Merge branch 'beta' of https://code-repo.d4science.org/D-Net/dnet-hadoop into beta
commit
ee1f1eeca2
@ -1,7 +1,8 @@
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van
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von
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der
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de
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dell
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sig
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mr
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mrs
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mrs
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@ -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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||||
|
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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
|
||||
.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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|
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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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||||
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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));
|
||||
} 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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||||
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||||
public class FileGZipCollectorPlugin extends AbstractSplittedRecordPlugin {
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||||
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private static final Logger log = LoggerFactory.getLogger(FileGZipCollectorPlugin.class);
|
||||
|
||||
public FileGZipCollectorPlugin(FileSystem fileSystem) {
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||||
super(fileSystem);
|
||||
}
|
||||
|
||||
@Override
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||||
protected BufferedInputStream getBufferedInputStream(final Path filePath) throws CollectorException {
|
||||
|
||||
log.info("filePath: {}", filePath);
|
||||
|
||||
try {
|
||||
FileSystem fs = super.getFileSystem();
|
||||
GZIPInputStream stream = new GZIPInputStream(fs.open(filePath));
|
||||
return new BufferedInputStream(stream);
|
||||
} catch (Exception e) {
|
||||
throw new CollectorException("Error reading file " + filePath, e);
|
||||
}
|
||||
}
|
||||
}
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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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||||
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||||
import java.io.InputStream;
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||||
import java.io.InputStreamReader;
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||||
import java.io.Reader;
|
||||
import java.io.StringWriter;
|
||||
import java.nio.charset.Charset;
|
||||
import java.nio.charset.CharsetDecoder;
|
||||
import java.nio.charset.CodingErrorAction;
|
||||
import java.util.Iterator;
|
||||
|
||||
import javax.xml.stream.XMLEventFactory;
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||||
import javax.xml.stream.XMLEventReader;
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||||
import javax.xml.stream.XMLEventWriter;
|
||||
import javax.xml.stream.XMLInputFactory;
|
||||
import javax.xml.stream.XMLOutputFactory;
|
||||
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> {
|
||||
|
||||
private static final Log log = LogFactory.getLog(XMLIterator.class);
|
||||
|
||||
private ThreadLocal<XMLInputFactory> inputFactory = new ThreadLocal<XMLInputFactory>() {
|
||||
|
||||
@Override
|
||||
protected XMLInputFactory initialValue() {
|
||||
return XMLInputFactory.newInstance();
|
||||
}
|
||||
};
|
||||
|
||||
private ThreadLocal<XMLOutputFactory> outputFactory = new ThreadLocal<XMLOutputFactory>() {
|
||||
|
||||
@Override
|
||||
protected XMLOutputFactory initialValue() {
|
||||
return XMLOutputFactory.newInstance();
|
||||
}
|
||||
};
|
||||
|
||||
private ThreadLocal<XMLEventFactory> eventFactory = new ThreadLocal<XMLEventFactory>() {
|
||||
|
||||
