Merge branch 'beta' into author_name_particles
commit
4829b96bb5
@ -0,0 +1,80 @@
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package eu.dnetlib.dhp.collection.plugin.file;
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import java.io.BufferedInputStream;
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import java.io.IOException;
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import java.util.Iterator;
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import java.util.Optional;
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import java.util.Spliterator;
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import java.util.Spliterators;
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import java.util.stream.Stream;
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import java.util.stream.StreamSupport;
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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.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.collection.ApiDescriptor;
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import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
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import eu.dnetlib.dhp.collection.plugin.utils.XMLIterator;
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import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
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import eu.dnetlib.dhp.common.collection.CollectorException;
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public abstract class AbstractSplittedRecordPlugin implements CollectorPlugin {
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private static final Logger log = LoggerFactory.getLogger(AbstractSplittedRecordPlugin.class);
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public static final String SPLIT_ON_ELEMENT = "splitOnElement";
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private final FileSystem fileSystem;
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public AbstractSplittedRecordPlugin(FileSystem fileSystem) {
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this.fileSystem = fileSystem;
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}
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@Override
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public Stream<String> collect(ApiDescriptor api, AggregatorReport report) throws CollectorException {
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// get path to file
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final Path filePath = Optional
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.ofNullable(api.getBaseUrl())
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.map(Path::new)
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.orElseThrow(() -> new CollectorException("missing baseUrl"));
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log.info("baseUrl: {}", filePath);
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// check that path to file exists
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try {
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if (!fileSystem.exists(filePath)) {
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throw new CollectorException("path does not exist: " + filePath);
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}
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} catch (IOException e) {
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throw new CollectorException(e);
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}
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// get split element
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final String splitOnElement = Optional
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.ofNullable(api.getParams().get(SPLIT_ON_ELEMENT))
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.orElseThrow(
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() -> new CollectorException(String
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.format("missing parameter '%s', required by the AbstractSplittedRecordPlugin", SPLIT_ON_ELEMENT)));
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log.info("splitOnElement: {}", splitOnElement);
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final BufferedInputStream bis = getBufferedInputStream(filePath);
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Iterator<String> xmlIterator = new XMLIterator(splitOnElement, bis);
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return StreamSupport
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.stream(
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Spliterators.spliteratorUnknownSize(xmlIterator, Spliterator.ORDERED),
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false);
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}
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abstract protected BufferedInputStream getBufferedInputStream(final Path filePath) throws CollectorException;
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public FileSystem getFileSystem() {
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return fileSystem;
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}
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}
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@ -0,0 +1,33 @@
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package eu.dnetlib.dhp.collection.plugin.file;
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import java.io.BufferedInputStream;
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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.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.common.collection.CollectorException;
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public class FileCollectorPlugin extends AbstractSplittedRecordPlugin {
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private static final Logger log = LoggerFactory.getLogger(FileCollectorPlugin.class);
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public FileCollectorPlugin(FileSystem fileSystem) {
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super(fileSystem);
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}
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@Override
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protected BufferedInputStream getBufferedInputStream(final Path filePath) throws CollectorException {
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log.info("filePath: {}", filePath);
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try {
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FileSystem fs = super.getFileSystem();
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return new BufferedInputStream(fs.open(filePath));
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} catch (Exception e) {
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throw new CollectorException("Error reading file " + filePath, e);
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}
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}
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}
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@ -0,0 +1,35 @@
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package eu.dnetlib.dhp.collection.plugin.file;
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import java.io.BufferedInputStream;
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import java.util.zip.GZIPInputStream;
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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.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.common.collection.CollectorException;
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public class FileGZipCollectorPlugin extends AbstractSplittedRecordPlugin {
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private static final Logger log = LoggerFactory.getLogger(FileGZipCollectorPlugin.class);
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public FileGZipCollectorPlugin(FileSystem fileSystem) {
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super(fileSystem);
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}
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@Override
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protected BufferedInputStream getBufferedInputStream(final Path filePath) throws CollectorException {
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log.info("filePath: {}", filePath);
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try {
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FileSystem fs = super.getFileSystem();
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GZIPInputStream stream = new GZIPInputStream(fs.open(filePath));
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return new BufferedInputStream(stream);
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} catch (Exception e) {
