added wf to extracting authors and works xml data from orcid dump to hdfs; added wf to download the lamda file (containing last orcid update informations) from orcid to hdfs
This commit is contained in:
parent
c796adae24
commit
c0c2e05eae
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@ -17,6 +17,7 @@ import org.apache.hadoop.io.SequenceFile;
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import org.apache.hadoop.io.Text;
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import org.apache.hadoop.io.Text;
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import org.apache.hadoop.io.compress.CompressionCodec;
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import org.apache.hadoop.io.compress.CompressionCodec;
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import org.apache.hadoop.io.compress.CompressionCodecFactory;
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import org.apache.hadoop.io.compress.CompressionCodecFactory;
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import org.apache.hadoop.io.compress.GzipCodec;
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import org.mortbay.log.Log;
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import org.mortbay.log.Log;
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import eu.dnetlib.doiboost.orcid.model.WorkData;
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import eu.dnetlib.doiboost.orcid.model.WorkData;
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@ -143,4 +144,64 @@ public class ActivitiesDecompressor {
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Log.info("Error from Orcid found: " + errorFromOrcidFound);
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Log.info("Error from Orcid found: " + errorFromOrcidFound);
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Log.info("Error parsing xml work found: " + xmlParserErrorFound);
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Log.info("Error parsing xml work found: " + xmlParserErrorFound);
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}
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}
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public static void extractXML(Configuration conf, String inputUri, Path outputPath)
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throws Exception {
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String uri = inputUri;
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FileSystem fs = FileSystem.get(URI.create(uri), conf);
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Path inputPath = new Path(uri);
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CompressionCodecFactory factory = new CompressionCodecFactory(conf);
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CompressionCodec codec = factory.getCodec(inputPath);
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if (codec == null) {
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System.err.println("No codec found for " + uri);
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System.exit(1);
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}
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CompressionCodecFactory.removeSuffix(uri, codec.getDefaultExtension());
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InputStream gzipInputStream = null;
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try {
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gzipInputStream = codec.createInputStream(fs.open(inputPath));
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int counter = 0;
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try (TarArchiveInputStream tais = new TarArchiveInputStream(gzipInputStream)) {
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TarArchiveEntry entry = null;
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try (SequenceFile.Writer writer = SequenceFile
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.createWriter(
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conf,
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SequenceFile.Writer.file(outputPath),
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SequenceFile.Writer.keyClass(Text.class),
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SequenceFile.Writer.valueClass(Text.class),
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SequenceFile.Writer.compression(SequenceFile.CompressionType.BLOCK, new GzipCodec()))) {
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while ((entry = tais.getNextTarEntry()) != null) {
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String filename = entry.getName();
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if (entry.isDirectory() || !filename.contains("works")) {
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} else {
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counter++;
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BufferedReader br = new BufferedReader(new InputStreamReader(tais));
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String line;
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StringBuffer buffer = new StringBuffer();
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while ((line = br.readLine()) != null) {
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buffer.append(line);
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}
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String xml = buffer.toString();
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String[] filenameParts = filename.split("/");
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final Text key = new Text(
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XMLRecordParser
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.retrieveOrcidIdFromActivity(
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xml.getBytes(), filenameParts[filenameParts.length - 1]));
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final Text value = new Text(xml);
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writer.append(key, value);
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if ((counter % 100000) == 0) {
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Log.info("Current xml works extracted: " + counter);
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}
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}
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}
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}
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}
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Log.info("Activities extraction completed");
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Log.info("Total XML works parsed: " + counter);
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} finally {
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Log.debug("Closing gzip stream");
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IOUtils.closeStream(gzipInputStream);
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}
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}
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}
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}
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@ -0,0 +1,54 @@
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package eu.dnetlib.doiboost.orcid;
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import java.io.IOException;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.Path;
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import org.mortbay.log.Log;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork;
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public class ExtractXMLActivitiesData extends OrcidDSManager {
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private String outputWorksPath;
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private String activitiesFileNameTarGz;
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public static void main(String[] args) throws IOException, Exception {
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ExtractXMLActivitiesData extractXMLActivitiesData = new ExtractXMLActivitiesData();
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extractXMLActivitiesData.loadArgs(args);
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extractXMLActivitiesData.extractWorks();
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}
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private void loadArgs(String[] args) throws IOException, Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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GenOrcidAuthorWork.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/doiboost/gen_orcid_works-no-doi_from_activities.json")));
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parser.parseArgument(args);
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hdfsServerUri = parser.get("hdfsServerUri");
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Log.info("HDFS URI: " + hdfsServerUri);
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workingPath = parser.get("workingPath");
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Log.info("Working Path: " + workingPath);
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activitiesFileNameTarGz = parser.get("activitiesFileNameTarGz");
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Log.info("Activities File Name: " + activitiesFileNameTarGz);
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outputWorksPath = parser.get("outputWorksPath");
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Log.info("Output Author Work Data: " + outputWorksPath);
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}
