new plugin to collect from a dump of BASE
This commit is contained in:
parent
3067ea390d
commit
3bcfc40293
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@ -19,6 +19,7 @@ import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.aggregation.common.ReporterCallback;
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import eu.dnetlib.dhp.aggregation.common.ReporterCallback;
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import eu.dnetlib.dhp.aggregation.common.ReportingJob;
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import eu.dnetlib.dhp.aggregation.common.ReportingJob;
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import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
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import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
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import eu.dnetlib.dhp.collection.plugin.base.BaseCollectorPlugin;
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import eu.dnetlib.dhp.collection.plugin.file.FileCollectorPlugin;
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import eu.dnetlib.dhp.collection.plugin.file.FileCollectorPlugin;
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import eu.dnetlib.dhp.collection.plugin.file.FileGZipCollectorPlugin;
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import eu.dnetlib.dhp.collection.plugin.file.FileGZipCollectorPlugin;
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import eu.dnetlib.dhp.collection.plugin.mongodb.MDStoreCollectorPlugin;
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import eu.dnetlib.dhp.collection.plugin.mongodb.MDStoreCollectorPlugin;
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@ -120,6 +121,8 @@ public class CollectorWorker extends ReportingJob {
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return new FileCollectorPlugin(fileSystem);
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return new FileCollectorPlugin(fileSystem);
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case fileGzip:
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case fileGzip:
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return new FileGZipCollectorPlugin(fileSystem);
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return new FileGZipCollectorPlugin(fileSystem);
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case baseDump:
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return new BaseCollectorPlugin(this.fileSystem);
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case other:
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case other:
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final CollectorPlugin.NAME.OTHER_NAME plugin = Optional
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final CollectorPlugin.NAME.OTHER_NAME plugin = Optional
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.ofNullable(api.getParams().get("other_plugin_type"))
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.ofNullable(api.getParams().get("other_plugin_type"))
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@ -10,7 +10,8 @@ import eu.dnetlib.dhp.common.collection.CollectorException;
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public interface CollectorPlugin {
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public interface CollectorPlugin {
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enum NAME {
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enum NAME {
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oai, other, rest_json2xml, file, fileGzip;
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oai, other, rest_json2xml, file, fileGzip, baseDump;
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public enum OTHER_NAME {
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public enum OTHER_NAME {
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mdstore_mongodb_dump, mdstore_mongodb
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mdstore_mongodb_dump, mdstore_mongodb
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@ -0,0 +1,171 @@
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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.StringWriter;
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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 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.events.EndElement;
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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.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.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<String> {
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private String nextElement;
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private final BlockingQueue<String> queue = new LinkedBlockingQueue<>(100);
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private static final Logger log = LoggerFactory.getLogger(BaseCollectorIterator.class);
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private static final String END_ELEM = "__END__";
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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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try {
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this.nextElement = 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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protected BaseCollectorIterator(final String resourcePath, final AggregatorReport report) {
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new Thread(() -> importTestFile(resourcePath, report)).start();
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try {
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this.nextElement = 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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@Override
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public synchronized boolean hasNext() {
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return (this.nextElement != null) & !END_ELEM.equals(this.nextElement);
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}
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@Override
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public synchronized String next() {
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try {
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return END_ELEM.equals(this.nextElement) ? null : this.nextElement;
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} finally {
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try {
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this.nextElement = 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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}
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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, report);
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} catch (final Throwable e) {
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throw new RuntimeException("Error processing BASE records", e);
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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, report);
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} catch (final Throwable e) {
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throw new RuntimeException("Error processing BASE records", e);
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}
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}
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private void importTarStream(final TarArchiveInputStream tarInputStream, final AggregatorReport report) {
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long count = 0;
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final XMLInputFactory xmlInputFactory = XMLInputFactory.newInstance();
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final XMLOutputFactory xmlOutputFactory = XMLOutputFactory.newInstance();
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try {
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TarArchiveEntry entry;
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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()
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.createCompressorInputStream(bzipBis)) {
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final XMLEventReader reader = xmlInputFactory.createXMLEventReader(bzipInput);
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XMLEventWriter eventWriter = null;
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StringWriter xmlWriter = null;
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while (reader.hasNext()) {
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final XMLEvent nextEvent = reader.nextEvent();
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if (nextEvent.isStartElement()) {
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final StartElement startElement = nextEvent.asStartElement();
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if ("record".equals(startElement.getName().getLocalPart())) {
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xmlWriter = new StringWriter();
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eventWriter = xmlOutputFactory.createXMLEventWriter(xmlWriter);
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}
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}
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if (eventWriter != null) {
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eventWriter.add(nextEvent);
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}
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if (nextEvent.isEndElement()) {
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final EndElement endElement = nextEvent.asEndElement();
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if ("record".equals(endElement.getName().getLocalPart())) {
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eventWriter.flush();
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eventWriter.close();
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this.queue.put(xmlWriter.toString());
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eventWriter = null;
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xmlWriter = null;
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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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this.queue.put(END_ELEM); // TO INDICATE THE END OF THE QUEUE
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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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log.info("Total records (written in queue): " + count);
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}
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}
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}
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@ -0,0 +1,152 @@
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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.sql.SQLException;
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import java.util.HashSet;
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import java.util.Iterator;
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import java.util.Optional;
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import java.util.Set;
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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.commons.io.IOUtils;
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import org.apache.commons.lang3.StringUtils;
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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.DocumentException;
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import org.dom4j.DocumentHelper;
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import org.dom4j.Node;
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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.file.AbstractSplittedRecordPlugin;
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import eu.dnetlib.dhp.common.DbClient;
