo.WorkspaceUndoUtil;
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import eu.etaxonomy.cdm.api.service.IClassificationService;
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import eu.etaxonomy.cdm.api.service.INameService;
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import eu.etaxonomy.cdm.api.service.ITaxonNodeService;
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import eu.etaxonomy.cdm.api.service.ITaxonService;
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import eu.etaxonomy.cdm.api.service.config.SynonymDeletionConfigurator;
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import eu.etaxonomy.cdm.api.service.config.TaxonBaseDeletionConfigurator;
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import eu.etaxonomy.cdm.api.service.config.TaxonDeletionConfigurator;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.name.HybridRelationship;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.taxon.ITaxonTreeNode;
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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.TaxonRelationship;
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import eu.etaxonomy.taxeditor.editor.CdmEntitySessionInput;
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import eu.etaxonomy.taxeditor.editor.ChooseFromMultipleAcceptedTaxaDialog;
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import eu.etaxonomy.taxeditor.editor.ChooseFromMultipleTaxonNodesDialog;
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import eu.etaxonomy.taxeditor.editor.l10n.Messages;
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import eu.etaxonomy.taxeditor.model.AbstractUtility;
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import eu.etaxonomy.taxeditor.model.MessagingUtils;
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import eu.etaxonomy.taxeditor.operation.AbstractPostOperation;
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import eu.etaxonomy.taxeditor.operation.IPostOperationEnabled;
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import eu.etaxonomy.taxeditor.preference.PreferencesUtil;
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import eu.etaxonomy.taxeditor.store.CdmStore;
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import eu.etaxonomy.taxeditor.store.internal.TaxeditorStorePlugin;
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/**
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* @author pplitzner
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* @date Aug 24, 2017
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*/
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public class TaxonEditorInput extends CdmEntitySessionInput<TaxonNode>{
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private static final String INCORRECT_STATE = Messages.TaxonEditorInput_INCORRECT_STATE;
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private TaxonNode taxonNode;
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private Map<TaxonBase, TaxonBaseDeletionConfigurator> toDeletes = new HashMap<>();
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private Set<Synonym> toSaveNewSynonyms = new HashSet<>();
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private Set<TaxonBase> toSaveConcepts = new HashSet<>();
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private Set<TaxonName> toSaveNewNames = new HashSet<>();
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private Set<AbstractPostOperation> operations = new HashSet<>();
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// private TaxonEditorInputDataChangeBehaviourE4 dataChangeBehavior;
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private TaxonBase<?> initiallySelectedTaxonBase;
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private UISynchronize sync;
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public void setSync(UISynchronize sync) {
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this.sync = sync;
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}
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private enum CdmType {
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TAXON_NODE,
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TAXON_BASE,
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PARENT_TAXON_NODE
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}
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private TaxonEditorInput(UUID uuid, CdmType type) {
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super(true);
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switch(type) {
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case PARENT_TAXON_NODE:
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initForParentTaxonNode(uuid);
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break;
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case TAXON_BASE:
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initForTaxonBase(uuid);
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break;
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case TAXON_NODE:
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initForTaxonNode(uuid);
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break;
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}
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}
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private void init(TaxonNode taxonNode) {
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this.taxonNode = taxonNode;
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}
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private void initForTaxonNode(UUID taxonNodeUuid) {
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this.getCdmEntitySession().bind();
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TaxonNode taxonNode = CdmStore.getService(ITaxonNodeService.class).load(taxonNodeUuid, getTaxonNodePropertyPaths());
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// TaxonNode taxonNode = getCdmEntitySession().remoteLoad(CdmStore.getService(ITaxonNodeService.class), taxonNodeUuid, getTaxonNodePropertyPaths());
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if(taxonNode == null){
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MessagingUtils.warningDialog(Messages.TaxonEditorInput_NOT_IMPLEMENTED, TaxonEditorInput.class, Messages.TaxonEditorInput_NOT_IMPLEMENTED_MESSAGE);