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private void extractWorks() throws Exception {
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Configuration conf = initConfigurationObject();
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FileSystem fs = initFileSystemObject(conf);
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String tarGzUri = hdfsServerUri.concat(workingPath).concat(activitiesFileNameTarGz);
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Path outputPath = new Path(
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hdfsServerUri
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.concat(workingPath)
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.concat(outputWorksPath));
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ActivitiesDecompressor.extractXML(conf, tarGzUri, outputPath);
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}
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}
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@ -0,0 +1,56 @@
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package eu.dnetlib.doiboost.orcid;
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import java.io.IOException;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.Path;
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import org.mortbay.log.Log;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork;
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public class ExtractXMLSummariesData extends OrcidDSManager {
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private String outputAuthorsPath;
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private String summariesFileNameTarGz;
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public static void main(String[] args) throws IOException, Exception {
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ExtractXMLSummariesData extractXMLSummariesData = new ExtractXMLSummariesData();
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extractXMLSummariesData.loadArgs(args);
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extractXMLSummariesData.extractAuthors();
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}
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private void loadArgs(String[] args) throws IOException, Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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GenOrcidAuthorWork.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/doiboost/gen_orcid_authors_from_summaries.json")));
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parser.parseArgument(args);
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hdfsServerUri = parser.get("hdfsServerUri");
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Log.info("HDFS URI: " + hdfsServerUri);
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workingPath = parser.get("workingPath");
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Log.info("Working Path: " + workingPath);
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summariesFileNameTarGz = parser.get("summariesFileNameTarGz");
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Log.info("Summaries File Name: " + summariesFileNameTarGz);
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outputAuthorsPath = parser.get("outputAuthorsPath");
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Log.info("Output Authors Data: " + outputAuthorsPath);
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}
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public void extractAuthors() throws Exception {
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Configuration conf = initConfigurationObject();
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FileSystem fs = initFileSystemObject(conf);
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String tarGzUri = hdfsServerUri.concat(workingPath).concat(summariesFileNameTarGz);
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Path outputPath = new Path(
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hdfsServerUri
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.concat(workingPath)
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.concat(outputAuthorsPath)
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.concat("xml_authors.seq"));
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SummariesDecompressor.extractXML(conf, tarGzUri, outputPath);
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}
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}
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@ -17,6 +17,7 @@ import org.apache.hadoop.io.SequenceFile;
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import org.apache.hadoop.io.Text;
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import org.apache.hadoop.io.Text;
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import org.apache.hadoop.io.compress.CompressionCodec;
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import org.apache.hadoop.io.compress.CompressionCodec;
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import org.apache.hadoop.io.compress.CompressionCodecFactory;
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import org.apache.hadoop.io.compress.CompressionCodecFactory;
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import org.apache.hadoop.io.compress.GzipCodec;
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import org.mortbay.log.Log;
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import org.mortbay.log.Log;
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import eu.dnetlib.dhp.schema.orcid.AuthorData;
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import eu.dnetlib.dhp.schema.orcid.AuthorData;
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@ -160,4 +161,67 @@ public class SummariesDecompressor {
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Log.info("Error from Orcid found: " + errorFromOrcidFound);
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Log.info("Error from Orcid found: " + errorFromOrcidFound);
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Log.info("Error parsing xml record found: " + xmlParserErrorFound);
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Log.info("Error parsing xml record found: " + xmlParserErrorFound);
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}
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}
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public static void extractXML(Configuration conf, String inputUri, Path outputPath)
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throws Exception {
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String uri = inputUri;
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FileSystem fs = FileSystem.get(URI.create(uri), conf);
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Path inputPath = new Path(uri);
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CompressionCodecFactory factory = new CompressionCodecFactory(conf);
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CompressionCodec codec = factory.getCodec(inputPath);
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if (codec == null) {
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System.err.println("No codec found for " + uri);
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System.exit(1);
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}
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CompressionCodecFactory.removeSuffix(uri, codec.getDefaultExtension());
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InputStream gzipInputStream = null;
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try {
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gzipInputStream = codec.createInputStream(fs.open(inputPath));
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int counter = 0;
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try (TarArchiveInputStream tais = new TarArchiveInputStream(gzipInputStream)) {
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TarArchiveEntry entry = null;
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CompressionCodec Codec = new GzipCodec();
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org.apache.hadoop.io.SequenceFile.Writer.Option optCom = SequenceFile.Writer
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.compression(SequenceFile.CompressionType.RECORD, Codec);
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try (SequenceFile.Writer writer = SequenceFile
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.createWriter(
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conf,
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SequenceFile.Writer.file(outputPath),
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SequenceFile.Writer.keyClass(Text.class),
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SequenceFile.Writer.valueClass(Text.class), optCom)) {
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while ((entry = tais.getNextTarEntry()) != null) {
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String filename = entry.getName();
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if (entry.isDirectory()) {
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Log.debug("Directory entry name: " + entry.getName());
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} else {
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Log.debug("XML record entry name: " + entry.getName());
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counter++;
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BufferedReader br = new BufferedReader(new InputStreamReader(tais));