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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 class BaseCollectorPlugin implements CollectorPlugin {
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private final FileSystem fs;
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private static final Logger log = LoggerFactory.getLogger(AbstractSplittedRecordPlugin.class);
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// MAPPING AND FILTERING ARE DEFINED HERE:
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// https://docs.google.com/document/d/1Aj-ZAV11b44MCrAAUCPiS2TUlXb6PnJEu1utCMAcCOU/edit
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public BaseCollectorPlugin(final FileSystem fs) {
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this.fs = fs;
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}
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@Override
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public Stream<String> collect(final ApiDescriptor api, final 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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final String dbUrl = api.getParams().get("dbUrl");
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final String dbUser = api.getParams().get("dbUser");
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final String dbPassword = api.getParams().get("dbPassword");
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final String acceptedNormTypesString = api.getParams().get("acceptedNormTypes");
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log.info("baseUrl: {}", filePath);
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log.info("dbUrl: {}", dbUrl);
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log.info("dbUser: {}", dbUser);
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log.info("dbPassword: {}", "***");
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log.info("acceptedNormTypes: {}", acceptedNormTypesString);
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try {
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if (!this.fs.exists(filePath)) {
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throw new CollectorException("path does not exist: " + filePath);
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}
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} catch (final Throwable e) {
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throw new CollectorException(e);
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}
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final Set<String> acceptedOpendoarIds = findAcceptedOpendoarIds(dbUrl, dbUser, dbPassword);
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final Set<String> acceptedNormTypes = new HashSet<>();
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if (StringUtils.isNotBlank(acceptedNormTypesString)) {
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for (final String s : StringUtils.split(acceptedNormTypesString, ",")) {
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if (StringUtils.isNotBlank(s)) {
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acceptedNormTypes.add(s.trim());
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}
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}
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}
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final Iterator<String> iterator = new BaseCollectorIterator(this.fs, filePath, report);
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final Spliterator<String> spliterator = Spliterators.spliteratorUnknownSize(iterator, Spliterator.ORDERED);
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return StreamSupport
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.stream(spliterator, false)
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.filter(doc -> filterXml(doc, acceptedOpendoarIds, acceptedNormTypes));
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}
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private Set<String> findAcceptedOpendoarIds(final String dbUrl, final String dbUser, final String dbPassword)
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throws CollectorException {
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final Set<String> accepted = new HashSet<>();
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try (final DbClient dbClient = new DbClient(dbUrl, dbUser, dbPassword)) {
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final String sql = IOUtils
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.toString(
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getClass().getResourceAsStream("/eu/dnetlib/dhp/collection/plugin/base/sql/opendoar-accepted.sql"));
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dbClient.processResults(sql, row -> {
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try {
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final String dsId = row.getString("id");
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log.info("Accepted Datasource: " + dsId);
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accepted.add(dsId);
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} catch (final SQLException e) {
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log.error("Error in SQL", e);
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throw new RuntimeException("Error in SQL", e);
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}
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});
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} catch (final IOException e) {
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log.error("Error accessong SQL", e);
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throw new CollectorException("Error accessong SQL", e);
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}
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log.info("Accepted Datasources (TOTAL): " + accepted.size());
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return accepted;
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}
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protected static boolean filterXml(final String xml,
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final Set<String> acceptedOpendoarIds,
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final Set<String> acceptedNormTypes) {
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try {
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final Document doc = DocumentHelper.parseText(xml);
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final String id = doc.valueOf("//*[local-name()='collection']/@opendoar_id").trim();
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if (StringUtils.isBlank(id) || !acceptedOpendoarIds.contains("opendoar____::" + id)) {
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return false;
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}
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if (acceptedNormTypes.isEmpty()) {
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return true;
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}
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for (final Object s : doc.selectNodes("//*[local-name()='typenorm']")) {
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if (acceptedNormTypes.contains(((Node) s).getText().trim())) {
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return true;
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}
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}
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return false;
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} catch (final DocumentException e) {
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log.error("Error parsing document", e);
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throw new RuntimeException("Error parsing document", e);
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}
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}
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}
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@ -0,0 +1,114 @@
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BEGIN;
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INSERT INTO dsm_services(
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_dnet_resource_identifier_,
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id,
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officialname,
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englishname,
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namespaceprefix,
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websiteurl,
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logourl,
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platform,
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contactemail,
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collectedfrom,
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provenanceaction,
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_typology_to_remove_,
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eosc_type,
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eosc_datasource_type,
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research_entity_types,
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thematic
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) VALUES (
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'openaire____::base_search',
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||||||
|
'openaire____::base_search',
|
||||||
|
'Bielefeld Academic Search Engine (BASE)',
|
||||||
|
'Bielefeld Academic Search Engine (BASE)',
|
||||||
|
'base_search_',
|
||||||
|
'https://www.base-search.net',
|
||||||
|
'https://www.base-search.net/about/download/logo_224x57_white.gif',
|
||||||
|
'BASE',
|
||||||
|
'openaire-helpdesk@uni-bielefeld.de',
|
||||||
|
'infrastruct_::openaire',
|
||||||
|
'user:insert',
|
||||||
|
'aggregator::pubsrepository::unknown',
|
||||||
|
'Data Source',
|
||||||
|
'Aggregator',
|
||||||
|
ARRAY['Research Products'],
|
||||||
|
false
|
||||||
|
);
|
||||||
|
|
||||||
|
INSERT INTO dsm_service_organization(
|
||||||
|
_dnet_resource_identifier_,
|
||||||
|
organization,
|
||||||
|
service
|
||||||
|
) VALUES (
|
||||||
|
'fairsharing_::org::214@@openaire____::base_search',
|
||||||
|
'fairsharing_::org::214',
|
||||||
|
'openaire____::base_search'
|
||||||
|
);
|
||||||
|
|
||||||
|
INSERT INTO dsm_api(
|
||||||
|
_dnet_resource_identifier_,
|
||||||
|
id,
|
||||||
|
service,
|
||||||
|
protocol,
|
||||||
|
baseurl,
|
||||||
|
metadata_identifier_path
|
||||||
|
) VALUES (
|
||||||
|
'api_________::openaire____::base_search::dump',
|
||||||
|
'api_________::openaire____::base_search::dump',
|
||||||
|
'openaire____::base_search',
|
||||||
|
'baseDump',
|
||||||
|
'/user/michele.artini/base-import/base_oaipmh_dump-current.tar',
|
||||||
|
'//*[local-name()=''header'']/*[local-name()=''identifier'']'
|
||||||
|
);
|
||||||
|
|
||||||
|
|
||||||
|
INSERT INTO dsm_apiparams(
|
||||||
|
_dnet_resource_identifier_,
|
||||||
|
api,
|
||||||
|
param,
|
||||||
|
value
|
||||||
|
) VALUES (
|
||||||
|
'api_________::openaire____::base_search::dump@@dbUrl',
|
||||||
|
'api_________::openaire____::base_search::dump',
|
||||||
|
'dbUrl',
|
||||||
|
'jdbc:postgresql://postgresql.services.openaire.eu:5432/dnet_openaireplus'
|
||||||
|
);
|
||||||
|
|
||||||
|
INSERT INTO dsm_apiparams(
|
||||||
|
_dnet_resource_identifier_,
|
||||||
|
api,
|
||||||
|
param,
|
||||||
|
value
|
||||||
|
) VALUES (
|
||||||
|
'api_________::openaire____::base_search::dump@@dbUser',
|
||||||
|
'api_________::openaire____::base_search::dump',
|
||||||
|
'dbUser',
|
||||||
|
'dnet'
|
||||||
|
);
|
||||||
|
|
||||||
|
INSERT INTO dsm_apiparams(
|
||||||
|
_dnet_resource_identifier_,
|
||||||
|
api,
|
||||||
|
param,
|
||||||
|
value
|
||||||
|
) VALUES (
|
||||||
|
'api_________::openaire____::base_search::dump@@dbPassword',
|
||||||
|
'api_________::openaire____::base_search::dump',