@Override
|
||||
protected XMLEventFactory initialValue() {
|
||||
return XMLEventFactory.newInstance();
|
||||
}
|
||||
};
|
||||
|
||||
public static final String UTF_8 = "UTF-8";
|
||||
|
||||
final XMLEventReader parser;
|
||||
|
||||
private XMLEvent current = null;
|
||||
|
||||
private String element;
|
||||
|
||||
private InputStream inputStream;
|
||||
|
||||
public XMLIterator(final String element, final InputStream inputStream) {
|
||||
super();
|
||||
this.element = element;
|
||||
this.inputStream = inputStream;
|
||||
this.parser = getParser();
|
||||
try {
|
||||
this.current = findElement(parser);
|
||||
} catch (XMLStreamException e) {
|
||||
log.warn("cannot init parser position. No element found: " + element);
|
||||
current = null;
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean hasNext() {
|
||||
return current != null;
|
||||
}
|
||||
|
||||
@Override
|
||||
public String next() {
|
||||
String result = null;
|
||||
try {
|
||||
result = copy(parser);
|
||||
current = findElement(parser);
|
||||
return result;
|
||||
} catch (XMLStreamException e) {
|
||||
throw new RuntimeException(String.format("error copying xml, built so far: '%s'", result), e);
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public void remove() {
|
||||
throw new UnsupportedOperationException();
|
||||
}
|
||||
|
||||
@SuppressWarnings("finally")
|
||||
private String copy(final XMLEventReader parser) throws XMLStreamException {
|
||||
final StringWriter result = new StringWriter();
|
||||
try {
|
||||
final XMLEventWriter writer = outputFactory.get().createXMLEventWriter(result);
|
||||
final StartElement start = current.asStartElement();
|
||||
final StartElement newRecord = eventFactory
|
||||
.get()
|
||||
.createStartElement(start.getName(), start.getAttributes(), start.getNamespaces());
|
||||
|
||||
// new root record
|
||||
writer.add(newRecord);
|
||||
|
||||
// copy the rest as it is
|
||||
while (parser.hasNext()) {
|
||||
final XMLEvent event = parser.nextEvent();
|
||||
|
||||
// TODO: replace with depth tracking instead of close tag tracking.
|
||||
if (event.isEndElement() && event.asEndElement().getName().getLocalPart().equals(element)) {
|
||||
writer.add(event);
|
||||
break;
|
||||
}
|
||||
|
||||
writer.add(event);
|
||||
}
|
||||
writer.close();
|
||||
} finally {
|
||||
return result.toString();
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Looks for the next occurrence of the splitter element.
|
||||
*
|
||||
* @param parser
|
||||
* @return
|
||||
* @throws XMLStreamException
|
||||
*/
|
||||
private XMLEvent findElement(final XMLEventReader parser) throws XMLStreamException {
|
||||
|
||||
/*
|
||||
* if (current != null && element.equals(current.asStartElement().getName().getLocalPart())) { return current; }
|
||||
*/
|
||||
|
||||
XMLEvent peek = parser.peek();
|
||||
if (peek != null && peek.isStartElement()) {
|
||||
String name = peek.asStartElement().getName().getLocalPart();
|
||||
if (element.equals(name)) {
|
||||
return peek;
|
||||
}
|
||||
}
|
||||
|
||||
while (parser.hasNext()) {
|
||||
final XMLEvent event = parser.nextEvent();
|
||||
if (event != null && event.isStartElement()) {
|
||||
String name = event.asStartElement().getName().getLocalPart();
|
||||
if (element.equals(name)) {
|
||||
return event;
|
||||
}
|
||||
}
|
||||
}
|
||||
return null;
|
||||
}
|
||||
|
||||
private XMLEventReader getParser() {
|
||||
try {
|
||||
return inputFactory.get().createXMLEventReader(sanitize(inputStream));
|
||||
} catch (XMLStreamException e) {
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
}
|
||||
|
||||
private Reader sanitize(final InputStream in) {
|
||||
final CharsetDecoder charsetDecoder = Charset.forName(UTF_8).newDecoder();
|
||||
charsetDecoder.onMalformedInput(CodingErrorAction.REPLACE);
|
||||
charsetDecoder.onUnmappableCharacter(CodingErrorAction.REPLACE);
|
||||
return new InputStreamReader(in, charsetDecoder);
|
||||
}
|
||||
|
||||
}
|
||||
@ -1,5 +1,5 @@
|
||||
|
||||
package eu.dnetlib.dhp.collection;
|
||||
package eu.dnetlib.dhp.collection.plugin.utils;
|
||||
|
||||
import java.util.HashMap;
|
||||
import java.util.HashSet;
|
||||
