126 lines
4.2 KiB
Java
126 lines
4.2 KiB
Java
package eu.dnetlib.dhp.collection.plugin.base;
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import java.io.BufferedInputStream;
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import java.io.ByteArrayInputStream;
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import java.io.InputStream;
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import java.io.InputStreamReader;
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import java.util.Iterator;
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import java.util.concurrent.BlockingQueue;
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import java.util.concurrent.LinkedBlockingQueue;
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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.commons.compress.compressors.CompressorInputStream;
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import org.apache.commons.compress.compressors.CompressorStreamFactory;
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import org.apache.commons.io.IOUtils;
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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.dom4j.Document;
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import org.dom4j.DocumentHelper;
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import org.dom4j.Element;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
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public class BaseCollectorIterator implements Iterator<Element> {
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private final BlockingQueue<Element> queue = new LinkedBlockingQueue<>();
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private static final Logger log = LoggerFactory.getLogger(BaseCollectorIterator.class);
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private boolean completed = false;
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public BaseCollectorIterator(final FileSystem fs, final Path filePath, final AggregatorReport report) {
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new Thread(() -> importHadoopFile(fs, filePath, report)).start();
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}
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protected BaseCollectorIterator(final String resourcePath, final AggregatorReport report) {
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new Thread(() -> importTestFile(resourcePath, report)).start();
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}
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@Override
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public synchronized boolean hasNext() {
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return !this.queue.isEmpty() || !isCompleted();
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}
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@Override
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public synchronized Element next() {
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try {
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return this.queue.take();
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} catch (final InterruptedException e) {
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throw new RuntimeException(e);
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}
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}
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private void importHadoopFile(final FileSystem fs, final Path filePath, final AggregatorReport report) {
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log.info("I start to read the TAR stream");
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try (InputStream origInputStream = fs.open(filePath);
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final TarArchiveInputStream tarInputStream = new TarArchiveInputStream(origInputStream)) {
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importTarStream(tarInputStream);
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} catch (final Throwable e) {
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log.error("Error processing BASE records", e);
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report.put(e.getClass().getName(), e.getMessage());
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throw new RuntimeException("Error processing BASE records", e);
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} finally {
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setCompleted(true);
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}
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}
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private void importTestFile(final String resourcePath, final AggregatorReport report) {
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try (final InputStream origInputStream = BaseCollectorIterator.class.getResourceAsStream(resourcePath);
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final TarArchiveInputStream tarInputStream = new TarArchiveInputStream(origInputStream)) {
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importTarStream(tarInputStream);
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} catch (final Throwable e) {
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log.error("Error processing BASE records", e);
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report.put(e.getClass().getName(), e.getMessage());
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throw new RuntimeException("Error processing BASE records", e);
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} finally {
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setCompleted(true);
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}
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}
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private void importTarStream(final TarArchiveInputStream tarInputStream) throws Exception {
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TarArchiveEntry entry;
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long count = 0;
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while ((entry = (TarArchiveEntry) tarInputStream.getNextEntry()) != null) {
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final String name = entry.getName();
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if (!entry.isDirectory() && name.contains("ListRecords") && name.endsWith(".bz2")) {
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log.info("Processing file (BZIP): " + name);
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final byte[] bzipData = new byte[(int) entry.getSize()];
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IOUtils.readFully(tarInputStream, bzipData);
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try (InputStream bzipIs = new ByteArrayInputStream(bzipData);
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final BufferedInputStream bzipBis = new BufferedInputStream(bzipIs);
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final CompressorInputStream bzipInput = new CompressorStreamFactory().createCompressorInputStream(bzipBis)) {
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final String xml = IOUtils.toString(new InputStreamReader(bzipInput));
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final Document doc = DocumentHelper.parseText(xml);
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for (final Object o : doc.selectNodes("//*[local-name()='ListRecords']/*[local-name()='record']")) {
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if (o instanceof Element) {
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this.queue.add((Element) o);
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count++;
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}
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}
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}
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}
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}
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log.info("Total records (written in queue): " + count);
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}
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private synchronized boolean isCompleted() {
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return this.completed;
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}
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private synchronized void setCompleted(final boolean completed) {
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this.completed = completed;
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}
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}
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