228 lines
7.6 KiB
Java
228 lines
7.6 KiB
Java
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package eu.dnetlib.doiboost.orcid;
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import java.io.BufferedReader;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.InputStreamReader;
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import java.net.URI;
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import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
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import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.Path;
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import org.apache.hadoop.io.IOUtils;
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import org.apache.hadoop.io.SequenceFile;
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import org.apache.hadoop.io.Text;
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import org.apache.hadoop.io.compress.CompressionCodec;
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import org.apache.hadoop.io.compress.CompressionCodecFactory;
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import org.apache.hadoop.io.compress.GzipCodec;
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import org.mortbay.log.Log;
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import eu.dnetlib.dhp.schema.orcid.AuthorData;
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import eu.dnetlib.doiboost.orcid.xml.XMLRecordParser;
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import eu.dnetlib.doiboost.orcidnodoi.json.JsonWriter;
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public class SummariesDecompressor {
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private static final int MAX_XML_RECORDS_PARSED = -1;
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public static void parseGzSummaries(Configuration conf, String inputUri, Path outputPath)
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throws Exception {
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String uri = inputUri;
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FileSystem fs = FileSystem.get(URI.create(uri), conf);
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Path inputPath = new Path(uri);
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CompressionCodecFactory factory = new CompressionCodecFactory(conf);
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CompressionCodec codec = factory.getCodec(inputPath);
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if (codec == null) {
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System.err.println("No codec found for " + uri);
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System.exit(1);
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}
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CompressionCodecFactory.removeSuffix(uri, codec.getDefaultExtension());
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InputStream gzipInputStream = null;
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try {
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gzipInputStream = codec.createInputStream(fs.open(inputPath));
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parseTarSummaries(fs, conf, gzipInputStream, outputPath);
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} finally {
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Log.debug("Closing gzip stream");
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IOUtils.closeStream(gzipInputStream);
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}
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}
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private static void parseTarSummaries(
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FileSystem fs, Configuration conf, InputStream gzipInputStream, Path outputPath) {
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int counter = 0;
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int nameFound = 0;
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int surnameFound = 0;
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int creditNameFound = 0;
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int otherNamesFound = 0;
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int errorFromOrcidFound = 0;
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int xmlParserErrorFound = 0;
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try (TarArchiveInputStream tais = new TarArchiveInputStream(gzipInputStream)) {
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TarArchiveEntry entry = null;
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try (SequenceFile.Writer writer = SequenceFile
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.createWriter(
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conf,
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SequenceFile.Writer.file(outputPath),
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SequenceFile.Writer.keyClass(Text.class),
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SequenceFile.Writer.valueClass(Text.class))) {
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while ((entry = tais.getNextTarEntry()) != null) {
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String filename = entry.getName();
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try {
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if (entry.isDirectory()) {
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Log.debug("Directory entry name: " + entry.getName());
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} else {
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Log.debug("XML record entry name: " + entry.getName());
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counter++;
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BufferedReader br = new BufferedReader(new InputStreamReader(tais)); // Read directly from
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// tarInput
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String line;
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StringBuffer buffer = new StringBuffer();
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while ((line = br.readLine()) != null) {
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buffer.append(line);
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}
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AuthorData authorData = XMLRecordParser.VTDParseAuthorData(buffer.toString().getBytes());
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if (authorData != null) {
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if (authorData.getErrorCode() != null) {
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errorFromOrcidFound += 1;
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Log
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.debug(
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"error from Orcid with code "
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+ authorData.getErrorCode()
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+ " for oid "
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+ entry.getName());
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continue;
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}
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String jsonData = JsonWriter.create(authorData);
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Log.debug("oid: " + authorData.getOid() + " data: " + jsonData);
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final Text key = new Text(authorData.getOid());
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final Text value = new Text(jsonData);
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try {
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writer.append(key, value);
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} catch (IOException e) {
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Log.debug("Writing to sequence file: " + e.getMessage());
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Log.debug(e);
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throw new RuntimeException(e);
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}
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if (authorData.getName() != null) {
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nameFound += 1;
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}
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if (authorData.getSurname() != null) {
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surnameFound += 1;
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}