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}
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init(taxonNode);
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setInitiallySelectedTaxonBase(getTaxon());
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}
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private void initForTaxonBase(UUID taxonBaseUuid) {
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this.getCdmEntitySession().bind();
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// TaxonBase taxonBase = CdmStore.getService(ITaxonService.class).load(taxonBaseUuid, getTaxonBasePropertyPaths());
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TaxonBase<?> taxonBase = getCdmEntitySession().remoteLoad(CdmStore.getService(ITaxonService.class), taxonBaseUuid, getTaxonBasePropertyPaths());
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if (taxonBase != null){
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if(taxonBase.isInstanceOf(Taxon.class)){
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Taxon taxon = CdmBase.deproxy(taxonBase, Taxon.class);
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setInitiallySelectedTaxonBase(taxon);
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if ( taxon.isMisapplication() || taxon.isProparteSynonym()){
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// TODO get accepted taxon
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MessagingUtils.info(Messages.TaxonEditorInput_OPEN_MISSAPPLIED_NAME);
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Set<Taxon> acceptedTaxa = new HashSet<Taxon>();
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Set<TaxonRelationship> relations = taxon.getRelationsFromThisTaxon();
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for(TaxonRelationship relation : relations){
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if(relation.getType().isAnyMisappliedName() || relation.getType().isAnySynonym()){
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acceptedTaxa.add(relation.getToTaxon());
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}
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}
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if (taxon.getTaxonNodes().size() > 0){
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acceptedTaxa.add(taxon);
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}
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setInputForRelatedTaxa(acceptedTaxa);
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}else{
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setInputForMultipleNodes(taxon.getTaxonNodes());
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}
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}else if(taxonBase instanceof Synonym){
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Synonym synonym = (Synonym) taxonBase;
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Set<Taxon> taxa = new HashSet<>();
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Taxon taxon = synonym.getAcceptedTaxon();
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if (taxon != null){
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taxa.add(taxon);
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}
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setInputForMultipleTaxa(taxa);
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setInitiallySelectedTaxonBase(synonym);
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}
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}
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}
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private void initForParentTaxonNode(UUID parentNodeUuid){
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this.getCdmEntitySession().bind();
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TaxonName name = PreferencesUtil.getPreferredNomenclaturalCode().getNewTaxonNameInstance(null);
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ITaxonTreeNode parentNode = CdmStore.getService(IClassificationService.class).getTreeNodeByUuid(parentNodeUuid);
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Taxon newTaxon = Taxon.NewInstance(name, parentNode.getReference());
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TaxonNode newTaxonNode = parentNode.addChildTaxon(newTaxon, parentNode.getReference(), parentNode.getMicroReference());
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// add the new taxon to the editors persistence context
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UUID newTaxonNodeUuid = CdmStore.getService(ITaxonNodeService.class).save(newTaxonNode).getUuid();
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initForTaxonNode(newTaxonNodeUuid);
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}
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private void setInputForMultipleNodes(Set<TaxonNode> taxonNodes){
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if(taxonNodes.size() == 1){
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TaxonNode taxonNode = taxonNodes.iterator().next();
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taxonNode = getCdmEntitySession().remoteLoad(CdmStore.getService(ITaxonNodeService.class), taxonNode.getUuid(), getTaxonNodePropertyPaths());
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init(taxonNode);
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}else if(taxonNodes.size() > 1){
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TaxonNode taxonNode = ChooseFromMultipleTaxonNodesDialog.choose(taxonNodes);
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if(taxonNode != null){
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taxonNode = CdmStore.getService(ITaxonNodeService.class).load(taxonNode.getUuid(), getTaxonNodePropertyPaths());
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}
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if(taxonNode != null){
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init(taxonNode);
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}
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} else if (taxonNodes.size() == 0) {
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// this is an undesired state
