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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.csv.redlist.out;
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import java.io.File;
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import java.io.FileNotFoundException;
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import java.io.FileOutputStream;
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import java.io.IOException;
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import java.io.OutputStream;
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import java.io.OutputStreamWriter;
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import java.io.PrintWriter;
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import java.io.UnsupportedEncodingException;
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import java.util.HashSet;
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import java.util.Set;
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import java.util.UUID;
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import javax.xml.stream.XMLOutputFactory;
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import javax.xml.stream.XMLStreamException;
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import javax.xml.stream.XMLStreamWriter;
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import org.apache.commons.lang.StringUtils;
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import org.apache.log4j.Logger;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.io.common.CdmExportBase;
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import eu.etaxonomy.cdm.io.common.ICdmExport;
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import eu.etaxonomy.cdm.io.common.mapping.out.IExportTransformer;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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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.reference.IOriginalSource;
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import eu.etaxonomy.cdm.model.reference.ISourceable;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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/**
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* @author a.mueller, a.oppermann
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* @since 18.10.2012
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*
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*/
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public abstract class CsvExportBaseRedlist
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extends CdmExportBase<CsvTaxExportConfiguratorRedlist, CsvTaxExportStateRedlist, IExportTransformer, File>
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implements ICdmExport<CsvTaxExportConfiguratorRedlist, CsvTaxExportStateRedlist>{
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private static final long serialVersionUID = 2719567114724597599L;
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private static final Logger logger = Logger.getLogger(CsvExportBaseRedlist.class);
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protected static final boolean IS_CORE = true;
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protected Set<Integer> existingRecordIds = new HashSet<Integer>();
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protected Set<UUID> existingRecordUuids = new HashSet<UUID>();
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/**
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* Creates the locationId, locality, countryCode triple
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* @param record
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* @param area
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*/
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protected void handleArea(ICsvAreaRecord record, NamedArea area, TaxonBase<?> taxon, boolean required) {
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if (area != null){
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record.setLocationId(area);
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record.setLocality(area.getLabel());
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if (area.isInstanceOf(Country.class)){
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Country country = CdmBase.deproxy(area, Country.class);
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record.setCountryCode(country.getIso3166_A2());
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}
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}else{
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if (required){
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String message = "Description requires area but area does not exist for taxon " + getTaxonLogString(taxon);
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logger.warn(message);
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}
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}
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}
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protected String getTaxonLogString(TaxonBase<?> taxon) {
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return taxon.getTitleCache() + "(" + taxon.getId() + ")";
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}
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/**
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* @param el
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* @return
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*/
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protected boolean recordExists(CdmBase el) {
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return existingRecordIds.contains(el.getId());
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}
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/**
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* @param sec
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*/
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protected void addExistingRecord(CdmBase cdmBase) {
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existingRecordIds.add(cdmBase.getId());
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}
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/**
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* @param el
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* @return
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*/
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protected boolean recordExistsUuid(CdmBase el) {
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return existingRecordUuids.contains(el.getUuid());
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}
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/**
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* @param sec
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*/
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protected void addExistingRecordUuid(CdmBase cdmBase) {
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existingRecordUuids.add(cdmBase.getUuid());
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}
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protected String getSources(ISourceable<?> sourceable, CsvTaxExportConfiguratorRedlist config) {
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String result = "";
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for (IOriginalSource source: sourceable.getSources()){
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if (StringUtils.isBlank(source.getIdInSource())){//idInSource indicates that this source is only data provenance, may be changed in future
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if (source.getCitation() != null){
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String ref = source.getCitation().getTitleCache();
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result = CdmUtils.concat(config.getSetSeparator(), result, ref);
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}
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}
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}
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return result;
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}
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/**
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* @param config
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* @return
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* @throws IOException
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* @throws FileNotFoundException
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*/
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protected FileOutputStream createFileOutputStream(CsvTaxExportConfiguratorRedlist config, String thisFileName) throws IOException, FileNotFoundException {
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String filePath = config.getDestinationNameString();
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String fileName = filePath + File.separatorChar + thisFileName;
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File f = new File(fileName);
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if (!f.exists()){
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f.createNewFile();
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}
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FileOutputStream fos = new FileOutputStream(f);
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return fos;
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}
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/**
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* @param config
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* @param factory
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* @return
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* @throws IOException
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* @throws FileNotFoundException
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* @throws XMLStreamException
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*/
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protected XMLStreamWriter createXmlStreamWriter(CsvTaxExportStateRedlist state, String fileName)
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throws IOException, FileNotFoundException, XMLStreamException {
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XMLOutputFactory factory = XMLOutputFactory.newInstance();
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OutputStream os;
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boolean useZip = state.isZip();
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if (useZip){
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os = state.getZipStream(fileName);
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}else{
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os = createFileOutputStream(state.getConfig(), fileName);
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}
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XMLStreamWriter writer = factory.createXMLStreamWriter(os);
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return writer;
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}
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/**
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* @param coreTaxFileName
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* @param config
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* @return
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* @throws IOException
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* @throws FileNotFoundException
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* @throws UnsupportedEncodingException
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*/
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protected PrintWriter createPrintWriter(final String fileName, CsvTaxExportStateRedlist state)
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throws IOException, FileNotFoundException, UnsupportedEncodingException {
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OutputStream os;
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boolean useZip = state.isZip();
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if (useZip){
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os = state.getZipStream(fileName);
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}else{
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os = createFileOutputStream(state.getConfig(), fileName);
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}
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PrintWriter writer = new PrintWriter(new OutputStreamWriter(os, "UTF8"), true);
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return writer;
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}
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/**
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* Closes the writer
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* @param writer
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* @param state
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*/
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protected void closeWriter(PrintWriter writer, CsvTaxExportStateRedlist state) {
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if (writer != null && state.isZip() == false){
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writer.close();
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}
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}
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/**
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* Closes the writer.
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* Note: XMLStreamWriter does not close the underlying stream.
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* @param writer
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* @param state
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*/
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protected void closeWriter(XMLStreamWriter writer, CsvTaxExportStateRedlist state) {
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if (writer != null && state.isZip() == false){
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try {
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writer.close();
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} catch (XMLStreamException e) {
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throw new RuntimeException(e);
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}
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}
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}
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protected void clearExistingRecordIds(){
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existingRecordIds.clear();
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}
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}
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