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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.cdm.app.wp6.palmae;
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import java.util.List;
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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 org.springframework.transaction.TransactionStatus;
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import eu.etaxonomy.cdm.api.application.CdmApplicationController;
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import eu.etaxonomy.cdm.app.common.CdmDestinations;
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import eu.etaxonomy.cdm.database.DbSchemaValidation;
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import eu.etaxonomy.cdm.database.ICdmDataSource;
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import eu.etaxonomy.cdm.model.common.OriginalSourceType;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.FeatureNode;
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import eu.etaxonomy.cdm.model.description.FeatureTree;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.description.TextData;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.reference.IReference;
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import eu.etaxonomy.cdm.model.reference.Reference;
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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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/**
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* @author a.mueller
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* @since 01.10.2009
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*/
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public class PalmaePostImportUpdater {
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private static final Logger logger = Logger.getLogger(PalmaePostImportUpdater.class);
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static final ICdmDataSource cdmDestination = CdmDestinations.localH2Palmae();
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private String relationships = "relationships";
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private String taxonomicAccounts = "taxonomic accounts";
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private String fossilRecord = "fossil record";
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public boolean updateMissingFeatures(ICdmDataSource dataSource) {
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try{
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int count = 0;
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UUID featureTreeUuid = PalmaeActivator.featureTreeUuid;
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CdmApplicationController cdmApp = CdmApplicationController.NewInstance(dataSource, DbSchemaValidation.VALIDATE);
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TransactionStatus tx = cdmApp.startTransaction();
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FeatureTree tree = cdmApp.getFeatureTreeService().find(featureTreeUuid);
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FeatureNode root = tree.getRoot();
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List<Feature> featureList = cdmApp.getTermService().list(Feature.class, null, null, null, null);
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for (Feature feature : featureList){
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String label = feature.getLabel();
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if (relationships.equals(label)){
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FeatureNode newNode = FeatureNode.NewInstance(feature);
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root.addChild(newNode);
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count++;
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}else if(taxonomicAccounts.equals(label)){
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FeatureNode newNode = FeatureNode.NewInstance(feature);
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root.addChild(newNode);
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count++;
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}else if(fossilRecord.equals(label)){
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FeatureNode newNode = FeatureNode.NewInstance(feature);
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root.addChild(newNode);
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count++;
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}
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}
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cdmApp.commitTransaction(tx);
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if (count != 3){
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logger.warn("Did not find 3 additional features but " + count);
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return false;
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}
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logger.info("Feature tree updated!");
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return true;
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} catch (Exception e) {
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e.printStackTrace();
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logger.error("ERROR in feature tree update");
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return false;
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}
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}
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public boolean updateNameUsage(ICdmDataSource dataSource) {
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try{
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boolean result = true;
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CdmApplicationController cdmApp = CdmApplicationController.NewInstance(dataSource, DbSchemaValidation.VALIDATE);
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TransactionStatus tx = cdmApp.startTransaction();
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int page = 0;
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int count = cdmApp.getTaxonService().count(Taxon.class);
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List<TaxonBase> taxonList = cdmApp.getTaxonService().list(TaxonBase.class, 100000, page, null, null);
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int i = 0;
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IReference treatmentReference = (IReference) cdmApp.getCommonService().getSourcedObjectByIdInSource(Reference.class, "palm_pub_ed_999999", "PublicationCitation");
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if (treatmentReference == null){
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logger.error("Treatment reference could not be found");
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result = false;
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}else{
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for (TaxonBase nameUsage : taxonList){
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if ((i++ % 100) == 0){System.out.println(i);};
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try {
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//if not in treatment
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if (! isInTreatment(nameUsage, treatmentReference, false)){
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//if connected treatment taxon can be found
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Taxon acceptedTaxon = getAcceptedTreatmentTaxon(nameUsage, treatmentReference);
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if (acceptedTaxon != null){
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//add as citation and delete
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addNameUsage(acceptedTaxon, nameUsage);
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cdmApp.getTaxonService().delete(nameUsage);
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}else{
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logger.warn("Non treatment taxon has no accepted taxon in treatment: " + nameUsage + " (" + nameUsage.getId() +")" );
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}
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}
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} catch (Exception e) {
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result = false;
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e.printStackTrace();
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}
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}
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}
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//add citation feature to feature tree
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UUID featureTreeUuid = PalmaeActivator.featureTreeUuid;
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FeatureTree tree = cdmApp.getFeatureTreeService().find(featureTreeUuid);
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FeatureNode root = tree.getRoot();
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List<Feature> featureList = cdmApp.getTermService().list(Feature.class, null, null, null, null);
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count = 0;
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for (Feature feature : featureList){
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if (feature.equals(Feature.CITATION())){
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FeatureNode newNode = FeatureNode.NewInstance(feature);
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root.addChild(newNode);
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count++;
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}
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}
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if (count != 1){
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logger.warn("Did not add exactly 1 features to the feature tree but " + count);
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result = false;
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}
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//commit
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cdmApp.commitTransaction(tx);
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logger.info("NameUsage updated!");