|
||||||
|
'dbPassword',
|
||||||
|
'***'
|
||||||
|
);
|
||||||
|
|
||||||
|
INSERT INTO dsm_apiparams(
|
||||||
|
_dnet_resource_identifier_,
|
||||||
|
api,
|
||||||
|
param,
|
||||||
|
value
|
||||||
|
) VALUES (
|
||||||
|
'api_________::openaire____::base_search::dump@@acceptedNormTypes',
|
||||||
|
'api_________::openaire____::base_search::dump',
|
||||||
|
'acceptedNormTypes',
|
||||||
|
''
|
||||||
|
);
|
||||||
|
|
||||||
|
COMMIT;
|
||||||
|
|
@ -0,0 +1,7 @@
|
||||||
|
select s.id as id
|
||||||
|
from dsm_services s
|
||||||
|
where collectedfrom = 'openaire____::opendoar'
|
||||||
|
and jurisdiction = 'Institutional'
|
||||||
|
and s.id not in (
|
||||||
|
select service from dsm_api where coalesce(compatibility_override, compatibility) like '%openaire%' or last_collection_total > 0
|
||||||
|
);
|
||||||
|
|
@ -0,0 +1,11 @@
|
||||||
|
select
|
||||||
|
s.id as id,
|
||||||
|
s.jurisdiction as jurisdiction,
|
||||||
|
array_remove(array_agg(a.id || ' (compliance: ' || coalesce(a.compatibility_override, a.compatibility, 'UNKNOWN') || ')@@@' || coalesce(a.last_collection_total, 0)), NULL) as aggregations
|
||||||
|
from
|
||||||
|
dsm_services s
|
||||||
|
join dsm_api a on (s.id = a.service)
|
||||||
|
where
|
||||||
|
collectedfrom = 'openaire____::opendoar'
|
||||||
|
group by
|
||||||
|
s.id;
|
||||||
|
|
@ -0,0 +1,180 @@
|
||||||
|
<RESOURCE_PROFILE>
|
||||||
|
<HEADER>
|
||||||
|
<RESOURCE_IDENTIFIER value="c67911d6-9988-4a3b-b965-7d39bdd4a31d_Vm9jYWJ1bGFyeURTUmVzb3VyY2VzL1ZvY2FidWxhcnlEU1Jlc291cmNlVHlwZQ==" />
|
||||||
|
<RESOURCE_TYPE value="VocabularyDSResourceType" />
|
||||||
|
<RESOURCE_KIND value="VocabularyDSResources" />
|
||||||
|
<RESOURCE_URI value="" />
|
||||||
|
<DATE_OF_CREATION value="2024-02-13T11:15:48+00:00" />
|
||||||
|
</HEADER>
|
||||||
|
<BODY>
|
||||||
|
<CONFIGURATION>
|
||||||
|
<VOCABULARY_NAME code="base:normalized_types">base:normalized_types</VOCABULARY_NAME>
|
||||||
|
<VOCABULARY_DESCRIPTION>base:normalized_types</VOCABULARY_DESCRIPTION>
|
||||||
|
<TERMS>
|
||||||
|
<TERM native_name="Text" code="Text" english_name="Text" encoding="BASE">
|
||||||
|
<SYNONYMS>
|
||||||
|
<SYNONYM term="1" encoding="BASE" />
|
||||||
|
</SYNONYMS>
|
||||||
|
<RELATIONS />
|
||||||
|
</TERM>
|
||||||
|
<TERM native_name="Book" code="Book" english_name="Book" encoding="BASE">
|
||||||
|
<SYNONYMS>
|
||||||
|
<SYNONYM term="11" encoding="BASE" />
|
||||||
|
</SYNONYMS>
|
||||||
|
<RELATIONS />
|
||||||
|
</TERM>
|
||||||
|
<TERM native_name="Book part" code="Book part" english_name="Book part" encoding="BASE">
|
||||||
|
<SYNONYMS>
|
||||||
|
<SYNONYM term="111" encoding="BASE" />
|
||||||
|
</SYNONYMS>
|
||||||
|
<RELATIONS />
|
||||||
|
</TERM>
|
||||||
|
<TERM native_name="Journal/Newspaper" code="Journal/Newspaper" english_name="Journal/Newspaper" encoding="BASE">
|
||||||
|
<SYNONYMS>
|
||||||
|
<SYNONYM term="12" encoding="BASE" />
|
||||||
|
</SYNONYMS>
|
||||||
|
<RELATIONS />
|
||||||
|
</TERM>
|
||||||
|
<TERM native_name="Article contribution" code="Article contribution" english_name="Article contribution" encoding="BASE">
|
||||||
|
<SYNONYMS>
|
||||||
|
<SYNONYM term="121" encoding="BASE" />
|
||||||
|
</SYNONYMS>
|
||||||
|
<RELATIONS />
|
||||||
|
</TERM>
|
||||||
|
<TERM native_name="Other non-article" code="Other non-article" english_name="Other non-article" encoding="BASE">
|
||||||
|
<SYNONYMS>
|
||||||
|
<SYNONYM term="122" encoding="BASE" />
|
||||||
|
</SYNONYMS>
|
||||||
|
<RELATIONS />
|
||||||
|
</TERM>
|
||||||
|
<TERM native_name="Conference object" code="Conference object" english_name="Conference object" encoding="BASE">
|
||||||
|
<SYNONYMS>
|
||||||
|
<SYNONYM term="13" encoding="BASE" />
|
||||||
|
</SYNONYMS>
|
||||||
|
<RELATIONS />
|
||||||
|
</TERM>
|
||||||
|
<TERM native_name="Report" code="Report" english_name="Report" encoding="BASE">
|
||||||
|
<SYNONYMS>
|
||||||
|
<SYNONYM term="14" encoding="BASE" />
|
||||||
|
</SYNONYMS>
|
||||||
|
<RELATIONS />
|
||||||
|
</TERM>
|
||||||
|
<TERM native_name="Review" code="Review" english_name="Review" encoding="BASE">
|
||||||
|
<SYNONYMS>
|
||||||
|
<SYNONYM term="15" encoding="BASE" />
|
||||||
|
</SYNONYMS>
|
||||||
|
<RELATIONS />
|
||||||
|
</TERM>
|
||||||
|
<TERM native_name="Course material" code="Course material" english_name="Course material" encoding="BASE">
|
||||||
|
<SYNONYMS>
|
||||||
|
<SYNONYM term="16" encoding="BASE" />
|
||||||
|
</SYNONYMS>
|
||||||
|
<RELATIONS />
|
||||||
|
</TERM>
|
||||||
|
<TERM native_name="Lecture" code="Lecture" english_name="Lecture" encoding="BASE">
|
||||||
|
<SYNONYMS>
|
||||||
|
<SYNONYM term="17" encoding="BASE" />
|
||||||
|
</SYNONYMS>
|
||||||
|
<RELATIONS />
|
||||||
|
</TERM>
|
||||||
|
<TERM native_name="Thesis" code="Thesis" english_name="Thesis" encoding="BASE">
|
||||||
|
<SYNONYMS>
|
||||||
|
<SYNONYM term="18" encoding="BASE" />
|
||||||
|
</SYNONYMS>
|
||||||
|
<RELATIONS />
|
||||||
|
</TERM>
|
||||||
|
<TERM native_name="Bachelor's thesis" code="Bachelor's thesis" english_name="Bachelor's thesis" encoding="BASE">
|
||||||
|
<SYNONYMS>
|
||||||
|
<SYNONYM term="181" encoding="BASE" />
|
||||||
|
</SYNONYMS>
|
||||||
|
<RELATIONS />
|
||||||
|
</TERM>
|
||||||
|
<TERM native_name="Master's thesis" code="Master's thesis" english_name="Master's thesis" encoding="BASE">
|
||||||
|
<SYNONYMS>
|
||||||
|
<SYNONYM term="182" encoding="BASE" />
|
||||||
|
</SYNONYMS>
|
||||||
|
<RELATIONS />
|
||||||
|
</TERM>
|
||||||
|
<TERM native_name="Doctoral and postdoctoral thesis" code="Doctoral and postdoctoral thesis" english_name="Doctoral and postdoctoral thesis" encoding="BASE">
|
||||||
|
<SYNONYMS>
|
||||||
|
<SYNONYM term="183" encoding="BASE" />
|
||||||
|
</SYNONYMS>
|
||||||
|
<RELATIONS />
|
||||||
|
</TERM>
|
||||||
|
<TERM native_name="Manuscript" code="Manuscript" english_name="Manuscript" encoding="BASE">
|
||||||
|
<SYNONYMS>
|
||||||
|
<SYNONYM term="19" encoding="BASE" />
|
||||||
|
</SYNONYMS>
|
||||||
|
<RELATIONS />
|
||||||
|
</TERM>
|
||||||
|
<TERM native_name="Patent" code="Patent" english_name="Patent" encoding="BASE">
|
||||||
|
<SYNONYMS>
|
||||||
|
<SYNONYM term="1A" encoding="BASE" />
|
||||||
|
</SYNONYMS>
|
||||||
|
<RELATIONS />
|
||||||
|
</TERM>
|
||||||
|
<TERM native_name="Musical notation" code="Musical notation" english_name="Musical notation" encoding="BASE">
|
||||||
|
<SYNONYMS>
|
||||||
|
<SYNONYM term="2" encoding="BASE" />
|
||||||
|
</SYNONYMS>
|
||||||
|
<RELATIONS />
|
||||||
|
</TERM>
|
||||||
|
<TERM native_name="Map" code="Map" english_name="Map" encoding="BASE">
|
||||||
|
<SYNONYMS>
|
||||||
|
<SYNONYM term="3" encoding="BASE" />
|
||||||
|
</SYNONYMS>
|
||||||
|
<RELATIONS />
|
||||||
|
</TERM>
|
||||||
|
<TERM native_name="Audio" code="Audio" english_name="Audio" encoding="BASE">
|
||||||
|
<SYNONYMS>
|
||||||
|
<SYNONYM term="4" encoding="BASE" />
|
||||||
|
</SYNONYMS>
|
||||||
|
<RELATIONS />
|
||||||
|
</TERM>
|
||||||
|
<TERM native_name="Image/Video" code="Image/Video" english_name="Image/Video" encoding="BASE">
|
||||||
|
<SYNONYMS>
|
||||||
|
<SYNONYM term="5" encoding="BASE" />
|
||||||
|
</SYNONYMS>
|
||||||
|
<RELATIONS />
|
||||||
|
</TERM>
|
||||||
|
<TERM native_name="Still image" code="Still image" english_name="Still image" encoding="BASE">
|
||||||
|
<SYNONYMS>
|
||||||
|
<SYNONYM term="51" encoding="BASE" />
|
||||||
|
</SYNONYMS>
|
||||||
|
<RELATIONS />
|
||||||
|
</TERM>
|
||||||
|
<TERM native_name="Moving image/Video" code="Moving image/Video" english_name="Moving image/Video" encoding="BASE">
|
||||||
|
<SYNONYMS>
|
||||||
|
<SYNONYM term="52" encoding="BASE" />
|
||||||
|
</SYNONYMS>
|
||||||
|
<RELATIONS />
|
||||||
|
</TERM>
|
||||||
|
<TERM native_name="Software" code="Software" english_name="Software" encoding="BASE">
|
||||||
|
<SYNONYMS>
|
||||||
|
<SYNONYM term="6" encoding="BASE" />
|
||||||
|
</SYNONYMS>
|
||||||
|
<RELATIONS />
|
||||||
|
</TERM>
|
||||||
|
<TERM native_name="Dataset" code="Dataset" english_name="Dataset" encoding="BASE">
|
||||||
|
<SYNONYMS>
|
||||||
|
<SYNONYM term="7" encoding="BASE" />
|
||||||
|
</SYNONYMS>
|
||||||
|
<RELATIONS />
|
||||||
|
</TERM>
|
||||||
|
<TERM native_name="Unknown" code="Unknown" english_name="Unknown" encoding="BASE">
|
||||||
|
<SYNONYMS>
|
||||||
|
<SYNONYM term="F" encoding="BASE" />
|
||||||
|
</SYNONYMS>
|
||||||
|
<RELATIONS />
|
||||||
|
</TERM>
|
||||||
|
|
||||||
|
</TERMS>
|
||||||
|
</CONFIGURATION>
|
||||||
|
<STATUS>
|
||||||
|
<LAST_UPDATE value="2013-11-18T10:46:36Z" />
|
||||||
|
</STATUS>
|
||||||
|
<SECURITY_PARAMETERS>String</SECURITY_PARAMETERS>
|
||||||
|
</BODY>
|
||||||
|
</RESOURCE_PROFILE>
|
||||||
|
|
||||||
|
|
||||||
|
|
@ -0,0 +1,298 @@
|
||||||
|
<RESOURCE_PROFILE>
|
||||||
|
<HEADER>
|
||||||
|
<RESOURCE_IDENTIFIER value="" />
|
||||||
|
<RESOURCE_TYPE value="TransformationRuleDSResourceType" />
|
||||||
|
<RESOURCE_KIND value="TransformationRuleDSResources" />
|
||||||
|
<RESOURCE_URI value="" />
|
||||||
|
<DATE_OF_CREATION value="2024-03-05T11:23:00+00:00" />
|
||||||
|
</HEADER>
|
||||||
|
<BODY>
|
||||||
|
<CONFIGURATION>
|
||||||
|
<SOURCE_METADATA_FORMAT interpretation="cleaned" layout="store" name="dc" />
|
||||||
|
<SINK_METADATA_FORMAT name="oaf_hbase" />
|
||||||
|
<IMPORTED />
|
||||||
|
<SCRIPT>
|
||||||
|
<TITLE>xslt_base2oaf_hadoop</TITLE>
|
||||||
|
<CODE>
|
||||||
|
<xsl:stylesheet xmlns:oaire="http://namespace.openaire.eu/schema/oaire/" xmlns:dateCleaner="http://eu/dnetlib/transform/dateISO"
|
||||||
|
xmlns:base_dc="http://oai.base-search.net/base_dc/"
|
||||||
|
xmlns:datacite="http://datacite.org/schema/kernel-4" xmlns:dr="http://www.driver-repository.eu/namespace/dr" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||||
|
xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xmlns:vocabulary="http://eu/dnetlib/transform/clean" xmlns:oaf="http://namespace.openaire.eu/oaf"
|
||||||
|
xmlns:oai="http://www.openarchives.org/OAI/2.0/" xmlns:dri="http://www.driver-repository.eu/namespace/dri" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:dc="http://purl.org/dc/elements/1.1/"
|
||||||
|
exclude-result-prefixes="xsl vocabulary dateCleaner base_dc" version="2.0">
|
||||||
|
<xsl:param name="varOfficialName" />
|
||||||
|
<xsl:param name="varDataSourceId" />
|
||||||
|
<xsl:param name="varFP7" select="'corda_______::'" />
|
||||||
|
<xsl:param name="varH2020" select="'corda__h2020::'" />
|
||||||
|
<xsl:param name="repoCode" select="substring-before(//*[local-name() = 'header']/*[local-name()='recordIdentifier'], ':')" />
|
||||||
|
<xsl:param name="index" select="0" />
|
||||||
|
<xsl:param name="transDate" select="current-dateTime()" />
|
||||||
|
|
||||||
|
<xsl:template name="terminate">
|
||||||
|
<xsl:message terminate="yes">
|
||||||
|
record is not compliant, transformation is interrupted.
|
||||||
|
</xsl:message>
|
||||||
|
</xsl:template>
|
||||||
|
|
||||||
|
<xsl:template match="/">
|
||||||
|
<record>
|
||||||
|
<xsl:apply-templates select="//*[local-name() = 'header']" />
|
||||||
|
|
||||||
|
|
||||||
|
<!-- TO EVALUATE
|
||||||
|
base_dc:authod_id
|
||||||
|
base_dc:authod_id/base_dc:creator_id
|
||||||
|
base_dc:authod_id/base_dc:creator_name
|
||||||
|
|
||||||
|
example:
|
||||||
|
|
||||||
|
<dc:creator>ALBU, Svetlana</dc:creator>
|
||||||
|
|
||||||
|
<base_dc:authod_id>
|
||||||
|
<base_dc:creator_name>ALBU, Svetlana</base_dc:creator_name>
|
||||||
|
<base_dc:creator_id>https://orcid.org/0000-0002-8648-950X</base_dc:creator_id>
|
||||||
|
</base_dc:authod_id>
|
||||||
|
-->
|
||||||
|
|
||||||
|
<!-- NOT USED
|
||||||
|
base_dc:global_id (I used oai:identifier)
|
||||||
|
base_dc:collection/text()
|
||||||
|
|
||||||
|
base_dc:continent
|
||||||
|
base_dc:country
|
||||||
|
base_dc:year (I used dc:date)
|
||||||
|
dc:coverage
|
||||||
|
dc:language (I used base_dc:lang)
|
||||||
|
base_dc:link (I used dc:identifier)
|
||||||
|
-->
|
||||||
|
|
||||||
|
|
||||||
|
<xsl:variable name="varBaseNormType" select="vocabulary:clean(//base_dc:typenorm, 'base:normalized_types')" />
|
||||||
|
|
||||||
|
|
||||||
|
<metadata>
|
||||||
|
<xsl:call-template name="allElements">
|
||||||
|
