partial refactoring
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c6db6335b9
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c974c75f83
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@ -13,35 +13,39 @@ 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.CompressorInputStream;
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import org.apache.commons.compress.compressors.CompressorStreamFactory;
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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.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.Document;
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import org.dom4j.DocumentHelper;
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import org.dom4j.DocumentHelper;
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import org.dom4j.Element;
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import org.dom4j.Element;
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import org.slf4j.Logger;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import org.slf4j.LoggerFactory;
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public class BaseCollectorIterator implements Iterator<Element> {
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import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
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private final InputStream origInputStream;
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public class BaseCollectorIterator implements Iterator<Element> {
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private boolean completed;
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private final BlockingQueue<Element> queue = new LinkedBlockingQueue<>();
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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 static final Logger log = LoggerFactory.getLogger(BaseCollectorIterator.class);
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public BaseCollectorIterator(final InputStream origInputStream) {
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private boolean completed = false;
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this.origInputStream = origInputStream;
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this.completed = false;
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new Thread(this::importFile).start();
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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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}
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@Override
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@Override
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public boolean hasNext() {
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public synchronized boolean hasNext() {
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return !this.completed || !this.queue.isEmpty();
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return !this.queue.isEmpty() || !isCompleted();
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}
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}
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@Override
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@Override
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public Element next() {
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public synchronized Element next() {
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try {
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try {
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return this.queue.take();
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return this.queue.take();
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} catch (final InterruptedException e) {
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} catch (final InterruptedException e) {
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@ -49,46 +53,73 @@ public class BaseCollectorIterator implements Iterator<Element> {
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}
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}
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}
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}
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private void importFile() {
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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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log.info("I start to read the TAR stream");
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final long count = 0;
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try (InputStream origInputStream = fs.open(filePath);
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try (final TarArchiveInputStream tarInputStream = new TarArchiveInputStream(this.origInputStream)) {
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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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TarArchiveEntry entry;
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private void importTestFile(final String resourcePath, final AggregatorReport report) {
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while ((entry = (TarArchiveEntry) tarInputStream.getNextEntry()) != null) {
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try (final InputStream origInputStream = BaseCollectorIterator.class.getResourceAsStream(resourcePath);
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final String name = entry.getName();
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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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if (!entry.isDirectory() && name.contains("ListRecords") && name.endsWith(".bz2")) {
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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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log.info("Processing file (BZIP): " + name);
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if (!entry.isDirectory() && name.contains("ListRecords") && name.endsWith(".bz2")) {
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final byte[] bzipData = new byte[(int) entry.getSize()];
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log.info("Processing file (BZIP): " + name);
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IOUtils.readFully(tarInputStream, bzipData);
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try (InputStream bzipIs = new ByteArrayInputStream(bzipData);
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final byte[] bzipData = new byte[(int) entry.getSize()];
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final BufferedInputStream bzipBis = new BufferedInputStream(bzipIs);
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IOUtils.readFully(tarInputStream, bzipData);
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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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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 Document doc = DocumentHelper.parseText(xml);
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final String xml = IOUtils.toString(new InputStreamReader(bzipInput));
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for (final Object o : doc.selectNodes("//*[local-name()='ListRecords']/*[local-name()='record']")) {
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final Document doc = DocumentHelper.parseText(xml);
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if (o instanceof Element) {
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this.queue.add((Element) o);
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for (final Object o : doc.selectNodes("//*[local-name()='ListRecords']/*[local-name()='record']")) {
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}
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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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}
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}
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}
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} catch (final Throwable e) {
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log.error("Error processing BASE records", e);
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throw new RuntimeException("Error processing BASE records", e);
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} finally {
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this.completed = true;
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log.info("Total records (written in queue): " + count);
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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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}
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}
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@ -1,7 +1,6 @@
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package eu.dnetlib.dhp.collection.plugin.base;
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package eu.dnetlib.dhp.collection.plugin.base;
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import java.io.IOException;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.StringWriter;
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import java.io.StringWriter;
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import java.util.Iterator;
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import java.util.Iterator;
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import java.util.Optional;
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import java.util.Optional;
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@ -52,16 +51,11 @@ public class BaseCollectorPlugin implements CollectorPlugin {
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throw new CollectorException(e);
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throw new CollectorException(e);
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}
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}
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try (InputStream is = this.fs.open(filePath)) {
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final Iterator<Element> iterator = new BaseCollectorIterator(this.fs, filePath, report);
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final Iterator<Element> iterator = new BaseCollectorIterator(is);
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final Spliterator<Element> spliterator = Spliterators.spliteratorUnknownSize(iterator, Spliterator.ORDERED);
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final Spliterator<Element> spliterator = Spliterators.spliteratorUnknownSize(iterator, Spliterator.ORDERED);
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return StreamSupport.stream(spliterator, false)
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return StreamSupport.stream(spliterator, false)
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.filter(elem -> filterXml(elem, report))
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.filter(elem -> filterXml(elem, report))
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.map(elem -> xmlToString(report, elem));
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.map(elem -> xmlToString(report, elem));
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} catch (final Throwable e) {
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report.put(e.getClass().getName(), e.getMessage());
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throw new CollectorException(e);
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}
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}
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}
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private boolean filterXml(final Element elem, final AggregatorReport report) {
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private boolean filterXml(final Element elem, final AggregatorReport report) {
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@ -2,27 +2,28 @@ package eu.dnetlib.dhp.collection.plugin.base;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import java.io.InputStream;
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import java.util.Iterator;
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import org.dom4j.Element;
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import org.dom4j.Element;
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import org.junit.jupiter.api.Test;
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import org.junit.jupiter.api.Test;
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import org.junit.jupiter.api.extension.ExtendWith;
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import org.mockito.junit.jupiter.MockitoExtension;
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import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
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@ExtendWith(MockitoExtension.class)
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public class BaseCollectorIteratorTest {
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public class BaseCollectorIteratorTest {
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@Test
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@Test
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void testImportFile() throws Exception {
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void testImportFile() throws Exception {
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long count = 0;
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long count = 0;
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try (final InputStream is = getClass().getResourceAsStream("base-sample.tar")) {
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final BaseCollectorIterator iterator = new BaseCollectorIterator("base-sample.tar", new AggregatorReport());
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final Iterator<Element> iterator = new BaseCollectorIterator(is);
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while (iterator.hasNext()) {
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final Element record = iterator.next();
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System.out.println(record.asXML());
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count++;
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}
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}
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while (iterator.hasNext()) {
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final Element record = iterator.next();
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// System.out.println(record.asXML());
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count++;
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}
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assertEquals(30000, count);
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assertEquals(30000, count);
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}
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}
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