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MessagingUtils.warningDialog(INCORRECT_STATE,TaxonEditorInput.class,Messages.TaxonEditorInput_TAXON_NOT_IN_CLASSIFICATION);
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}
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}
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private void setInputForMultipleTaxa(Set<Taxon> taxa){
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if(taxa.size() == 1){
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Taxon taxon = taxa.iterator().next();
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Set<TaxonNode> nodes = taxon.getTaxonNodes();
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setInputForMultipleNodes(nodes);
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}else if(taxa.size() > 1){
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Set<TaxonNode> taxonNodes = new HashSet<TaxonNode>();
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for ( Taxon taxon : taxa ){
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taxonNodes.addAll(taxon.getTaxonNodes());
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}
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setInputForMultipleNodes(taxonNodes);
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}else if(taxa.size() == 0){
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// this is an undesired state
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MessagingUtils.warningDialog(INCORRECT_STATE, TaxonEditorInput.class, Messages.TaxonEditorInput_NO_ACCEPTED_TAXON_PRESENT);
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}
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}
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private void setInputForRelatedTaxa(Set<Taxon> taxa){
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if(taxa.size() == 1){
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Taxon taxon = taxa.iterator().next();
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Set<TaxonNode> nodes = taxon.getTaxonNodes();
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TaxonNode taxonNode = null;
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if (nodes.size()>1){
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taxonNode = ChooseFromMultipleTaxonNodesDialog.choose(nodes);
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}else if (nodes.size()==1){
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taxonNode = nodes.iterator().next();
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}else{
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MessagingUtils.warningDialog(INCORRECT_STATE,TaxonEditorInput.class,Messages.TaxonEditorInput_TAXON_NOT_IN_CLASSIFICATION);
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}
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init(taxonNode);
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}else if(taxa.size() > 1){
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Iterator<Taxon> taxonIterator = taxa.iterator();
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Set<TaxonNode> nodes = new HashSet<>();
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while (taxonIterator.hasNext()){
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nodes.addAll(taxonIterator.next().getTaxonNodes());
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}
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TaxonNode taxonNode = ChooseFromMultipleAcceptedTaxaDialog.choose(nodes);
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if(taxonNode != null){
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taxonNode = CdmStore.getService(ITaxonNodeService.class).load(taxonNode.getUuid(), getTaxonNodePropertyPaths());
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}
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if(taxonNode != null){
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init(taxonNode);
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}
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} else if (taxa.size() == 0) {
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// this is an undesired state
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MessagingUtils.warningDialog(INCORRECT_STATE,TaxonEditorInput.class,Messages.TaxonEditorInput_TAXON_NOT_IN_CLASSIFICATION);
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}
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}
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public static TaxonEditorInput NewInstance(UUID taxonNodeUuid) {
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return new TaxonEditorInput(taxonNodeUuid, CdmType.TAXON_NODE);
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}
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public static TaxonEditorInput NewInstanceFromTaxonBase(UUID taxonBaseUuid){
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return new TaxonEditorInput(taxonBaseUuid, CdmType.TAXON_BASE);
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}
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public static TaxonEditorInput NewEmptyInstance(UUID parentNodeUuid){
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return new TaxonEditorInput(parentNodeUuid, CdmType.PARENT_TAXON_NODE);
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}
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public Object getAdapter(Class adapter) {
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if (adapter == Taxon.class) {
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return getTaxon();
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}
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if (adapter == TaxonNode.class) {
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return taxonNode;
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}
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return null;
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}
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/**
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* {@inheritDoc}
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*
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* Overrides equals to ensure that a taxon can only be edited by
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* one editor at a time.