<xsl:with-param name="sourceElement" select="//dc:title" />
|
||||||
|
<xsl:with-param name="targetElement" select="'dc:title'" />
|
||||||
|
</xsl:call-template>
|
||||||
|
|
||||||
|
<xsl:call-template name="allElements">
|
||||||
|
<xsl:with-param name="sourceElement" select="//dc:creator/replace(., '^(.*)\|.*$', '$1')" />
|
||||||
|
<xsl:with-param name="targetElement" select="'dc:creator'" />
|
||||||
|
</xsl:call-template>
|
||||||
|
|
||||||
|
<xsl:call-template name="allElements">
|
||||||
|
<xsl:with-param name="sourceElement" select="//dc:contributor" />
|
||||||
|
<xsl:with-param name="targetElement" select="'dc:contributor'" />
|
||||||
|
</xsl:call-template>
|
||||||
|
|
||||||
|
<xsl:call-template name="allElements">
|
||||||
|
<xsl:with-param name="sourceElement" select="//dc:description" />
|
||||||
|
<xsl:with-param name="targetElement" select="'dc:description'" />
|
||||||
|
</xsl:call-template>
|
||||||
|
|
||||||
|
<xsl:call-template name="allElements">
|
||||||
|
<xsl:with-param name="sourceElement" select="//dc:subject" />
|
||||||
|
<xsl:with-param name="targetElement" select="'dc:subject'" />
|
||||||
|
</xsl:call-template>
|
||||||
|
|
||||||
|
<!-- TODO: I'm not sure if this is the correct encoding -->
|
||||||
|
<xsl:for-each select="//base_dc:classcode|//base_dc:autoclasscode">
|
||||||
|
<dc:subject><xsl:value-of select="concat(@type, ':', .)" /></dc:subject>
|
||||||
|
</xsl:for-each>
|
||||||
|
<!-- END TODO -->
|
||||||
|
|
||||||
|
<xsl:call-template name="allElements">
|
||||||
|
<xsl:with-param name="sourceElement" select="//dc:publisher" />
|
||||||
|
<xsl:with-param name="targetElement" select="'dc:publisher'" />
|
||||||
|
</xsl:call-template>
|
||||||
|
|
||||||
|
<xsl:call-template name="allElements">
|
||||||
|
<xsl:with-param name="sourceElement" select="//dc:format" />
|
||||||
|
<xsl:with-param name="targetElement" select="'dc:format'" />
|
||||||
|
</xsl:call-template>
|
||||||
|
|
||||||
|
<dc:type>
|
||||||
|
<xsl:value-of select="$varBaseNormType" />
|
||||||
|
</dc:type>
|
||||||
|
<xsl:call-template name="allElements">
|
||||||
|
<xsl:with-param name="sourceElement" select="//dc:type" />
|
||||||
|
<xsl:with-param name="targetElement" select="'dc:type'" />
|
||||||
|
</xsl:call-template>
|
||||||
|
|
||||||
|
|
||||||
|
<xsl:call-template name="allElements">
|
||||||
|
<xsl:with-param name="sourceElement" select="//dc:source" />
|
||||||
|
<xsl:with-param name="targetElement" select="'dc:source'" />
|
||||||
|
</xsl:call-template>
|
||||||
|
|
||||||
|
<dc:language>
|
||||||
|
<xsl:value-of select="vocabulary:clean( //base_dc:lang, 'dnet:languages')" />
|
||||||
|
</dc:language>
|
||||||
|
|
||||||
|
<xsl:call-template name="allElements">
|
||||||
|
<xsl:with-param name="sourceElement" select="//dc:rights" />
|
||||||
|
<xsl:with-param name="targetElement" select="'dc:rights'" />
|
||||||
|
</xsl:call-template>
|
||||||
|
|
||||||
|
<xsl:call-template name="allElements">
|
||||||
|
<xsl:with-param name="sourceElement" select="//dc:relation" />
|
||||||
|
<xsl:with-param name="targetElement" select="'dc:relation'" />
|
||||||
|
</xsl:call-template>
|
||||||
|
|
||||||
|
<xsl:if test="not(//dc:identifier[starts-with(., 'http')])">
|
||||||
|
<xsl:call-template name="terminate" />
|
||||||
|
</xsl:if>
|
||||||
|
|
||||||
|
<xsl:call-template name="allElements">
|
||||||
|
<xsl:with-param name="sourceElement" select="//dc:identifier[starts-with(., 'http')]" />
|
||||||
|
<xsl:with-param name="targetElement" select="'dc:identifier'" />
|
||||||
|
</xsl:call-template>
|
||||||
|
|
||||||
|
<xsl:for-each select="//dc:relation">
|
||||||
|
<xsl:if test="matches(normalize-space(.), '(info:eu-repo/grantagreement/ec/fp7/)(\d\d\d\d\d\d)(.*)', 'i')">
|
||||||
|
<oaf:projectid>
|
||||||
|
<xsl:value-of select="concat($varFP7, replace(normalize-space(.), '(info:eu-repo/grantagreement/ec/fp7/)(\d\d\d\d\d\d)(.*)', '$2', 'i'))" />
|
||||||
|
</oaf:projectid>
|
||||||
|
</xsl:if>
|
||||||
|
<xsl:if test="matches(normalize-space(.), '(info:eu-repo/grantagreement/ec/h2020/)(\d\d\d\d\d\d)(.*)', 'i')">
|
||||||
|
<oaf:projectid>
|
||||||
|
<xsl:value-of select="concat($varH2020, replace(normalize-space(.), '(info:eu-repo/grantagreement/ec/h2020/)(\d\d\d\d\d\d)(.*)', '$2', 'i'))" />
|
||||||
|
</oaf:projectid>
|
||||||
|
</xsl:if>
|
||||||
|
</xsl:for-each>
|
||||||
|
|
||||||
|
<dr:CobjCategory>
|
||||||
|
<xsl:variable name="varCobjCategory" select="vocabulary:clean($varBaseNormType, 'dnet:publication_resource')" />
|
||||||
|
<xsl:variable name="varSuperType" select="vocabulary:clean($varCobjCategory, 'dnet:result_typologies')" />
|
||||||
|
<xsl:attribute name="type" select="$varSuperType" />
|
||||||
|
<xsl:value-of select="$varCobjCategory" />
|
||||||
|
</dr:CobjCategory>
|
||||||
|
|
||||||
|
<oaf:accessrights>
|
||||||
|
<xsl:choose>
|
||||||
|
<xsl:when test="//base_dc:oa[.='1']">OPEN</xsl:when>
|
||||||
|
<xsl:when test="//base_dc:rightsnorm">
|
||||||
|
<xsl:value-of select="vocabulary:clean(//base_dc:rightsnorm, 'dnet:access_modes')" />
|
||||||
|
</xsl:when>
|
||||||
|
<xsl:when test="//dc:rights">
|
||||||
|
<xsl:value-of select="vocabulary:clean( //dc:rights, 'dnet:access_modes')" />
|
||||||
|
</xsl:when>
|
||||||
|
<xsl:otherwise>UNKNOWN</xsl:otherwise>
|
||||||
|
</xsl:choose>
|
||||||
|
</oaf:accessrights>
|
||||||
|
|
||||||
|
<xsl:for-each select="//base_dc:doi">
|
||||||
|
<oaf:identifier identifierType="doi">
|
||||||
|
<xsl:value-of select="." />
|
||||||
|
</oaf:identifier>
|
||||||
|
</xsl:for-each>
|
||||||
|
|
||||||
|
<xsl:for-each select="distinct-values(//dc:identifier[starts-with(., 'http') and (not(contains(., '://dx.doi.org/') or contains(., '://doi.org/') or contains(., '://hdl.handle.net/')))])">
|
||||||
|
<oaf:identifier identifierType="url">
|
||||||
|
<xsl:value-of select="." />
|
||||||
|
</oaf:identifier>
|
||||||
|
</xsl:for-each>
|
||||||
|
|
||||||
|
<xsl:for-each select="distinct-values(//dc:identifier[starts-with(., 'http') and contains(., '://hdl.handle.net/')]/substring-after(., 'hdl.handle.net/'))">
|
||||||
|
<oaf:identifier identifierType="handle">
|
||||||
|
<xsl:value-of select="." />
|
||||||
|
</oaf:identifier>
|
||||||
|
</xsl:for-each>
|
||||||
|
|
||||||
|
<xsl:for-each select="distinct-values(//dc:identifier[starts-with(., 'urn:nbn:nl:') or starts-with(., 'URN:NBN:NL:')])">
|
||||||
|
<oaf:identifier identifierType='urn'>
|
||||||
|
<xsl:value-of select="." />
|
||||||
|
</oaf:identifier>
|
||||||
|
</xsl:for-each>
|
||||||
|
|
||||||
|
<oaf:identifier identifierType="oai-original">
|
||||||
|
<xsl:value-of
|
||||||
|
select="//*[local-name() = 'about']/*[local-name() = 'provenance']//*[local-name() = 'originDescription' and not(./*[local-name() = 'originDescription'])]/*[local-name() = 'identifier']" />
|
||||||
|
</oaf:identifier>
|
||||||
|
|
||||||
|
<oaf:hostedBy>
|
||||||
|
<xsl:attribute name="name">
|
||||||
|
<xsl:value-of select="//base_dc:collname" />
|
||||||
|
</xsl:attribute>
|
||||||
|
<xsl:attribute name="id">
|
||||||
|
<xsl:value-of select="concat('opendoar____::', //base_dc:collection/@opendoar_id)" />
|
||||||
|
</xsl:attribute>
|
||||||
|
</oaf:hostedBy>
|
||||||
|
|
||||||
|
<oaf:collectedFrom>
|
||||||
|
<xsl:attribute name="name">
|
||||||
|
<xsl:value-of select="$varOfficialName" />
|
||||||
|
</xsl:attribute>
|
||||||
|
<xsl:attribute name="id">
|
||||||
|
<xsl:value-of select="$varDataSourceId" />
|
||||||
|
</xsl:attribute>
|
||||||
|
</oaf:collectedFrom>
|
||||||
|
|
||||||
|
<oaf:dateAccepted>
|
||||||
|
<xsl:value-of select="dateCleaner:dateISO( //dc:date[1] )" />
|
||||||
|
</oaf:dateAccepted>
|
||||||
|
|
||||||
|
<xsl:if test="//base_dc:oa[.='1']">
|
||||||
|
<xsl:for-each select="//dc:relation[starts-with(., 'http')]">
|
||||||
|
<oaf:fulltext>
|
||||||
|
<xsl:value-of select="normalize-space(.)" />
|
||||||
|
</oaf:fulltext>
|
||||||
|
</xsl:for-each>
|
||||||
|
</xsl:if>
|
||||||
|
|
||||||
|
<xsl:for-each select="//base_dc:collection/@ror_id">
|
||||||
|
<oaf:relation relType="resultOrganization"
|
||||||
|
subRelType="affiliation"
|
||||||
|
relClass="hasAuthorInstitution"
|
||||||
|
targetType="organization">
|
||||||
|
<xsl:choose>
|
||||||
|
<xsl:when test="contains(.,'https://ror.org/')">
|
||||||
|
<xsl:value-of select="concat('ror_________::', normalize-space(.))" />
|
||||||
|
</xsl:when>
|
||||||
|
<xsl:otherwise>
|
||||||
|
<xsl:value-of select="concat('ror_________::https://ror.org/', normalize-space(.))" />
|
||||||
|
</xsl:otherwise>
|
||||||
|
</xsl:choose>
|
||||||
|
</oaf:relation>
|
||||||
|
</xsl:for-each>
|
||||||
|
</metadata>
|
||||||
|
<xsl:copy-of select="//*[local-name() = 'about']" />
|
||||||
|
</record>
|
||||||
|
</xsl:template>
|
||||||
|
|
||||||
|
<xsl:template name="allElements">
|
||||||
|
<xsl:param name="sourceElement" />
|
||||||
|
<xsl:param name="targetElement" />
|
||||||
|
<xsl:for-each select="$sourceElement">
|
||||||
|
<xsl:element name="{$targetElement}">
|
||||||
|
<xsl:value-of select="normalize-space(.)" />
|
||||||
|
</xsl:element>
|
||||||
|
</xsl:for-each>
|
||||||
|
</xsl:template>
|
||||||
|
|
||||||
|
<xsl:template match="//*[local-name() = 'header']">
|
||||||
|
<xsl:if test="//oai:header/@status='deleted'">
|
||||||
|
<xsl:call-template name="terminate" />
|
||||||
|
</xsl:if>
|
||||||
|
<xsl:copy>
|
||||||
|
<xsl:apply-templates select="node()|@*" />
|
||||||
|
<xsl:element name="dr:dateOfTransformation">
|
||||||
|
<xsl:value-of select="$transDate" />
|
||||||
|
</xsl:element>
|
||||||
|
</xsl:copy>
|
||||||
|
</xsl:template>
|
||||||
|
|
||||||
|
<xsl:template match="node()|@*">
|
||||||
|
<xsl:copy>
|
||||||
|
<xsl:apply-templates select="node()|@*" />
|
||||||
|
</xsl:copy>
|
||||||
|
</xsl:template>
|
||||||
|
</xsl:stylesheet>
|
||||||
|
</CODE>
|
||||||
|
</SCRIPT>
|
||||||
|
</CONFIGURATION>
|
||||||
|
<STATUS />
|
||||||
|
<SECURITY_PARAMETERS />
|
||||||
|
</BODY>
|
||||||
|
</RESOURCE_PROFILE>
|
||||||
|
|
@ -0,0 +1,322 @@
|
||||||
|
<RESOURCE_PROFILE>
|
||||||
|
<HEADER>
|
||||||
|
<RESOURCE_IDENTIFIER value="2ad0cdd9-c96c-484c-8b0e-ed56d86891fe_VHJhbnNmb3JtYXRpb25SdWxlRFNSZXNvdXJjZXMvVHJhbnNmb3JtYXRpb25SdWxlRFNSZXNvdXJjZVR5cGU=" />
|
||||||
|
<RESOURCE_TYPE value="TransformationRuleDSResourceType" />
|
||||||
|
<RESOURCE_KIND value="TransformationRuleDSResources" />
|
||||||
|
<RESOURCE_URI value="" />
|
||||||
|
<DATE_OF_CREATION value="2024-03-05T11:23:00+00:00" />
|
||||||
|
</HEADER>
|
||||||
|
<BODY>
|
||||||
|
<CONFIGURATION>
|
||||||
|
<SOURCE_METADATA_FORMAT interpretation="cleaned" layout="store" name="dc" />
|
||||||
|
<SINK_METADATA_FORMAT name="odf_hbase" />
|
||||||
|
<IMPORTED />
|
||||||
|
<SCRIPT>
|
||||||
|
<TITLE>xslt_base2odf_hadoop</TITLE>
|
||||||
|
<CODE>
|
||||||
|
<xsl:stylesheet xmlns:oaire="http://namespace.openaire.eu/schema/oaire/" xmlns:dateCleaner="http://eu/dnetlib/transform/dateISO" xmlns:base_dc="http://oai.base-search.net/base_dc/"
|
||||||
|
xmlns:datacite="http://datacite.org/schema/kernel-4" xmlns:dr="http://www.driver-repository.eu/namespace/dr" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||||
|
xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xmlns:vocabulary="http://eu/dnetlib/transform/clean" xmlns:oaf="http://namespace.openaire.eu/oaf"
|
||||||
|
xmlns:oai="http://www.openarchives.org/OAI/2.0/" xmlns:dri="http://www.driver-repository.eu/namespace/dri" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:dc="http://purl.org/dc/elements/1.1/"
|
||||||
|
exclude-result-prefixes="xsl vocabulary dateCleaner base_dc" version="2.0">
|
||||||
|
<xsl:param name="varOfficialName" />
|
||||||
|
<xsl:param name="varDataSourceId" />
|
||||||
|
<xsl:param name="varFP7" select="'corda_______::'" />
|
||||||
|
<xsl:param name="varH2020" select="'corda__h2020::'" />
|
||||||
|
<xsl:param name="repoCode" select="substring-before(//*[local-name() = 'header']/*[local-name()='recordIdentifier'], ':')" />
|
||||||
|
<xsl:param name="index" select="0" />
|
||||||
|
<xsl:param name="transDate" select="current-dateTime()" />
|
||||||
|
|
||||||
|
<xsl:template name="terminate">
|
||||||
|
<xsl:message terminate="yes">
|
||||||
|
record is not compliant, transformation is interrupted.