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return result;
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} catch (Exception e) {
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e.printStackTrace();
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logger.error("ERROR in name usage update");
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return false;
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}
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}
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/**
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* @param nameUsage
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* @return
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*/
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private Taxon getAcceptedTreatmentTaxon(TaxonBase nameUsage, IReference treatmentReference) {
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boolean hasSynonymInTreatment = false;
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TaxonName name = nameUsage.getName();
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Set<TaxonBase> candidateList = name.getTaxonBases();
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for (TaxonBase candidate : candidateList){
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if (candidate instanceof Taxon){
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if (isInTreatment(candidate, treatmentReference, false)){
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return (Taxon)candidate;
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}
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}else if (candidate instanceof Synonym){
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Synonym synonym = (Synonym)candidate;
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Taxon accTaxon = synonym.getAcceptedTaxon();
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if (isInTreatment(synonym, treatmentReference, true)){
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hasSynonymInTreatment = true;
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}
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if (accTaxon != null){
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if (isInTreatment(accTaxon, treatmentReference, false)){
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return accTaxon;
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}
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}
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}else{
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throw new IllegalStateException("TaxonBase should be either a Taxon or a Synonym but was " + nameUsage.getClass().getName());
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}
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}
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if (hasSynonymInTreatment){
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logger.warn("Non treatment taxon has synonym in treatment but no accepted taxon: " + nameUsage + " (" + nameUsage.getId() +")" );
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}
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return null;
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}
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/**
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* @param taxonBase
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* @param treatmentReference
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* @return
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*/
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private boolean isInTreatment(TaxonBase taxonBase, IReference treatmentReference, boolean silent) {
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if (taxonBase.getSec().equals(treatmentReference)){
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//treatment taxa
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if (! silent){
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if (taxonBase instanceof Taxon){
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if (((Taxon)taxonBase).getTaxonNodes().size()< 1){
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logger.warn("Taxon has treatment sec but is not in tree: " + taxonBase + " (" + taxonBase.getId() +")" );
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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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boolean hasAccTaxonInTreatment = false;
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Taxon accTaxon = synonym.getAcceptedTaxon();
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if (accTaxon != null){
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hasAccTaxonInTreatment |= isInTreatment(accTaxon, treatmentReference, false);
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}
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if (hasAccTaxonInTreatment == false){
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logger.warn("Synonym has treatment reference but has no accepted taxon in tree: " + taxonBase + " (" + taxonBase.getId() +")" );
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}
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}else{
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throw new IllegalStateException("TaxonBase should be either Taxon or Synonym");
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}
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}
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return true;
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}else{
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//taxon not in treatment
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if (! silent){
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if (taxonBase instanceof Taxon){
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if (((Taxon)taxonBase).getTaxonNodes().size()> 0){
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logger.warn("Taxon has no treatment sec but is in tree: " + taxonBase + " (" + taxonBase.getId() +")" );
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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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boolean hasAccTaxonInTreatment = false;
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Taxon accTaxon = synonym.getAcceptedTaxon();
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if (accTaxon != null){
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hasAccTaxonInTreatment |= isInTreatment(accTaxon, treatmentReference, false);
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}
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if (hasAccTaxonInTreatment == true){
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logger.warn("Synonym has no treatment reference but has accepted taxon in treatment: " + taxonBase + " (" + taxonBase.getId() +")" );
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}
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}else{
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throw new IllegalStateException("TaxonBase should be either Taxon or Synonym but was ");
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}
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}
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return false;
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}
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}
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/**
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* @param taxonCandidate
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* @param taxon
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*/
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private boolean addNameUsage(Taxon taxon, TaxonBase nameUsageTaxon) {
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TaxonDescription myDescription = null;
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for (TaxonDescription desc : taxon.getDescriptions()){
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if (! desc.isImageGallery()){
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myDescription = desc;
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break;
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}
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}
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if (myDescription == null){
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return false;
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}
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TextData textData = TextData.NewInstance(Feature.CITATION());
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//creates text (name: reference)
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//textData.putText(nameUsageTaxon.getName().getTitleCache()+": " + nameUsageTaxon.getSec().getTitleCache(), Language.DEFAULT());
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textData.addSource(OriginalSourceType.PrimaryTaxonomicSource, null, null, nameUsageTaxon.getSec(), null, nameUsageTaxon.getName(), nameUsageTaxon.getName().getTitleCache());
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myDescription.addElement(textData);
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return true;
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}
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/**
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* @param args
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*/
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public static void main(String[] args) {
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PalmaePostImportUpdater updater = new PalmaePostImportUpdater();
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try {
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updater.updateMissingFeatures(cdmDestination);
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updater.updateNameUsage(cdmDestination);
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} catch (Exception e) {
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e.printStackTrace();
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logger.error("ERROR in feature tree update");
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}
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}
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}
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