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if (authorData.getCreditName() != null) {
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creditNameFound += 1;
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}
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if (authorData.getOtherNames() != null && authorData.getOtherNames().size() > 1) {
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otherNamesFound += authorData.getOtherNames().size();
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}
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} else {
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Log.warn("Data not retrievable [" + entry.getName() + "] " + buffer.toString());
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xmlParserErrorFound += 1;
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}
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}
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} catch (Exception e) {
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Log
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.warn(
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"Parsing record from tar archive and xml record: "
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+ filename
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+ " "
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+ e.getMessage());
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Log.warn(e);
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}
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if ((counter % 100000) == 0) {
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Log.info("Current xml records parsed: " + counter);
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}
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if ((MAX_XML_RECORDS_PARSED > -1) && (counter > MAX_XML_RECORDS_PARSED)) {
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break;
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}
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}
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}
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} catch (IOException e) {
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Log.warn("Parsing record from gzip archive: " + e.getMessage());
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Log.warn(e);
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throw new RuntimeException(e);
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}
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Log.info("Summaries parse completed");
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Log.info("Total XML records parsed: " + counter);
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Log.info("Name found: " + nameFound);
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Log.info("Surname found: " + surnameFound);
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Log.info("Credit name found: " + creditNameFound);
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Log.info("Other names found: " + otherNamesFound);
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Log.info("Error from Orcid found: " + errorFromOrcidFound);
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Log.info("Error parsing xml record found: " + xmlParserErrorFound);
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}
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public static void extractXML(Configuration conf, String inputUri, Path outputPath)
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throws Exception {
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String uri = inputUri;
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FileSystem fs = FileSystem.get(URI.create(uri), conf);
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Path inputPath = new Path(uri);
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CompressionCodecFactory factory = new CompressionCodecFactory(conf);
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CompressionCodec codec = factory.getCodec(inputPath);
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if (codec == null) {
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System.err.println("No codec found for " + uri);
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System.exit(1);
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}
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CompressionCodecFactory.removeSuffix(uri, codec.getDefaultExtension());
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InputStream gzipInputStream = null;
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try {
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gzipInputStream = codec.createInputStream(fs.open(inputPath));
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int counter = 0;
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try (TarArchiveInputStream tais = new TarArchiveInputStream(gzipInputStream)) {
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TarArchiveEntry entry = null;
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CompressionCodec Codec = new GzipCodec();
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org.apache.hadoop.io.SequenceFile.Writer.Option optCom = SequenceFile.Writer
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.compression(SequenceFile.CompressionType.RECORD, Codec);
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try (SequenceFile.Writer writer = SequenceFile
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.createWriter(
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conf,
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SequenceFile.Writer.file(outputPath),
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SequenceFile.Writer.keyClass(Text.class),
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SequenceFile.Writer.valueClass(Text.class), optCom)) {
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while ((entry = tais.getNextTarEntry()) != null) {
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String filename = entry.getName();
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if (entry.isDirectory()) {
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Log.debug("Directory entry name: " + entry.getName());
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} else {
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Log.debug("XML record entry name: " + entry.getName());
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counter++;
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BufferedReader br = new BufferedReader(new InputStreamReader(tais));
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String line;
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StringBuffer buffer = new StringBuffer();
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while ((line = br.readLine()) != null) {
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buffer.append(line);
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}
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String xml = buffer.toString();
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final Text key = new Text(
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XMLRecordParser
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.retrieveOrcidIdFromSummary(
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xml.getBytes(), filename.split("/")[2].substring(0, 19)));
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final Text value = new Text(xml);
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writer.append(key, value);
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}
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if ((counter % 100000) == 0) {
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Log.info("Current xml records extracted: " + counter);
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}
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}
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}
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}
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Log.info("Summaries extract completed");
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Log.info("Total XML records parsed: " + counter);
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} finally {
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Log.debug("Closing gzip stream");
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IOUtils.closeStream(gzipInputStream);
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}
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}
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}
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