|
||||||
|
</xsl:message>
|
||||||
|
</xsl:template>
|
||||||
|
|
||||||
|
<xsl:template match="/">
|
||||||
|
<record>
|
||||||
|
<xsl:apply-templates select="//*[local-name() = 'header']" />
|
||||||
|
|
||||||
|
|
||||||
|
<!-- NOT USED
|
||||||
|
base_dc:global_id (I used oai:identifier)
|
||||||
|
base_dc:collection/text()
|
||||||
|
base_dc:continent
|
||||||
|
base_dc:country
|
||||||
|
dc:coverage
|
||||||
|
dc:source
|
||||||
|
dc:relation
|
||||||
|
dc:type (I used //base_dc:typenorm)
|
||||||
|
dc:language (I used base_dc:lang)
|
||||||
|
base_dc:link (I used dc:identifier)
|
||||||
|
-->
|
||||||
|
|
||||||
|
|
||||||
|
<xsl:variable name="varBaseNormType" select="vocabulary:clean(//base_dc:typenorm, 'base:normalized_types')" />
|
||||||
|
|
||||||
|
|
||||||
|
<metadata>
|
||||||
|
<datacite:resource>
|
||||||
|
|
||||||
|
<xsl:for-each select="//base_dc:doi">
|
||||||
|
<datacite:identifier identifierType="DOI">
|
||||||
|
<xsl:value-of select="." />
|
||||||
|
</datacite:identifier>
|
||||||
|
</xsl:for-each>
|
||||||
|
|
||||||
|
<datacite:alternateIdentifiers>
|
||||||
|
<xsl:for-each
|
||||||
|
select="distinct-values(//dc:identifier[starts-with(., 'http') and (not(contains(., '://dx.doi.org/') or contains(., '://doi.org/') or contains(., '://hdl.handle.net/')))])">
|
||||||
|
<datacite:identifier alternateIdentifierType="url">
|
||||||
|
<xsl:value-of select="." />
|
||||||
|
</datacite:identifier>
|
||||||
|
</xsl:for-each>
|
||||||
|
|
||||||
|
<xsl:for-each select="distinct-values(//dc:identifier[starts-with(., 'http') and contains(., '://hdl.handle.net/')]/substring-after(., 'hdl.handle.net/'))">
|
||||||
|
<datacite:identifier alternateIdentifierType="handle">
|
||||||
|
<xsl:value-of select="." />
|
||||||
|
</datacite:identifier>
|
||||||
|
</xsl:for-each>
|
||||||
|
|
||||||
|
<xsl:for-each select="distinct-values(//dc:identifier[starts-with(., 'urn:nbn:nl:') or starts-with(., 'URN:NBN:NL:')])">
|
||||||
|
<datacite:identifier alternateIdentifierType='urn'>
|
||||||
|
<xsl:value-of select="." />
|
||||||
|
</datacite:identifier>
|
||||||
|
</xsl:for-each>
|
||||||
|
|
||||||
|
<datacite:identifier alternateIdentifierType="oai-original">
|
||||||
|
<xsl:value-of
|
||||||
|
select="//*[local-name() = 'about']/*[local-name() = 'provenance']//*[local-name() = 'originDescription' and not(./*[local-name() = 'originDescription'])]/*[local-name() = 'identifier']" />
|
||||||
|
</datacite:identifier>
|
||||||
|
</datacite:alternateIdentifiers>
|
||||||
|
|
||||||
|
<datacite:relatedIdentifiers />
|
||||||
|
|
||||||
|
|
||||||
|
<datacite:resourceType><xsl:value-of select="$varBaseNormType" /></datacite:resourceType>
|
||||||
|
|
||||||
|
<datacite:titles>
|
||||||
|
<xsl:for-each select="//dc:title">
|
||||||
|
<datacite:title>
|
||||||
|
<xsl:value-of select="normalize-space(.)" />
|
||||||
|
</datacite:title>
|
||||||
|
</xsl:for-each>
|
||||||
|
</datacite:titles>
|
||||||
|
|
||||||
|
<datacite:creators>
|
||||||
|
<xsl:for-each select="//dc:creator">
|
||||||
|
<xsl:variable name="author" select="normalize-space(.)" />
|
||||||
|
<datacite:creator>
|
||||||
|
<datacite:creatorName>
|
||||||
|
<xsl:value-of select="$author" />
|
||||||
|
</datacite:creatorName>
|
||||||
|
<xsl:for-each select="//base_dc:authod_id[normalize-space(./base_dc:creator_name) = $author]/base_dc:creator_id ">
|
||||||
|
<xsl:if test="contains(.,'https://orcid.org/')">
|
||||||
|
<nameIdentifier schemeURI="https://orcid.org/" nameIdentifierScheme="ORCID">
|
||||||
|
<xsl:value-of select="substring-after(., 'https://orcid.org/')" />
|
||||||
|
</nameIdentifier>
|
||||||
|
</xsl:if>
|
||||||
|
</xsl:for-each>
|
||||||
|
</datacite:creator>
|
||||||
|
</xsl:for-each>
|
||||||
|
</datacite:creators>
|
||||||
|
|
||||||
|
<datacite:contributors>
|
||||||
|
<xsl:for-each select="//dc:contributor">
|
||||||
|
<datacite:contributor>
|
||||||
|
<datacite:contributorName>
|
||||||
|
<xsl:value-of select="normalize-space(.)" />
|
||||||
|
</datacite:contributorName>
|
||||||
|
</datacite:contributor>
|
||||||
|
</xsl:for-each>
|
||||||
|
</datacite:contributors>
|
||||||
|
|
||||||
|
<datacite:descriptions>
|
||||||
|
<xsl:for-each select="//dc:description">
|
||||||
|
<datacite:description descriptionType="Abstract">
|
||||||
|
<xsl:value-of select="normalize-space(.)" />
|
||||||
|
</datacite:description>
|
||||||
|
</xsl:for-each>
|
||||||
|
</datacite:descriptions>
|
||||||
|
|
||||||
|
<datacite:subjects>
|
||||||
|
<xsl:for-each select="//dc:subject">
|
||||||
|
<datacite:subject>
|
||||||
|
<xsl:value-of select="normalize-space(.)" />
|
||||||
|
</datacite:subject>
|
||||||
|
</xsl:for-each>
|
||||||
|
|
||||||
|
<xsl:for-each select="//base_dc:classcode|//base_dc:autoclasscode">
|
||||||
|
<datacite:subject subjectScheme="{@type}" classificationCode="{normalize-space(.)}">
|
||||||
|
<!-- TODO the value should be obtained by the Code -->
|
||||||
|
<xsl:value-of select="normalize-space(.)" />
|
||||||
|
</datacite:subject>
|
||||||
|
</xsl:for-each>
|
||||||
|
</datacite:subjects>
|
||||||
|
|
||||||
|
<datacite:publisher>
|
||||||
|
<xsl:value-of select="normalize-space(//dc:publisher)" />
|
||||||
|
</datacite:publisher>
|
||||||
|
|
||||||
|
<datacite:publicationYear>
|
||||||
|
<xsl:value-of select="normalize-space(//base_dc:year)" />
|
||||||
|
</datacite:publicationYear>
|
||||||
|
|
||||||
|
<datacite:formats>
|
||||||
|
<xsl:for-each select="//dc:format">
|
||||||
|
<datacite:format>
|
||||||
|
<xsl:value-of select="normalize-space(.)" />
|
||||||
|
</datacite:format>
|
||||||
|
</xsl:for-each>
|
||||||
|
</datacite:formats>
|
||||||
|
|
||||||
|
<datacite:language>
|
||||||
|
<xsl:value-of select="vocabulary:clean( //base_dc:lang, 'dnet:languages')" />
|
||||||
|
</datacite:language>
|
||||||
|
|
||||||
|
<oaf:accessrights>
|
||||||
|
<xsl:if test="//base_dc:oa[.='1']">
|
||||||
|
<datacite:rights rightsURI="http://purl.org/coar/access_right/c_abf2">open access</datacite:rights>
|
||||||
|
</xsl:if>
|
||||||
|
<xsl:for-each select="//dc:rights|//base_dc:rightsnorm">
|
||||||
|
<datacite:rights><xsl:value-of select="vocabulary:clean(., 'dnet:access_modes')" /></datacite:rights>
|
||||||
|
</xsl:for-each>
|
||||||
|
</oaf:accessrights>
|
||||||
|
|
||||||
|
</datacite:resource>
|
||||||
|
|
||||||
|
<xsl:for-each select="//dc:relation">
|
||||||
|
<xsl:if test="matches(normalize-space(.), '(info:eu-repo/grantagreement/ec/fp7/)(\d\d\d\d\d\d)(.*)', 'i')">
|
||||||
|
<oaf:projectid>
|
||||||
|
<xsl:value-of select="concat($varFP7, replace(normalize-space(.), '(info:eu-repo/grantagreement/ec/fp7/)(\d\d\d\d\d\d)(.*)', '$2', 'i'))" />
|
||||||
|
</oaf:projectid>
|
||||||
|
</xsl:if>
|
||||||
|
<xsl:if test="matches(normalize-space(.), '(info:eu-repo/grantagreement/ec/h2020/)(\d\d\d\d\d\d)(.*)', 'i')">
|
||||||
|
<oaf:projectid>
|
||||||
|
<xsl:value-of select="concat($varH2020, replace(normalize-space(.), '(info:eu-repo/grantagreement/ec/h2020/)(\d\d\d\d\d\d)(.*)', '$2', 'i'))" />
|
||||||
|
</oaf:projectid>
|
||||||
|
</xsl:if>
|
||||||
|
</xsl:for-each>
|
||||||
|
|
||||||
|
<dr:CobjCategory>
|
||||||
|
<xsl:variable name="varCobjCategory" select="vocabulary:clean($varBaseNormType, 'dnet:publication_resource')" />
|
||||||
|
<xsl:variable name="varSuperType" select="vocabulary:clean($varCobjCategory, 'dnet:result_typologies')" />
|
||||||
|
<xsl:attribute name="type" select="$varSuperType" />
|
||||||
|
<xsl:value-of select="$varCobjCategory" />
|
||||||
|
</dr:CobjCategory>
|
||||||
|
|
||||||
|
<oaf:accessrights>
|
||||||
|
<xsl:choose>
|
||||||
|
<xsl:when test="//base_dc:oa[.='1']">OPEN</xsl:when>
|
||||||
|
<xsl:when test="//base_dc:rightsnorm">
|
||||||
|
<xsl:value-of select="vocabulary:clean(//base_dc:rightsnorm, 'dnet:access_modes')" />
|
||||||
|
</xsl:when>
|
||||||
|
<xsl:when test="//dc:rights">
|
||||||
|
<xsl:value-of select="vocabulary:clean( //dc:rights, 'dnet:access_modes')" />
|
||||||
|
</xsl:when>
|
||||||
|
<xsl:otherwise>UNKNOWN</xsl:otherwise>
|
||||||
|
</xsl:choose>
|
||||||
|
</oaf:accessrights>
|
||||||
|
|
||||||
|
<xsl:for-each select="//base_dc:doi">
|
||||||
|
<oaf:identifier identifierType="doi">
|
||||||
|
<xsl:value-of select="." />
|
||||||
|
</oaf:identifier>
|
||||||
|
</xsl:for-each>
|
||||||
|
|
||||||
|
<xsl:for-each
|
||||||
|
select="distinct-values(//dc:identifier[starts-with(., 'http') and ( not(contains(., '://dx.doi.org/') or contains(., '://doi.org/') or contains(., '://hdl.handle.net/')))])">
|
||||||
|
<oaf:identifier identifierType="url">
|
||||||
|
<xsl:value-of select="." />
|
||||||
|
</oaf:identifier>
|
||||||
|
</xsl:for-each>
|
||||||
|
|
||||||
|
<xsl:for-each select="distinct-values(//dc:identifier[starts-with(., 'http') and contains(., '://hdl.handle.net/')]/substring-after(., 'hdl.handle.net/'))">
|
||||||
|
<oaf:identifier identifierType="handle">
|
||||||
|
<xsl:value-of select="." />
|
||||||
|
</oaf:identifier>