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throw new CollectorException("Error reading file " + filePath, e);
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}
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}
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}
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@ -1,5 +1,5 @@
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package eu.dnetlib.dhp.collection;
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package eu.dnetlib.dhp.collection.plugin.utils;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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@ -0,0 +1,177 @@
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package eu.dnetlib.dhp.collection.plugin.utils;
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import java.io.InputStream;
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import java.io.InputStreamReader;
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import java.io.Reader;
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import java.io.StringWriter;
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import java.nio.charset.Charset;
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import java.nio.charset.CharsetDecoder;
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import java.nio.charset.CodingErrorAction;
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import java.util.Iterator;
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import javax.xml.stream.XMLEventFactory;
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import javax.xml.stream.XMLEventReader;
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import javax.xml.stream.XMLEventWriter;
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import javax.xml.stream.XMLInputFactory;
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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.events.StartElement;
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import javax.xml.stream.events.XMLEvent;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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public class XMLIterator implements Iterator<String> {
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private static final Log log = LogFactory.getLog(XMLIterator.class);
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private ThreadLocal<XMLInputFactory> inputFactory = new ThreadLocal<XMLInputFactory>() {
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@Override
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protected XMLInputFactory initialValue() {
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return XMLInputFactory.newInstance();
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}
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};
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private ThreadLocal<XMLOutputFactory> outputFactory = new ThreadLocal<XMLOutputFactory>() {
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@Override
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protected XMLOutputFactory initialValue() {
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return XMLOutputFactory.newInstance();
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}
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};
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private ThreadLocal<XMLEventFactory> eventFactory = new ThreadLocal<XMLEventFactory>() {
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@Override
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protected XMLEventFactory initialValue() {
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return XMLEventFactory.newInstance();
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}
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};
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public static final String UTF_8 = "UTF-8";
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final XMLEventReader parser;
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private XMLEvent current = null;
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private String element;
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private InputStream inputStream;
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public XMLIterator(final String element, final InputStream inputStream) {
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super();
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this.element = element;
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this.inputStream = inputStream;
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this.parser = getParser();
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try {
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this.current = findElement(parser);
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} catch (XMLStreamException e) {
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log.warn("cannot init parser position. No element found: " + element);
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current = null;
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}
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}
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@Override
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public boolean hasNext() {
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return current != null;
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}
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@Override
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public String next() {
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String result = null;
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try {
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result = copy(parser);
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current = findElement(parser);
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return result;
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} catch (XMLStreamException e) {
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throw new RuntimeException(String.format("error copying xml, built so far: '%s'", result), e);
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}
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}
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@Override
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public void remove() {
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throw new UnsupportedOperationException();
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}
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@SuppressWarnings("finally")
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private String copy(final XMLEventReader parser) throws XMLStreamException {
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final StringWriter result = new StringWriter();
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try {
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final XMLEventWriter writer = outputFactory.get().createXMLEventWriter(result);
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final StartElement start = current.asStartElement();
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final StartElement newRecord = eventFactory
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.get()
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.createStartElement(start.getName(), start.getAttributes(), start.getNamespaces());
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// new root record
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writer.add(newRecord);
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// copy the rest as it is
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while (parser.hasNext()) {
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final XMLEvent event = parser.nextEvent();
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// TODO: replace with depth tracking instead of close tag tracking.
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if (event.isEndElement() && event.asEndElement().getName().getLocalPart().equals(element)) {
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writer.add(event);
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break;
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}
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writer.add(event);
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}
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writer.close();
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} finally {
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return result.toString();
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}
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}
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/**
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* Looks for the next occurrence of the splitter element.