@ -0,0 +1,61 @@
|
||||
|
||||
package eu.dnetlib.dhp.collection.plugin.file;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.util.HashMap;
|
||||
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.Assertions;
|
||||
import org.junit.jupiter.api.BeforeEach;
|
||||
import org.junit.jupiter.api.Test;
|
||||
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;
|
||||
import net.bytebuddy.asm.Advice;
|
||||
|
||||
public class FileCollectorPluginTest {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(FileGZipCollectorPluginTest.class);
|
||||
|
||||
private final ApiDescriptor api = new ApiDescriptor();
|
||||
|
||||
private FileCollectorPlugin plugin;
|
||||
|
||||
private static final String SPLIT_ON_ELEMENT = "repository";
|
||||
|
||||
@BeforeEach
|
||||
public void setUp() throws IOException {
|
||||
|
||||
final String gzipFile = this
|
||||
.getClass()
|
||||
.getResource("/eu/dnetlib/dhp/collection/plugin/file/opendoar.xml")
|
||||
.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 FileCollectorPlugin(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);
|
||||
});
|
||||
}
|
||||
}
|
||||
@ -0,0 +1,68 @@
|
||||
|
||||
package eu.dnetlib.dhp.collection.plugin.file;
|
||||
|
||||
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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@ -0,0 +1,69 @@
|
||||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<record xmlns:oaf="http://namespace.openaire.eu/oaf"
|
||||
xmlns:oai="http://www.openarchives.org/OAI/2.0/"
|
||||
xmlns:datacite="http://datacite.org/schema/kernel-3"
|
||||
xmlns:dr="http://www.driver-repository.eu/namespace/dr"
|
||||
xmlns:dri="http://www.driver-repository.eu/namespace/dri">>
|
||||
<header xmlns="http://www.openarchives.org/OAI/2.0/">
|
||||
<identifier>oai:zenodo.org:3406824</identifier>
|
||||
<datestamp>2020-01-20T16:45:20Z</datestamp>
|
||||
<setSpec>openaire</setSpec>
|
||||
<dr:dateOfTransformation>2022-06-07T10:21:24.06Z</dr:dateOfTransformation>
|
||||
<dri:objIdentifier>test________::92fe3efa47883b2f3401e6a4bd92e9d7</dri:objIdentifier>
|
||||
<dri:dateOfCollection>2020-05-21T05:26:15.93Z</dri:dateOfCollection>
|
||||
<dri:dateOfTransformation>2020-08-01T11:06:26.977Z</dri:dateOfTransformation>
|
||||
</header>
|
||||
<metadata>
|
||||
<resource xmlns="http://datacite.org/schema/kernel-4"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||
xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4.1/metadata.xsd">
|
||||
<identifier identifierType="DOI">10.5281/zenodo.3406824</identifier>
|
||||
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<description descriptionType="Abstract"><p>In the 1880s Robert Graves published a biography about Sir William Rowan Hamilton (1805-1865), to which in a 1980 biography Thomas Hankins added further information. From these biographies a picture emerged of a man who was unhappily married because he had lost the love of his life, which raised the question how such an unhappy man could produce so much beautiful mathematics. In this article it is stated that a main cause for the unhappy picture is that Graves ignored the influence on one another of Hamilton and his wife Helen Bayly, and Hankins that of Hamilton and his first and lost love Catherine Disney. It is then shown that if these influences are taken into account a very different view on Hamilton;s private life arises, in which he was happily married to a wife who enabled him to work as he needed to.</p></description>
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<dc:description descriptionType="Abstract">The COVID-19 pandemic has led to significant reductions in economic activity, especially during lockdowns. Several studies has shown that the concentration of nitrogen dioxyde and particulate matter levels have reduced during lockdown events. Reductions in transportation sector emissions are most likely largely responsible for the NO2 anomalies. In this study, we analyze the impact of lockdown events on the air quality using data from Copernicus Atmosphere Monitoring Service over Europe and at selected locations.</dc:description>
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Loading…
Reference in New Issue