|
||||||
|
</xsl:for-each>
|
||||||
|
|
||||||
|
<xsl:for-each select="distinct-values(//dc:identifier[starts-with(., 'urn:nbn:nl:') or starts-with(., 'URN:NBN:NL:')])">
|
||||||
|
<oaf:identifier identifierType='urn'>
|
||||||
|
<xsl:value-of select="." />
|
||||||
|
</oaf:identifier>
|
||||||
|
</xsl:for-each>
|
||||||
|
|
||||||
|
<oaf:identifier identifierType="oai-original">
|
||||||
|
<xsl:value-of
|
||||||
|
select="//*[local-name() = 'about']/*[local-name() = 'provenance']//*[local-name() = 'originDescription' and not(./*[local-name() = 'originDescription'])]/*[local-name() = 'identifier']" />
|
||||||
|
</oaf:identifier>
|
||||||
|
|
||||||
|
<oaf:hostedBy>
|
||||||
|
<xsl:attribute name="name">
|
||||||
|
<xsl:value-of select="//base_dc:collname" />
|
||||||
|
</xsl:attribute>
|
||||||
|
<xsl:attribute name="id">
|
||||||
|
<xsl:value-of select="concat('opendoar____::', //base_dc:collection/@opendoar_id)" />
|
||||||
|
</xsl:attribute>
|
||||||
|
</oaf:hostedBy>
|
||||||
|
|
||||||
|
<oaf:collectedFrom>
|
||||||
|
<xsl:attribute name="name">
|
||||||
|
<xsl:value-of select="$varOfficialName" />
|
||||||
|
</xsl:attribute>
|
||||||
|
<xsl:attribute name="id">
|
||||||
|
<xsl:value-of select="$varDataSourceId" />
|
||||||
|
</xsl:attribute>
|
||||||
|
</oaf:collectedFrom>
|
||||||
|
|
||||||
|
<oaf:dateAccepted>
|
||||||
|
<xsl:value-of select="dateCleaner:dateISO( //dc:date[1] )" />
|
||||||
|
</oaf:dateAccepted>
|
||||||
|
|
||||||
|
<xsl:if test="//base_dc:oa[.='1']">
|
||||||
|
<xsl:for-each select="//dc:relation[starts-with(., 'http')]">
|
||||||
|
<oaf:fulltext>
|
||||||
|
<xsl:value-of select="normalize-space(.)" />
|
||||||
|
</oaf:fulltext>
|
||||||
|
</xsl:for-each>
|
||||||
|
</xsl:if>
|
||||||
|
|
||||||
|
<xsl:for-each select="//base_dc:collection/@ror_id">
|
||||||
|
<oaf:relation relType="resultOrganization" subRelType="affiliation" relClass="hasAuthorInstitution" targetType="organization">
|
||||||
|
<xsl:choose>
|
||||||
|
<xsl:when test="contains(.,'https://ror.org/')">
|
||||||
|
<xsl:value-of select="concat('ror_________::', normalize-space(.))" />
|
||||||
|
</xsl:when>
|
||||||
|
<xsl:otherwise>
|
||||||
|
<xsl:value-of select="concat('ror_________::https://ror.org/', normalize-space(.))" />
|
||||||
|
</xsl:otherwise>
|
||||||
|
</xsl:choose>
|
||||||
|
</oaf:relation>
|
||||||
|
</xsl:for-each>
|
||||||
|
</metadata>
|
||||||
|
<xsl:copy-of select="//*[local-name() = 'about']" />
|
||||||
|
</record>
|
||||||
|
</xsl:template>
|
||||||
|
|
||||||
|
<xsl:template match="//*[local-name() = 'header']">
|
||||||
|
<xsl:if test="//oai:header/@status='deleted'">
|
||||||
|
<xsl:call-template name="terminate" />
|
||||||
|
</xsl:if>
|
||||||
|
<xsl:copy>
|
||||||
|
<xsl:apply-templates select="node()|@*" />
|
||||||
|
<xsl:element name="dr:dateOfTransformation">
|
||||||
|
<xsl:value-of select="$transDate" />
|
||||||
|
</xsl:element>
|
||||||
|
</xsl:copy>
|
||||||
|
</xsl:template>
|
||||||
|
|
||||||
|
<xsl:template match="node()|@*">
|
||||||
|
<xsl:copy>
|
||||||
|
<xsl:apply-templates select="node()|@*" />
|
||||||
|
</xsl:copy>
|
||||||
|
</xsl:template>
|
||||||
|
</xsl:stylesheet>
|
||||||
|
</CODE>
|
||||||
|
</SCRIPT>
|
||||||
|
</CONFIGURATION>
|
||||||
|
<STATUS />
|
||||||
|
<SECURITY_PARAMETERS />
|
||||||
|
</BODY>
|
||||||
|
</RESOURCE_PROFILE>
|
||||||
|
|
@ -11,6 +11,7 @@ import org.apache.spark.SparkConf
|
||||||
import org.apache.spark.sql.{Encoder, Encoders, SparkSession}
|
import org.apache.spark.sql.{Encoder, Encoders, SparkSession}
|
||||||
import org.slf4j.{Logger, LoggerFactory}
|
import org.slf4j.{Logger, LoggerFactory}
|
||||||
import eu.dnetlib.dhp.utils.DHPUtils.{MAPPER, writeHdfsFile}
|
import eu.dnetlib.dhp.utils.DHPUtils.{MAPPER, writeHdfsFile}
|
||||||
|
|
||||||
object SparkTransformBioDatabaseToOAF {
|
object SparkTransformBioDatabaseToOAF {
|
||||||
|
|
||||||
def main(args: Array[String]): Unit = {
|
def main(args: Array[String]): Unit = {
|
||||||
|
|
|
||||||
|
|
@ -0,0 +1,38 @@
|
||||||
|
|
||||||
|
package eu.dnetlib.dhp.collection.plugin.base;
|
||||||
|
|
||||||
|
import java.io.Serializable;
|
||||||
|
|
||||||
|
public class BaseCollectionInfo implements Serializable {
|
||||||
|
|
||||||
|
private static final long serialVersionUID = 5766333937429419647L;
|
||||||
|
|
||||||
|
private String id;
|
||||||
|
private String opendoarId;
|
||||||
|
private String rorId;
|
||||||
|
|
||||||
|
public String getId() {
|
||||||
|
return this.id;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void setId(final String id) {
|
||||||
|
this.id = id;
|
||||||
|
}
|
||||||
|
|
||||||
|
public String getOpendoarId() {
|
||||||
|
return this.opendoarId;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void setOpendoarId(final String opendoarId) {
|
||||||
|
this.opendoarId = opendoarId;
|
||||||
|
}
|
||||||
|
|
||||||
|
public String getRorId() {
|
||||||
|
return this.rorId;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void setRorId(final String rorId) {
|
||||||
|
this.rorId = rorId;
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,184 @@
|
||||||
|
|
||||||
|
package eu.dnetlib.dhp.collection.plugin.base;
|
||||||
|
|
||||||
|
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||||
|
|
||||||
|
import java.util.ArrayList;
|
||||||
|
import java.util.HashMap;
|
||||||
|
import java.util.HashSet;
|
||||||
|
import java.util.LinkedHashSet;
|
||||||
|
import java.util.List;
|
||||||
|
import java.util.Map;
|
||||||
|
import java.util.Map.Entry;
|
||||||
|
import java.util.Set;
|
||||||
|
import java.util.concurrent.atomic.AtomicInteger;
|
||||||
|
|
||||||
|
import org.apache.commons.io.IOUtils;
|
||||||
|
import org.apache.commons.lang3.StringUtils;
|
||||||
|
import org.apache.spark.api.java.JavaRDD;
|
||||||
|
import org.apache.spark.api.java.JavaSparkContext;
|
||||||
|
import org.apache.spark.sql.Dataset;
|
||||||
|
import org.apache.spark.sql.Encoders;
|
||||||
|
import org.apache.spark.sql.SparkSession;
|
||||||
|
import org.dom4j.Attribute;
|
||||||
|
import org.dom4j.Document;
|
||||||
|
import org.dom4j.DocumentException;
|
||||||
|
import org.dom4j.DocumentHelper;
|
||||||
|
import org.dom4j.Element;
|
||||||
|
import org.dom4j.Node;
|
||||||
|
import org.junit.jupiter.api.Disabled;
|
||||||
|
import org.junit.jupiter.api.Test;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
|
||||||
|
|
||||||
|
@Disabled
|
||||||
|
public class BaseCollectorIteratorTest {
|
||||||
|
|
||||||
|
@Test
|
||||||
|
void testImportFile() throws Exception {
|
||||||
|
|
||||||
|
long count = 0;
|
||||||
|
|
||||||
|
final BaseCollectorIterator iterator = new BaseCollectorIterator("base-sample.tar", new AggregatorReport());
|
||||||
|
|
||||||
|
final Map<String, Map<String, String>> collections = new HashMap<>();
|
||||||
|
final Map<String, AtomicInteger> fields = new HashMap<>();
|
||||||
|
final Set<String> types = new HashSet<>();
|
||||||
|
|
||||||
|
while (iterator.hasNext()) {
|
||||||
|
|
||||||
|
final Document record = DocumentHelper.parseText(iterator.next());
|
||||||
|
|
||||||
|
count++;
|
||||||
|
|
||||||
|
if ((count % 1000) == 0) {
|
||||||
|
System.out.println("# Read records: " + count);
|
||||||
|
}
|
||||||
|
|
||||||
|
// System.out.println(record.asXML());
|
||||||
|
|
||||||
|
for (final Object o : record.selectNodes("//*|//@*")) {
|
||||||
|
final String path = ((Node) o).getPath();
|
||||||
|
|
||||||
|
if (fields.containsKey(path)) {
|
||||||
|
fields.get(path).incrementAndGet();
|
||||||
|
} else {
|
||||||
|
fields.put(path, new AtomicInteger(1));
|
||||||
|
}
|
||||||
|
|
||||||
|
if (o instanceof Element) {
|
||||||
|
final Element n = (Element) o;
|
||||||
|
|
||||||
|
if ("collection".equals(n.getName())) {
|
||||||
|
final String collName = n.getText().trim();
|
||||||
|
if (StringUtils.isNotBlank(collName) && !collections.containsKey(collName)) {
|
||||||
|
final Map<String, String> collAttrs = new HashMap<>();
|
||||||
|
for (final Object ao : n.attributes()) {
|
||||||
|
collAttrs.put(((Attribute) ao).getName(), ((Attribute) ao).getValue());
|
||||||
|
}
|
||||||
|
collections.put(collName, collAttrs);
|
||||||
|
}
|
||||||
|
} else if ("type".equals(n.getName())) {
|
||||||
|
types.add(n.getText().trim());
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
final ObjectMapper mapper = new ObjectMapper();
|
||||||
|
for (final Entry<String, Map<String, String>> e : collections.entrySet()) {
|
||||||
|
System.out.println(e.getKey() + ": " + mapper.writeValueAsString(e.getValue()));
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
for (final Entry<String, AtomicInteger> e : fields.entrySet()) {
|
||||||
|
System.out.println(e.getKey() + ": " + e.getValue().get());
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
System.out.println("TYPES: ");
|
||||||
|
for (final String s : types) {
|
||||||
|
System.out.println(s);
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