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*/
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@Override
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public boolean equals(Object obj) {
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if (TaxonEditorInput.class.equals(obj.getClass())
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&& getTaxon() != null
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&& getTaxon().equals(((TaxonEditorInput) obj).getTaxon())) {
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if (((TaxonEditorInput) obj).getInitiallySelectedTaxonBase() != null){
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setInitiallySelectedTaxonBase(((TaxonEditorInput) obj).getInitiallySelectedTaxonBase());
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}
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return true;
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}
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return false;
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}
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public Taxon getTaxon(){
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if(taxonNode!=null){
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Taxon taxon = CdmBase.deproxy(taxonNode.getTaxon());
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return taxon;
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}
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return null;
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}
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public TaxonNode getTaxonNode() {
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return taxonNode;
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}
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public void setInitiallySelectedTaxonBase(TaxonBase taxonBase) {
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this.initiallySelectedTaxonBase = taxonBase;
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}
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public TaxonBase getInitiallySelectedTaxonBase() {
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return initiallySelectedTaxonBase;
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}
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public void addOperation(AbstractPostOperation operation) {
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this.operations.add(operation);
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}
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public void addToSaveNewSynonym(Synonym toSaveNew) {
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this.toSaveNewSynonyms.add(toSaveNew);
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}
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public void addToSaveConcept(Taxon toSaveNew) {
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this.toSaveConcepts.add(toSaveNew);
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}
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@Override
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public List<TaxonNode> getRootEntities() {
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return Arrays.asList(taxonNode);
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}
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@Override
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public void merge() {
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if (!this.getCdmEntitySession().isActive()){
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this.getCdmEntitySession().bind();
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}
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for(Entry<TaxonBase, TaxonBaseDeletionConfigurator> entry:toDeletes.entrySet()){
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delete(entry.getKey(), entry.getValue());
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}
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toDeletes.clear();
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// new concepts needs to be saved separately, the list contains all concepts, the
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for (TaxonBase<?> concept: toSaveConcepts){
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if (concept != null){
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if (concept.getName() != null){
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for (HybridRelationship rel : concept.getName().getHybridChildRelations()){
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toSaveNewNames.add(rel.getParentName());
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toSaveNewNames.add(rel.getHybridName());
