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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.io.pesi.indexFungorum;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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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 org.apache.commons.lang.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.common.CdmUtils;
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import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
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import eu.etaxonomy.cdm.io.pesi.out.PesiTransformer;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.name.BotanicalName;
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import eu.etaxonomy.cdm.model.name.NonViralName;
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import eu.etaxonomy.cdm.model.name.Rank;
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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.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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* @created 27.02.2012
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*/
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@Component
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public class IndexFungorumGeneraImport extends IndexFungorumImportBase {
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private static final Logger logger = Logger.getLogger(IndexFungorumGeneraImport.class);
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private static final String pluralString = "genera";
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private static final String dbTableName = "tblGenera";
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public IndexFungorumGeneraImport(){
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super(pluralString, dbTableName, null);
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}
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@Override
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protected String getIdQuery() {
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String result = " SELECT [RECORD NUMBER] FROM " + getTableName() +
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" ORDER BY [NAME OF FUNGUS] ";
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return result;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getRecordQuery(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator)
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*/
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@Override
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protected String getRecordQuery(IndexFungorumImportConfigurator config) {
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String strRecordQuery =
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" SELECT DISTINCT c.[Family name], c.[Order name], c.[Subclass name], c.[Class name], c.[Subphylum name], c.[Phylum name], c.[Kingdom name], g.* " +
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" FROM tblGenera AS g LEFT OUTER JOIN dbo.[tblPESIfungi-Classification] AS c ON g.[RECORD NUMBER] = c.PreferredNameFDCnumber " +
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" WHERE ( g.[RECORD NUMBER] IN (" + ID_LIST_TOKEN + ") )" +
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"";
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return strRecordQuery;
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}
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@Override
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public boolean doPartition(ResultSetPartitioner partitioner, IndexFungorumImportState state) {
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boolean success =true;
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Reference<?> sourceReference = state.getRelatedObject(NAMESPACE_REFERENCE, SOURCE_REFERENCE, Reference.class);
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ResultSet rs = partitioner.getResultSet();
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Classification classification = getClassification(state);
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try {
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while (rs.next()){
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//TODO
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//DisplayName, NomRefCache
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Double id = (Double)rs.getObject("RECORD NUMBER");
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String preferredName = rs.getString("NAME OF FUNGUS");
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if (StringUtils.isBlank(preferredName)){
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logger.warn("Preferred name is blank. This case is not yet handled by IF import. RECORD NUMBER" + id);
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}
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Rank rank = Rank.GENUS();
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NonViralName<?> name = BotanicalName.NewInstance(rank);
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name.setGenusOrUninomial(preferredName);
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Taxon taxon = Taxon.NewInstance(name, sourceReference);
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Taxon parent = getParentTaxon(state, rs);
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classification.addParentChild(parent, taxon, null, null);
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//author + publication
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makeAuthorAndPublication(state, rs, name);
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//source
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//makeSource(state, taxon, id, NAMESPACE_GENERA );
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if (id != null){
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makeSource(state, taxon, id.intValue(), NAMESPACE_GENERA );
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} else{
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makeSource(state, taxon, null,NAMESPACE_GENERA);
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}
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getTaxonService().saveOrUpdate(taxon);
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}
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} catch (Exception e) {
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e.printStackTrace();
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logger.error(e.getMessage());
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state.setSuccess(false);
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success = false;
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}
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return success;
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}
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private Taxon getParentTaxon(IndexFungorumImportState state, ResultSet rs) throws SQLException {
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String parentName = getParentNameString(rs);
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if (parentName == null){
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logger.warn("Parent name not found for: " + rs.getString("NAME OF FUNGUS"));
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}
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Taxon taxon = state.getRelatedObject(NAMESPACE_SUPRAGENERIC_NAMES, parentName, Taxon.class);
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if (taxon == null){
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logger.warn("Taxon not found for " + parentName + " name of fungus: " +rs.getString("NAME OF FUNGUS") );
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}
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return taxon;
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}
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private String getParentNameString(ResultSet rs) throws SQLException {
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String parentName = rs.getString("Family name");
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if (parentName == null){
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logger.warn(rs.getObject("NAME OF FUNGUS") + " has no family name. ");
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return null;
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}
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if (parentName.equalsIgnoreCase(INCERTAE_SEDIS)){
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parentName = rs.getString("Order name");
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if (parentName.equalsIgnoreCase(INCERTAE_SEDIS)){
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parentName = rs.getString("Subclass name");
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if (parentName.equalsIgnoreCase(INCERTAE_SEDIS)){
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parentName = rs.getString("Class name");
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if (parentName.equalsIgnoreCase(INCERTAE_SEDIS)){
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parentName = rs.getString("Subphylum name");
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if (parentName.equalsIgnoreCase(INCERTAE_SEDIS)){
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parentName = rs.getString("Phylum name");
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if (parentName.equalsIgnoreCase(INCERTAE_SEDIS) || parentName.equalsIgnoreCase(FOSSIL_FUNGI) ){
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parentName = rs.getString("Kingdom name");
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}
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}
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}
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}
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}
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}
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return parentName;
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}
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@Override
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public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, IndexFungorumImportState state) {
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String nameSpace;
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Class<?> cdmClass;
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Set<String> idSet;
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Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
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try{
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Set<String> taxonNameSet = new HashSet<String>();
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while (rs.next()){
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// handleForeignKey(rs, taxonIdSet,"tu_acctaxon" );
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}
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//taxon map
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nameSpace = NAMESPACE_SUPRAGENERIC_NAMES ;
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cdmClass = TaxonBase.class;
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// idSet = taxonNameSet;
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Map<String, TaxonBase<?>> taxonMap = new HashMap<String, TaxonBase<?>>();
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List<TaxonBase> list = getTaxonService().listTaxaByName(Taxon.class, "*", null, null, null, null, 1000000, null);
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for (TaxonBase<?> taxon : list){
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taxonMap.put(CdmBase.deproxy(taxon.getName(), NonViralName.class).getGenusOrUninomial(), taxon);
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}
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result.put(nameSpace, taxonMap);
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//sourceReference
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Reference<?> sourceReference = getReferenceService().find(PesiTransformer.uuidSourceRefIndexFungorum);
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Map<String, Reference> referenceMap = new HashMap<String, Reference>();
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referenceMap.put(SOURCE_REFERENCE, sourceReference);
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result.put(NAMESPACE_REFERENCE, referenceMap);
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} catch (SQLException e) {
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throw new RuntimeException(e);
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}
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return result;
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}
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@Override
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protected boolean doCheck(IndexFungorumImportState state){
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return true;
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}
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@Override
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protected boolean isIgnore(IndexFungorumImportState state){
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return ! state.getConfig().isDoTaxa();
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}
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}
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