assertEquals(30000, count);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void testParquet() throws Exception {
|
||||||
|
|
||||||
|
final String xml = IOUtils.toString(getClass().getResourceAsStream("record.xml"));
|
||||||
|
|
||||||
|
final SparkSession spark = SparkSession.builder().master("local[*]").getOrCreate();
|
||||||
|
|
||||||
|
final List<BaseRecordInfo> ls = new ArrayList<>();
|
||||||
|
|
||||||
|
for (int i = 0; i < 10; i++) {
|
||||||
|
ls.add(extractInfo(xml));
|
||||||
|
}
|
||||||
|
|
||||||
|
final JavaRDD<BaseRecordInfo> rdd = JavaSparkContext
|
||||||
|
.fromSparkContext(spark.sparkContext())
|
||||||
|
.parallelize(ls);
|
||||||
|
|
||||||
|
final Dataset<BaseRecordInfo> df = spark
|
||||||
|
.createDataset(rdd.rdd(), Encoders.bean(BaseRecordInfo.class));
|
||||||
|
|
||||||
|
df.printSchema();
|
||||||
|
|
||||||
|
df.show(false);
|
||||||
|
}
|
||||||
|
|
||||||
|
private BaseRecordInfo extractInfo(final String s) {
|
||||||
|
try {
|
||||||
|
final Document record = DocumentHelper.parseText(s);
|
||||||
|
|
||||||
|
final BaseRecordInfo info = new BaseRecordInfo();
|
||||||
|
|
||||||
|
final Set<String> paths = new LinkedHashSet<>();
|
||||||
|
final Set<String> types = new LinkedHashSet<>();
|
||||||
|
final List<BaseCollectionInfo> colls = new ArrayList<>();
|
||||||
|
|
||||||
|
for (final Object o : record.selectNodes("//*|//@*")) {
|
||||||
|
paths.add(((Node) o).getPath());
|
||||||
|
|
||||||
|
if (o instanceof Element) {
|
||||||
|
final Element n = (Element) o;
|
||||||
|
|
||||||
|
final String nodeName = n.getName();
|
||||||
|
|
||||||
|
if ("collection".equals(nodeName)) {
|
||||||
|
final String collName = n.getText().trim();
|
||||||
|
|
||||||
|
if (StringUtils.isNotBlank(collName)) {
|
||||||
|
final BaseCollectionInfo coll = new BaseCollectionInfo();
|
||||||
|
coll.setId(collName);
|
||||||
|
coll.setOpendoarId(n.valueOf("@opendoar_id").trim());
|
||||||
|
coll.setRorId(n.valueOf("@ror_id").trim());
|
||||||
|
colls.add(coll);
|
||||||
|
}
|
||||||
|
} else if ("type".equals(nodeName)) {
|
||||||
|
types.add("TYPE: " + n.getText().trim());
|
||||||
|
} else if ("typenorm".equals(nodeName)) {
|
||||||
|
types.add("TYPE_NORM: " + n.getText().trim());
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
info.setId(record.valueOf("//*[local-name() = 'header']/*[local-name() = 'identifier']").trim());
|
||||||
|
info.getTypes().addAll(types);
|
||||||
|
info.getPaths().addAll(paths);
|
||||||
|
info.setCollections(colls);
|
||||||
|
|
||||||
|
return info;
|
||||||
|
} catch (final DocumentException e) {
|
||||||
|
throw new RuntimeException(e);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,32 @@
|
||||||
|
|
||||||
|
package eu.dnetlib.dhp.collection.plugin.base;
|
||||||
|
|
||||||
|
import static org.junit.jupiter.api.Assertions.assertFalse;
|
||||||
|
import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||||
|
|
||||||
|
import java.util.Arrays;
|
||||||
|
import java.util.HashSet;
|
||||||
|
import java.util.Set;
|
||||||
|
|
||||||
|
import org.apache.commons.io.IOUtils;
|
||||||
|
import org.junit.jupiter.api.Test;
|
||||||
|
|
||||||
|
class BaseCollectorPluginTest {
|
||||||
|
|
||||||
|
@Test
|
||||||
|
void testFilterXml() throws Exception {
|
||||||
|
final String xml = IOUtils.toString(getClass().getResourceAsStream("record.xml"));
|
||||||
|
|
||||||
|
final Set<String> validIds = new HashSet<>(Arrays.asList("opendoar____::1234", "opendoar____::4567"));
|
||||||
|
final Set<String> validTypes = new HashSet<>(Arrays.asList("1", "121"));
|
||||||
|
final Set<String> validTypes2 = new HashSet<>(Arrays.asList("1", "11"));
|
||||||
|
|
||||||
|
assertTrue(BaseCollectorPlugin.filterXml(xml, validIds, validTypes));
|
||||||
|
assertTrue(BaseCollectorPlugin.filterXml(xml, validIds, new HashSet<>()));
|
||||||
|
|
||||||
|
assertFalse(BaseCollectorPlugin.filterXml(xml, new HashSet<>(), validTypes));
|
||||||
|
assertFalse(BaseCollectorPlugin.filterXml(xml, validIds, validTypes2));
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,49 @@
|
||||||
|
|
||||||
|
package eu.dnetlib.dhp.collection.plugin.base;
|
||||||
|
|
||||||
|
import java.io.Serializable;
|
||||||
|
import java.util.ArrayList;
|
||||||
|
import java.util.List;
|
||||||
|
|
||||||
|
public class BaseRecordInfo implements Serializable {
|
||||||
|
|
||||||
|
private static final long serialVersionUID = -8848232018350074593L;
|
||||||
|
|
||||||
|
private String id;
|
||||||
|
private List<BaseCollectionInfo> collections = new ArrayList<>();
|
||||||
|
private List<String> paths = new ArrayList<>();
|
||||||
|
private List<String> types = new ArrayList<>();
|
||||||
|
|
||||||
|
public String getId() {
|
||||||
|
return this.id;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void setId(final String id) {
|
||||||
|
this.id = id;
|
||||||
|
}
|
||||||
|
|
||||||
|
public List<String> getPaths() {
|
||||||
|
return this.paths;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void setPaths(final List<String> paths) {
|
||||||
|
this.paths = paths;
|
||||||
|
}
|
||||||
|
|
||||||
|
public List<String> getTypes() {
|
||||||
|
return this.types;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void setTypes(final List<String> types) {
|
||||||
|
this.types = types;
|
||||||
|
}
|
||||||
|
|
||||||
|
public List<BaseCollectionInfo> getCollections() {
|
||||||
|
return this.collections;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void setCollections(final List<BaseCollectionInfo> collections) {
|
||||||
|
this.collections = collections;
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,78 @@
|
||||||
|
|
||||||
|
package eu.dnetlib.dhp.collection.plugin.base;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
|
||||||
|
import org.apache.commons.io.IOUtils;
|
||||||
|
import org.apache.spark.SparkConf;
|
||||||
|
import org.apache.spark.util.LongAccumulator;
|
||||||
|
import org.dom4j.io.SAXReader;
|
||||||
|
import org.junit.jupiter.api.BeforeEach;
|
||||||
|
import org.junit.jupiter.api.Disabled;
|
||||||
|
import org.junit.jupiter.api.Test;
|
||||||
|
import org.junit.jupiter.api.extension.ExtendWith;
|
||||||
|
import org.mockito.junit.jupiter.MockitoExtension;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest;
|
||||||
|
import eu.dnetlib.dhp.aggregation.common.AggregationCounter;
|
||||||
|
import eu.dnetlib.dhp.schema.mdstore.MetadataRecord;
|
||||||
|
import eu.dnetlib.dhp.schema.mdstore.Provenance;
|
||||||
|
import eu.dnetlib.dhp.transformation.xslt.XSLTTransformationFunction;
|
||||||
|
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
||||||
|
|
||||||
|
@Disabled
|
||||||
|
@ExtendWith(MockitoExtension.class)
|
||||||
|
public class BaseTransfomationTest extends AbstractVocabularyTest {
|
||||||
|
|
||||||
|
private SparkConf sparkConf;
|
||||||
|
|
||||||
|
@BeforeEach
|
||||||
|
public void setUp() throws IOException, ISLookUpException {
|
||||||
|
setUpVocabulary();
|
||||||
|
|
||||||
|
this.sparkConf = new SparkConf();
|
||||||
|
this.sparkConf.setMaster("local[*]");
|
||||||
|
this.sparkConf.set("spark.driver.host", "localhost");
|
||||||
|
this.sparkConf.set("spark.ui.enabled", "false");
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
void testBase2ODF() throws Exception {
|
||||||
|
|
||||||
|
final MetadataRecord mr = new MetadataRecord();
|
||||||
|
mr.setProvenance(new Provenance("DSID", "DSNAME", "PREFIX"));
|
||||||
|
mr.setBody(IOUtils.toString(getClass().getResourceAsStream("record.xml")));
|
||||||
|
|
||||||
|
final XSLTTransformationFunction tr = loadTransformationRule("xml/base2odf.transformationRule.xml");
|
||||||
|
|
||||||
|
final MetadataRecord result = tr.call(mr);
|
||||||
|
|
||||||
|
System.out.println(result.getBody());
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
void testBase2OAF() throws Exception {
|
||||||
|
|
||||||
|
final MetadataRecord mr = new MetadataRecord();
|
||||||
|
mr.setProvenance(new Provenance("DSID", "DSNAME", "PREFIX"));
|
||||||
|
mr.setBody(IOUtils.toString(getClass().getResourceAsStream("record.xml")));
|
||||||
|
|
||||||
|
final XSLTTransformationFunction tr = loadTransformationRule("xml/base2oaf.transformationRule.xml");
|
||||||
|
|
||||||
|
final MetadataRecord result = tr.call(mr);
|
||||||
|
|
||||||
|
System.out.println(result.getBody());
|
||||||
|
}
|
||||||
|
|
||||||
|
private XSLTTransformationFunction loadTransformationRule(final String path) throws Exception {
|
||||||
|
final String xslt = new SAXReader()
|
||||||
|
.read(this.getClass().getResourceAsStream(path))
|
||||||
|
.selectSingleNode("//CODE/*")
|
||||||
|
.asXML();
|
||||||
|
|
||||||
|
final LongAccumulator la = new LongAccumulator();
|
||||||
|
|
||||||
|
return new XSLTTransformationFunction(new AggregationCounter(la, la, la), xslt, 0, this.vocabularies);
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
Binary file not shown.