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*
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* @param parser
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* @return
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* @throws XMLStreamException
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*/
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private XMLEvent findElement(final XMLEventReader parser) throws XMLStreamException {
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/*
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* if (current != null && element.equals(current.asStartElement().getName().getLocalPart())) { return current; }
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*/
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XMLEvent peek = parser.peek();
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if (peek != null && peek.isStartElement()) {
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String name = peek.asStartElement().getName().getLocalPart();
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if (element.equals(name)) {
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return peek;
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}
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}
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while (parser.hasNext()) {
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final XMLEvent event = parser.nextEvent();
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if (event != null && event.isStartElement()) {
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String name = event.asStartElement().getName().getLocalPart();
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if (element.equals(name)) {
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return event;
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}
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}
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}
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return null;
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}
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private XMLEventReader getParser() {
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try {
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return inputFactory.get().createXMLEventReader(sanitize(inputStream));
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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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private Reader sanitize(final InputStream in) {
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final CharsetDecoder charsetDecoder = Charset.forName(UTF_8).newDecoder();
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charsetDecoder.onMalformedInput(CodingErrorAction.REPLACE);
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charsetDecoder.onUnmappableCharacter(CodingErrorAction.REPLACE);
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return new InputStreamReader(in, charsetDecoder);
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}
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}
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@ -1,5 +1,5 @@
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package eu.dnetlib.dhp.collection;
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package eu.dnetlib.dhp.collection.plugin.utils;
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import java.util.HashMap;
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import java.util.HashSet;
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@ -0,0 +1,61 @@
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package eu.dnetlib.dhp.collection.plugin.file;
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import java.io.IOException;
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import java.util.HashMap;
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import java.util.stream.Stream;
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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.LocalFileSystem;
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import org.junit.jupiter.api.Assertions;
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import org.junit.jupiter.api.BeforeEach;
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import org.junit.jupiter.api.Test;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.collection.ApiDescriptor;
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import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
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import eu.dnetlib.dhp.common.collection.CollectorException;
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import net.bytebuddy.asm.Advice;
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public class FileCollectorPluginTest {
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private static final Logger log = LoggerFactory.getLogger(FileGZipCollectorPluginTest.class);
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private final ApiDescriptor api = new ApiDescriptor();
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private FileCollectorPlugin plugin;
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private static final String SPLIT_ON_ELEMENT = "repository";
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@BeforeEach
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public void setUp() throws IOException {
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final String gzipFile = this
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.getClass()
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.getResource("/eu/dnetlib/dhp/collection/plugin/file/opendoar.xml")
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.getFile();
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api.setBaseUrl(gzipFile);
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HashMap<String, String> params = new HashMap<>();
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params.put("splitOnElement", SPLIT_ON_ELEMENT);
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api.setParams(params);
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FileSystem fs = FileSystem.get(new Configuration());
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plugin = new FileCollectorPlugin(fs);
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}
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@Test
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void test() throws CollectorException {
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final Stream<String> stream = plugin.collect(api, new AggregatorReport());
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stream.limit(10).forEach(s -> {
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Assertions.assertTrue(s.length() > 0);
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log.info(s);
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});
|
||||
}
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||||
}
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@ -0,0 +1,68 @@
|
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package eu.dnetlib.dhp.collection.plugin.file;
|
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|
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import java.io.File;
|
||||
import java.io.IOException;
|
||||
import java.nio.file.Files;
|
||||
import java.util.HashMap;
|
||||
import java.util.Objects;
|
||||
import java.util.stream.Stream;
|
||||
|
||||
import org.apache.hadoop.conf.Configuration;
|
||||
import org.apache.hadoop.fs.FileSystem;
|
||||
import org.apache.hadoop.fs.LocalFileSystem;
|
||||
import org.junit.jupiter.api.*;
|
||||
import org.junit.jupiter.api.extension.ExtendWith;
|
||||
import org.mockito.Mockito;
|
||||
import org.mockito.junit.jupiter.MockitoExtension;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import eu.dnetlib.dhp.collection.ApiDescriptor;
|
||||
import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
|
||||
import eu.dnetlib.dhp.common.collection.CollectorException;
|
||||
|
||||
@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
|
||||
@ExtendWith(MockitoExtension.class)
|
||||
public class FileGZipCollectorPluginTest {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(FileGZipCollectorPluginTest.class);
|
||||
|
||||
private final ApiDescriptor api = new ApiDescriptor();
|
||||
|
||||
private FileGZipCollectorPlugin plugin;
|
||||
|
||||
private static final String SPLIT_ON_ELEMENT = "repository";
|
||||
|
||||
@BeforeEach
|
||||
public void setUp() throws IOException {
|
||||
|
||||
final String gzipFile = Objects
|
||||
.requireNonNull(
|
||||
this
|
||||
.getClass()
|
||||
.getResource("/eu/dnetlib/dhp/collection/plugin/file/opendoar.xml.gz"))
|
||||
.getFile();
|
||||
|
||||
api.setBaseUrl(gzipFile);
|
||||
|
||||
HashMap<String, String> params = new HashMap<>();
|
||||
params.put("splitOnElement", SPLIT_ON_ELEMENT);
|
||||
|
||||
api.setParams(params);
|
||||
|
||||
FileSystem fs = FileSystem.get(new Configuration());
|
||||
plugin = new FileGZipCollectorPlugin(fs);
|
||||
}
|
||||
|
||||
@Test
|
||||
void test() throws CollectorException {
|
||||
|
||||
final Stream<String> stream = plugin.collect(api, new AggregatorReport());
|
||||
|
||||
stream.limit(10).forEach(s -> {
|
||||
Assertions.assertTrue(s.length() > 0);
|
||||
log.info(s);
|
||||
});
|
||||
}
|
||||
}
|
||||
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