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/**
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* Copyright (C) 2016 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.mexico;
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import java.net.URI;
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import java.util.HashMap;
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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.commons.lang3.StringUtils;
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import org.apache.log4j.Logger;
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import org.springframework.stereotype.Component;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.OriginalSourceType;
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import eu.etaxonomy.cdm.model.common.TermType;
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import eu.etaxonomy.cdm.model.common.TermVocabulary;
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import eu.etaxonomy.cdm.model.description.CommonTaxonName;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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/**
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* @author a.mueller
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* @date 16.06.2016
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*
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*/
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@Component
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public class MexicoConabioCommonNamesImport<CONFIG extends MexicoConabioImportConfigurator>
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extends SimpleExcelTaxonImport<CONFIG>{
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private static final long serialVersionUID = 3579868489510261569L;
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private static final Logger logger = Logger.getLogger(MexicoConabioCommonNamesImport.class);
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private TermVocabulary<Language> languagesVoc;
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private Map<String, Language> languagesMap = new HashMap<>();
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private Map<String, Taxon> taxonIdMap;
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@Override
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protected String getWorksheetName() {
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return "NombresComunes";
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}
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@Override
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protected void firstPass(SimpleExcelTaxonImportState<CONFIG> state) {
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initLanguageVocabulary(state);
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initTaxa();
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String line = state.getCurrentLine() + ": ";
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HashMap<String, String> record = state.getOriginalRecord();
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String idCat = getValue(record, "IdCAT");
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Taxon taxon = taxonIdMap.get(idCat);
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if (taxon == null){
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logger.warn(line + "Taxon could not be found: " + idCat);
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}else{
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TaxonDescription desc = getTaxonDescription(taxon);
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String nomComunStr = getValue(record, "NomComun");
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String langStr = getValueNd(record, "Lengua");
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Language language = languagesMap.get(langStr);
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if (language == null && langStr != null){
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logger.warn("Language not found: " + langStr);
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}
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String refStr = getValue(record, "ReferenciasNombreComun");
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CommonTaxonName commonName = CommonTaxonName.NewInstance(nomComunStr,
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language, null);
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desc.addElement(commonName);
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Reference ref = getReference(state, refStr);
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if (ref != null){
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commonName.addSource(OriginalSourceType.PrimaryTaxonomicSource,
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null, null, ref, null);
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}
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getTaxonService().save(taxon);
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}
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}
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@SuppressWarnings("unchecked")
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private void initTaxa() {
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if (taxonIdMap == null){
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Set<String> existingKeys = MexicoConabioTaxonImport.taxonIdMap.keySet();
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taxonIdMap = (Map<String, Taxon>)getCommonService().getSourcedObjectsByIdInSource(Taxon.class,
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existingKeys, MexicoConabioTaxonImport.TAXON_NAMESPACE);
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}
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}
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/**
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* @param state
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*/
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@SuppressWarnings("unchecked")
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private void initLanguageVocabulary(SimpleExcelTaxonImportState<CONFIG> state) {
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if (languagesVoc == null){
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languagesVoc = this.getVocabularyService().find(MexicoConabioTransformer.uuidMexicanLanguagesVoc);
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if (languagesVoc == null){
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createLanguagesVoc(state);
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}
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}
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}
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/**
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* @param state
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* @return
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*/
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private void createLanguagesVoc(SimpleExcelTaxonImportState<CONFIG> state) {
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URI termSourceUri = null;
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String label = "Mexican States";
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String description = "Mexican languages as used by the CONABIO Rubiaceae database";
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languagesVoc = TermVocabulary.NewInstance(TermType.Language,
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description, label, null, termSourceUri);
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languagesVoc.setUuid(MexicoConabioTransformer.uuidMexicanLanguagesVoc);
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addLanguage(state, "Chontal", MexicoConabioTransformer.uuidChontal);
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addLanguage(state, "Chinanteco", MexicoConabioTransformer.uuidChinanteco);
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addLanguage(state, "Chiapaneca", MexicoConabioTransformer.uuidChiapaneca);
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addLanguage(state, "Huasteco", MexicoConabioTransformer.uuidHuasteco);
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addLanguage(state, "Español-Maya", MexicoConabioTransformer.uuidEspanol_Maya);
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addLanguage(state, "Guarijío", MexicoConabioTransformer.uuidGuarijio);
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addLanguage(state, "Huave", MexicoConabioTransformer.uuidHuave);
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addLanguage(state, "Español", MexicoConabioTransformer.uuidEspanol);
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addLanguage(state, "Maya", MexicoConabioTransformer.uuidMaya);
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addLanguage(state, "Lacandón", MexicoConabioTransformer.uuidLacandon);
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addLanguage(state, "Inglés", MexicoConabioTransformer.uuidIngles);
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addLanguage(state, "Itzmal", MexicoConabioTransformer.uuidItzmal);
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addLanguage(state, "Náhuatl", MexicoConabioTransformer.uuidNahuatl);
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addLanguage(state, "Tarahumara", MexicoConabioTransformer.uuidTarahumara);
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addLanguage(state, "Otomí", MexicoConabioTransformer.uuidOtomi);
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addLanguage(state, "Mixe", MexicoConabioTransformer.uuidMixe);
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addLanguage(state, "Tseltal", MexicoConabioTransformer.uuidTseltal);
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addLanguage(state, "Zapoteco", MexicoConabioTransformer.uuidZapoteco);
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addLanguage(state, "Totonaco", MexicoConabioTransformer.uuidTotonaco);
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addLanguage(state, "Tarasco", MexicoConabioTransformer.uuidTarasco);
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this.getVocabularyService().save(languagesVoc);
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return;
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}
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/**
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* @param state
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* @param string
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* @param uuidaguascalientes
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*/
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private void addLanguage(SimpleExcelTaxonImportState<CONFIG> state, String label, UUID uuid) {
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String abbrev = null;
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Language language = Language.NewInstance(
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label, label, abbrev);
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language.setUuid(uuid);
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languagesVoc.addTerm(language);
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languagesMap.put(label, language);
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}
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/**
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* @param state
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* @param refStr
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* @return
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*/
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private Reference getReference(SimpleExcelTaxonImportState<CONFIG> state, String refStr) {
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if (StringUtils.isNoneBlank(refStr)){
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return null;
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}
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Reference ref = state.getReference(refStr);
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if (ref == null){
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ref = ReferenceFactory.newBook();
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ref.setTitleCache(refStr, true);
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state.putReference(refStr, ref);
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}
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return ref;
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}
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/**
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* @param taxon
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* @return
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*/
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private TaxonDescription getTaxonDescription(Taxon taxon) {
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if (!taxon.getDescriptions().isEmpty()){
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return taxon.getDescriptions().iterator().next();
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}else{
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TaxonDescription desc = TaxonDescription.NewInstance(taxon);
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return desc;
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}
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}
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private String getValueNd(HashMap<String, String> record, String string) {
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String value = getValue(record, string);
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if ("ND".equals(value)){
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return null;
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}else{
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return value;
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}
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}
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@Override
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protected boolean isIgnore(SimpleExcelTaxonImportState<CONFIG> state) {
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return ! state.getConfig().isDoCommonNames();
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}
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}
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