|
|
@ -0,0 +1,58 @@
|
||||||
|
<record>
|
||||||
|
<header xmlns="http://www.openarchives.org/OAI/2.0/">
|
||||||
|
<identifier>ftdoajarticles:oai:doaj.org/article:e2d5b5126b2d4e479933cc7f9a9ae0c1</identifier>
|
||||||
|
<datestamp>2022-12-31T11:48:55Z</datestamp>
|
||||||
|
</header>
|
||||||
|
<metadata xmlns="http://www.openarchives.org/OAI/2.0/" xmlns:base_dc="http://oai.base-search.net/base_dc/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:dc="http://purl.org/dc/elements/1.1/">
|
||||||
|
<base_dc:dc xsi:schemaLocation="http://oai.base-search.net/base_dc/ http://oai.base-search.net/base_dc/base_dc.xsd">
|
||||||
|
<base_dc:global_id>ftdoajarticles:oai:doaj.org/article:e2d5b5126b2d4e479933cc7f9a9ae0c1</base_dc:global_id>
|
||||||
|
<base_dc:continent>cww</base_dc:continent>
|
||||||
|
<base_dc:country>org</base_dc:country>
|
||||||
|
<base_dc:collection opendoar_id="1234" ror_id="ror1234">ftdoajarticles</base_dc:collection>
|
||||||
|
<base_dc:collname>TEST REPO</base_dc:collname>
|
||||||
|
<dc:title>Assessment of cultural heritage: the legislative and methodological framework of Russian Federation</dc:title>
|
||||||
|
<dc:creator>ALBU, Svetlana</dc:creator>
|
||||||
|
<dc:creator>LEȘAN, Anna</dc:creator>
|
||||||
|
<dc:subject>architectural heritage</dc:subject>
|
||||||
|
<dc:subject>evaluation of architectural heritage</dc:subject>
|
||||||
|
<dc:subject>types of values</dc:subject>
|
||||||
|
<dc:subject>experience of russian federation</dc:subject>
|
||||||
|
<dc:subject>Social Sciences</dc:subject>
|
||||||
|
<dc:subject>H</dc:subject>
|
||||||
|
<dc:description>Architectural heritage is the real estate inheritance by population of a country becoming an extremely valuable and specific category, preserving and capitalizing on those assets requires considerable effort. The state does not have sufficient means to maintain and preserve cultural heritage, as a result it is included in the civil circuit. The transfer of property right or of some partial rights over the architectural patrimony is accompanied by the necessity to estimate the value of goods. In this article, the authors examine the experience of Russian Federation (one of the largest countries with a huge architectural heritage) on the legislative framework of architectural and methodological heritage of architectural heritage assessment. The particularities of cultural assets valuation compared to other categories of real estate are examined, as well as the methodological aspects (types of values, methods applied in valuation, approaches according to the purpose of valuation) regarding the valuation of real estate with architectural value in Russian Federation.</dc:description>
|
||||||
|
<dc:publisher>Technical University of Moldova</dc:publisher>
|
||||||
|
<dc:date>2020-09-01T00:00:00Z</dc:date>
|
||||||
|
<base_dc:year>2020</base_dc:year>
|
||||||
|
<dc:type>article</dc:type>
|
||||||
|
<base_dc:typenorm>121</base_dc:typenorm>
|
||||||
|
<dc:identifier>https://doi.org/10.5281/zenodo.3971988</dc:identifier>
|
||||||
|
<dc:identifier>https://doaj.org/article/e2d5b5126b2d4e479933cc7f9a9ae0c1</dc:identifier>
|
||||||
|
<base_dc:link>https://doi.org/10.5281/zenodo.3971988</base_dc:link>
|
||||||
|
<dc:source>Journal of Social Sciences, Vol 3, Iss 3, Pp 134-143 (2020)</dc:source>
|
||||||
|
<dc:language>EN</dc:language>
|
||||||
|
<dc:language>FR</dc:language>
|
||||||
|
<dc:language>RO</dc:language>
|
||||||
|
<dc:relation>http://ibn.idsi.md/sites/default/files/imag_file/JSS-3-2020_134-143.pdf</dc:relation>
|
||||||
|
<dc:relation>https://doaj.org/toc/2587-3490</dc:relation>
|
||||||
|
<dc:relation>https://doaj.org/toc/2587-3504</dc:relation>
|
||||||
|
<dc:relation>doi:10.5281/zenodo.3971988</dc:relation>
|
||||||
|
<dc:relation>2587-3490</dc:relation>
|
||||||
|
<dc:relation>2587-3504</dc:relation>
|
||||||
|
<dc:relation>https://doaj.org/article/e2d5b5126b2d4e479933cc7f9a9ae0c1</dc:relation>
|
||||||
|
<base_dc:autoclasscode type="ddc">720</base_dc:autoclasscode>
|
||||||
|
<base_dc:authod_id>
|
||||||
|
<base_dc:creator_name>ALBU, Svetlana</base_dc:creator_name>
|
||||||
|
<base_dc:creator_id>https://orcid.org/0000-0002-8648-950X</base_dc:creator_id>
|
||||||
|
</base_dc:authod_id>
|
||||||
|
<base_dc:authod_id>
|
||||||
|
<base_dc:creator_name>LEȘAN, Anna</base_dc:creator_name>
|
||||||
|
<base_dc:creator_id>https://orcid.org/0000-0003-3284-0525</base_dc:creator_id>
|
||||||
|
</base_dc:authod_id>
|
||||||
|
<base_dc:doi>https://doi.org/10.5281/zenodo.3971988</base_dc:doi>
|
||||||
|
<base_dc:oa>1</base_dc:oa>
|
||||||
|
<base_dc:lang>eng</base_dc:lang>
|
||||||
|
<base_dc:lang>fre</base_dc:lang>
|
||||||
|
<base_dc:lang>rum</base_dc:lang>
|
||||||
|
</base_dc:dc>
|
||||||
|
</metadata>
|
||||||
|
</record>
|
||||||
|
|
@ -1497,3 +1497,29 @@ cnr:institutes @=@ https://ror.org/0263zy895 @=@ CDS132
|
||||||
cnr:institutes @=@ https://ror.org/0263zy895 @=@ SCITEC - Istituto di Scienze e Tecnologie Chimiche \"Giulio Natta\"
|
cnr:institutes @=@ https://ror.org/0263zy895 @=@ SCITEC - Istituto di Scienze e Tecnologie Chimiche \"Giulio Natta\"
|
||||||
cnr:institutes @=@ __CDS133__ @=@ CDS133
|
cnr:institutes @=@ __CDS133__ @=@ CDS133
|
||||||
cnr:institutes @=@ __CDS133__ @=@ STEMS - Istituto di Scienze e Tecnologie per l'Energia e la Mobilità Sostenibili
|
cnr:institutes @=@ __CDS133__ @=@ STEMS - Istituto di Scienze e Tecnologie per l'Energia e la Mobilità Sostenibili
|
||||||
|
base:normalized_types @=@ Text @=@ 1
|
||||||
|
base:normalized_types @=@ Book @=@ 11
|
||||||
|
base:normalized_types @=@ Book part @=@ 111
|
||||||
|
base:normalized_types @=@ Journal/Newspaper @=@ 12
|
||||||
|
base:normalized_types @=@ Article contribution @=@ 121
|
||||||
|
base:normalized_types @=@ Other non-article @=@ 122
|
||||||
|
base:normalized_types @=@ Conference object @=@ 13
|
||||||
|
base:normalized_types @=@ Report @=@ 14
|
||||||
|
base:normalized_types @=@ Review @=@ 15
|
||||||
|
base:normalized_types @=@ Course material @=@ 16
|
||||||
|
base:normalized_types @=@ Lecture @=@ 17
|
||||||
|
base:normalized_types @=@ Thesis @=@ 18
|
||||||
|
base:normalized_types @=@ Bachelor's thesis @=@ 181
|
||||||
|
base:normalized_types @=@ Master's thesis @=@ 182
|
||||||
|
base:normalized_types @=@ Doctoral and postdoctoral thesis @=@ 183
|
||||||
|
base:normalized_types @=@ Manuscript @=@ 19
|
||||||
|
base:normalized_types @=@ Patent @=@ 1A
|
||||||
|
base:normalized_types @=@ Musical notation @=@ 2
|
||||||
|
base:normalized_types @=@ Map @=@ 3
|
||||||
|
base:normalized_types @=@ Audio @=@ 4
|
||||||
|
base:normalized_types @=@ Image/Video @=@ 5
|
||||||
|
base:normalized_types @=@ Still image @=@ 51
|
||||||
|
base:normalized_types @=@ Moving image/Video @=@ 52
|
||||||
|
base:normalized_types @=@ Software @=@ 6
|
||||||
|
base:normalized_types @=@ Dataset @=@ 7
|
||||||
|
base:normalized_types @=@ Unknown @=@ F
|
||||||
|
|
|
||||||
|
|
@ -1210,4 +1210,29 @@ cnr:institutes @=@ cnr:institutes @=@ __CDS130__ @=@ __CDS130__
|
||||||
cnr:institutes @=@ cnr:institutes @=@ __CDS131__ @=@ __CDS131__
|
cnr:institutes @=@ cnr:institutes @=@ __CDS131__ @=@ __CDS131__
|
||||||
cnr:institutes @=@ cnr:institutes @=@ https://ror.org/0263zy895 @=@ https://ror.org/0263zy895
|
cnr:institutes @=@ cnr:institutes @=@ https://ror.org/0263zy895 @=@ https://ror.org/0263zy895
|
||||||
cnr:institutes @=@ cnr:institutes @=@ __CDS133__ @=@ __CDS133__
|
cnr:institutes @=@ cnr:institutes @=@ __CDS133__ @=@ __CDS133__
|
||||||
|
base:normalized_types @=@ base:normalized_types @=@ Text @=@ Text
|
||||||
|
base:normalized_types @=@ base:normalized_types @=@ Book @=@ Book
|
||||||
|
base:normalized_types @=@ base:normalized_types @=@ Book part @=@ Book part
|
||||||
|
base:normalized_types @=@ base:normalized_types @=@ Journal/Newspaper @=@ Journal/Newspaper
|
||||||
|
base:normalized_types @=@ base:normalized_types @=@ Article contribution @=@ Article contribution
|
||||||
|
base:normalized_types @=@ base:normalized_types @=@ Other non-article @=@ Other non-article
|
||||||
|
base:normalized_types @=@ base:normalized_types @=@ Conference object @=@ Conference object
|
||||||
|
base:normalized_types @=@ base:normalized_types @=@ Report @=@ Report
|
||||||
|
base:normalized_types @=@ base:normalized_types @=@ Review @=@ Review
|
||||||
|
base:normalized_types @=@ base:normalized_types @=@ Course material @=@ Course material
|
||||||
|
base:normalized_types @=@ base:normalized_types @=@ Lecture @=@ Lecture
|
||||||
|
base:normalized_types @=@ base:normalized_types @=@ Thesis @=@ Thesis
|
||||||
|
base:normalized_types @=@ base:normalized_types @=@ Bachelor's thesis @=@ Bachelor's thesis
|
||||||
|
base:normalized_types @=@ base:normalized_types @=@ Master's thesis @=@ Master's thesis
|
||||||
|
base:normalized_types @=@ base:normalized_types @=@ Doctoral and postdoctoral thesis @=@ Doctoral and postdoctoral thesis
|
||||||
|
base:normalized_types @=@ base:normalized_types @=@ Manuscript @=@ Manuscript
|
||||||
|
base:normalized_types @=@ base:normalized_types @=@ Patent @=@ Patent
|
||||||
|
base:normalized_types @=@ base:normalized_types @=@ Musical notation @=@ Musical notation
|
||||||
|
base:normalized_types @=@ base:normalized_types @=@ Map @=@ Map
|
||||||
|
base:normalized_types @=@ base:normalized_types @=@ Audio @=@ Audio
|
||||||
|
base:normalized_types @=@ base:normalized_types @=@ Image/Video @=@ Image/Video
|
||||||
|
base:normalized_types @=@ base:normalized_types @=@ Still image @=@ Still image
|
||||||
|
base:normalized_types @=@ base:normalized_types @=@ Moving image/Video @=@ Moving image/Video
|
||||||
|
base:normalized_types @=@ base:normalized_types @=@ Software @=@ Software
|
||||||
|
base:normalized_types @=@ base:normalized_types @=@ Dataset @=@ Dataset
|
||||||
|
base:normalized_types @=@ base:normalized_types @=@ Unknown @=@ Unknown
|
||||||
Loading…
Reference in New Issue