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}
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}
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}
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}
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//handle cascading for hybrid relationshis
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//accepted taxa
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if (taxonNode.getTaxon().getName() != null){
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for (HybridRelationship rel : taxonNode.getTaxon().getName().getHybridChildRelations()){
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toSaveNewNames.add(rel.getParentName());
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toSaveNewNames.add(rel.getHybridName());
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}
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}
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//synonyms
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for (TaxonName synonymName : taxonNode.getTaxon().getSynonymNames()){
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if (synonymName != null){
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for (HybridRelationship rel : synonymName.getHybridChildRelations()){
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toSaveNewNames.add(rel.getParentName());
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toSaveNewNames.add(rel.getHybridName());
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}
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}
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}
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if (!toSaveNewNames.isEmpty()){
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List<TaxonName> listNames = new ArrayList(toSaveNewNames);
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CdmStore.getService(INameService.class).merge(listNames, true);
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}
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if (!toSaveConcepts.isEmpty()){
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List<TaxonBase> listTaxa = new ArrayList(toSaveConcepts);
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CdmStore.getService(ITaxonService.class).merge(listTaxa, true);
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}
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toSaveNewNames.clear();
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toSaveConcepts.clear();
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for(AbstractPostOperation<?> entry:operations){
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IStatus status = Status.CANCEL_STATUS;
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final IAdaptable uiInfoAdapter = WorkspaceUndoUtil
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.getUIInfoAdapter(AbstractUtility.getShell());
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String operationlabel = entry.getLabel();
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try {
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entry.addContext(IOperationHistory.GLOBAL_UNDO_CONTEXT);
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status = entry.execute(new NullProgressMonitor(), uiInfoAdapter);
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} catch (ExecutionException e) {
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MessagingUtils.operationDialog(AbstractUtility.class, e, TaxeditorStorePlugin.PLUGIN_ID, operationlabel, null);
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}
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IPostOperationEnabled postOperationEnabled = entry
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.getPostOperationEnabled();
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if (postOperationEnabled != null) {
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postOperationEnabled.onComplete();
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}
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401
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//AbstractUtility.executeOperation(entry,sync);
|
402
|
}
|
403
|
|
404
|
operations.clear();
|
405
|
CdmStore.getService(ITaxonNodeService.class).merge(taxonNode, true);
|
406
|
}
|
407
|
|
408
|
private void delete(TaxonBase key, TaxonBaseDeletionConfigurator value) {
|
409
|
if (key instanceof Synonym){
|
410
|
CdmStore.getService(ITaxonService.class).deleteSynonym(((Synonym)key).getUuid(), (SynonymDeletionConfigurator) value);
|
411
|
}else{
|
412
|
CdmStore.getService(ITaxonService.class).deleteTaxon(((Taxon)key).getUuid(), (TaxonDeletionConfigurator) value, null);
|
413
|
}
|
414
|
}
|
415
|
|
416
|
@Override
|
417
|
public Map<Object, List<String>> getPropertyPathsMap() {
|
418
|
return null;
|
419
|
}
|
420
|
|
421
|
private List<String> getTaxonNodePropertyPaths() {
|
422
|
List<String> taxonNodePropertyPaths = new ArrayList<String>();
|
423
|
for(String propertyPath : getTaxonBasePropertyPaths()) {
|
424
|
taxonNodePropertyPaths.add("taxon." + propertyPath); //$NON-NLS-1$
|
425
|
}
|
426
|
return taxonNodePropertyPaths;
|
427
|
}
|
428
|
|
429
|
private List<String> getTaxonBasePropertyPaths() {
|
430
|
List<String> taxonBasePropertyPaths = Arrays.asList(new String[] {
|
431
|
"sec", //$NON-NLS-1$
|
432
|
"createdBy", //$NON-NLS-1$
|
433
|
"updatedBy", //$NON-NLS-1$
|
434
|
"annotations", //$NON-NLS-1$
|
435
|
"markers", //$NON-NLS-1$
|
436
|
"credits", //$NON-NLS-1$
|
437
|
"extensions", //$NON-NLS-1$
|
438
|
"rights", //$NON-NLS-1$
|
439
|
"sources", //$NON-NLS-1$
|
440
|
"sources.links", //$NON-NLS-1$
|
441
|
"identifiers",
|
442
|
"descriptions", //$NON-NLS-1$
|
443
|
"taxonNodes", //$NON-NLS-1$
|
444
|
"descriptions.descriptionElements.feature", //$NON-NLS-1$
|
445
|
"descriptions.descriptionElements.area", //$NON-NLS-1$
|
446
|
"descriptions.descriptionElements.status", //$NON-NLS-1$
|
447
|
"descriptions.descriptionElements.markers", //$NON-NLS-1$
|
448
|
"descriptions.descriptionElements.sources", //$NON-NLS-1$
|
449
|
"descriptions.descriptionElements.annotations", //$NON-NLS-1$
|
450
|
"descriptions.markers", //$NON-NLS-1$
|
451
|
"descriptions.descriptionSources", //$NON-NLS-1$
|
452
|
"descriptions.sources", //$NON-NLS-1$
|
453
|
"descriptions.annotations", //$NON-NLS-1$
|
454
|
"descriptions.links", //$NON-NLS-1$
|
455
|
"name.descriptions", //$NON-NLS-1$
|
456
|
"name.typeDesignations.typeSpecimen.derivedFrom.originals", //$NON-NLS-1$
|
457
|
"name.typeDesignations.source", //$NON-NLS-1$
|
458
|
"name.typeDesignations.source.nameUsedInSource", //$NON-NLS-1$
|
459
|
"name.typeDesignations.source.citation", //$NON-NLS-1$
|
460
|
"name.typeDesignations.source.links", //$NON-NLS-1$
|
461
|
"name.typeDesignations.text", //$NON-NLS-1$
|
462
|
"name.typeDesignations.sources", //$NON-NLS-1$
|
463
|
"name.typeDesignations.sources.links", //$NON-NLS-1$
|
464
|
"name.status", //$NON-NLS-1$
|
465
|
"name.nomenclaturalSource", //$NON-NLS-1$
|
466
|
"name.nomenclaturalSource.nameUsedInSource", //$NON-NLS-1$
|
467
|
"name.nomenclaturalSource.links.description", //$NON-NLS-1$
|
468
|
"name.nomenclaturalSource.citation", //$NON-NLS-1$
|
469
|
"name.nomenclaturalSource.citation.inReference", //$NON-NLS-1$
|
470
|
"name.nomenclaturalSource.cdmSource", //$NON-NLS-1$
|
471
|
"name.nomenclaturalSource.cdmSource.description", //$NON-NLS-1$
|
472
|
"name.status.source", //$NON-NLS-1$
|
473
|
"name.status.source.links", //$NON-NLS-1$
|
474
|
"name.taxonBases.taxonNodes", //$NON-NLS-1$
|
475
|
"name.relationsFromThisName", //$NON-NLS-1$
|
476
|
"name.relationsFromThisName.source", //$NON-NLS-1$
|
477
|
"name.relationsFromThisName.source.links", //$NON-NLS-1$
|
478
|
"name.relationsToThisName", //$NON-NLS-1$
|
479
|
"name.relationsToThisName.source", //$NON-NLS-1$
|
480
|
"name.relationsToThisName.source.links", //$NON-NLS-1$
|
481
|
"name.homotypicalGroup.typifiedNames.taxonBases.synonyms.synonym.name.status", //$NON-NLS-1$
|
482
|
"name.homotypicalGroup.typifiedNames.relationsToThisName.fromName", //$NON-NLS-1$
|
483
|
"name.rank.vocabulary", //$NON-NLS-1$
|
484
|
"synonyms.name.status.type", //$NON-NLS-1$
|
485
|
"synonyms.name.relationsToThisName.relatedFrom", //$NON-NLS-1$
|
486
|
"synonyms.name.relationsFromThisName.relatedTo", //$NON-NLS-1$
|
487
|
"synonyms.name.nomenclaturalSource", //$NON-NLS-1$
|
488
|
"synonyms.name.nomenclaturalSource.nameUsedInSource", //$NON-NLS-1$
|
489
|
"synonyms.name.nomenclaturalSource.links", //$NON-NLS-1$
|
490
|
"synonyms.name.nomenclaturalSource.citation", //$NON-NLS-1$
|
491
|
"synonyms.name.nomenclaturalSource.citation.inReference", //$NON-NLS-1$
|
492
|
"synonyms.name.nomenclaturalSource.cdmSource", //$NON-NLS-1$
|
493
|
"synonyms.name.nomenclaturalSource.cdmSource.description", //$NON-NLS-1$
|
494
|
"synonyms.name.nomenclaturalSource.citation.inReference.authorship", //$NON-NLS-1$
|
495
|
"synonyms.name.nomenclaturalSource.citation.authorship", //$NON-NLS-1$
|
496
|
"synonyms.name.homotypicalGroup.typifiedNames.taxonBases.synonyms", //$NON-NLS-1$
|
497
|
"relationsFromThisTaxon",//$NON-NLS-1$
|
498
|
"relationsToThisTaxon"//$NON-NLS-1$
|
499
|
|
500
|
});
|
501
|
|
502
|
return taxonBasePropertyPaths;
|
503
|
}
|
504
|
|
505
|
public void addTaxonBaseToDelete(TaxonBase selectedElement, TaxonBaseDeletionConfigurator deleteConfig) {
|
506
|
this.toDeletes.put(selectedElement, deleteConfig);
|
507
|
|
508
|
}
|
509
|
|
510
|
public void addToSaveNewName(TaxonName newName) {
|
511
|
this.toSaveNewNames.add(newName);
|
512
|
}
|
513
|
}
|