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String line;
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StringBuffer buffer = new StringBuffer();
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while ((line = br.readLine()) != null) {
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buffer.append(line);
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}
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String xml = buffer.toString();
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final Text key = new Text(
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XMLRecordParser
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.retrieveOrcidIdFromSummary(
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xml.getBytes(), filename.split("/")[2].substring(0, 19)));
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final Text value = new Text(xml);
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writer.append(key, value);
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}
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if ((counter % 100000) == 0) {
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Log.info("Current xml records extracted: " + counter);
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}
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}
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}
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}
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Log.info("Summaries extract completed");
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Log.info("Total XML records parsed: " + counter);
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} finally {
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Log.debug("Closing gzip stream");
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IOUtils.closeStream(gzipInputStream);
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}
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}
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}
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}
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@ -4,6 +4,8 @@ package eu.dnetlib.doiboost.orcid.xml;
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import java.util.Arrays;
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import java.util.Arrays;
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import java.util.List;
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import java.util.List;
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import org.mortbay.log.Log;
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import com.ximpleware.AutoPilot;
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import com.ximpleware.AutoPilot;
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import com.ximpleware.EOFException;
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import com.ximpleware.EOFException;
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import com.ximpleware.EncodingException;
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import com.ximpleware.EncodingException;
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@ -126,4 +128,33 @@ public class XMLRecordParser {
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}
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}
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return workData;
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return workData;
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}
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}
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public static String retrieveOrcidIdFromSummary(byte[] bytes, String defaultValue)
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throws VtdException, ParseException {
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return retrieveOrcidId(bytes, defaultValue, NS_RECORD, NS_RECORD_URL, "//record:record", "path").substring(1);
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}
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public static String retrieveOrcidIdFromActivity(byte[] bytes, String defaultValue)
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throws VtdException, ParseException {
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return retrieveOrcidId(bytes, defaultValue, NS_WORK, NS_WORK_URL, "//work:work", "put-code");
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}
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private static String retrieveOrcidId(byte[] bytes, String defaultValue, String ns, String nsUrl, String xpath,
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String idAttributeName)
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throws VtdException, ParseException {
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final VTDGen vg = new VTDGen();
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vg.setDoc(bytes);
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vg.parse(true);
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final VTDNav vn = vg.getNav();
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final AutoPilot ap = new AutoPilot(vn);
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ap.declareXPathNameSpace(ns, nsUrl);
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List<VtdUtilityParser.Node> recordNodes = VtdUtilityParser
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.getTextValuesWithAttributes(
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ap, vn, xpath, Arrays.asList(idAttributeName));
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if (!recordNodes.isEmpty()) {
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return (recordNodes.get(0).getAttributes().get(idAttributeName));
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}
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Log.info("id not found - default: " + defaultValue);
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return defaultValue;
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}
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}
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}
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@ -1,45 +0,0 @@
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<workflow-app name="Orcid Download" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>workingPathOrcid</name>
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<description>the working dir base path</description>
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</property>
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<property>
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<name>token</name>
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<description>access token</description>
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</property>
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</parameters>
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<start to="ResetWorkingPath"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="ResetWorkingPath">
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<fs>
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<delete path='${workingPathOrcid}/download'/>
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<mkdir path='${workingPathOrcid}/download'/>
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</fs>
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<ok to="DownloadOrcidData"/>
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<error to="Kill"/>
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</action>
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<action name="DownloadOrcidData">
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<java>
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<main-class>eu.dnetlib.doiboost.orcid.OrcidDownloader</main-class>
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<arg>-d</arg><arg>${workingPathOrcid}/</arg>
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<arg>-n</arg><arg>${nameNode}</arg>
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<arg>-f</arg><arg>last_modified.csv</arg>
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<arg>-o</arg><arg>download/</arg>
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<arg>-t</arg><arg>${token}</arg>
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</java>
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<ok to="End"/>
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<error to="Kill"/>
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</action>
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<end name="End"/>
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</workflow-app>
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|
|
@ -0,0 +1,232 @@
|
||||||
|
<workflow-app name="Extract Orcid XML Works From Activities" xmlns="uri:oozie:workflow:0.5">
|
||||||
|
<parameters>
|
||||||
|
<property>
|
||||||
|
<name>workingPath</name>
|
||||||
|
<description>the working dir base path</description>
|
||||||
|
</property>
|
||||||
|
</parameters>
|
||||||
|
|
||||||
|
<global>
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<configuration>
|
||||||
|
<property>
|
||||||
|
<name>oozie.action.sharelib.for.java</name>
|
||||||
|
<value>${oozieActionShareLibForSpark2}</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>oozie.launcher.mapreduce.user.classpath.first</name>
|
||||||
|
<value>true</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>oozie.launcher.mapreduce.map.java.opts</name>
|
||||||
|
<value>-Xmx2g</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>oozie.use.system.libpath</name>
|
||||||
|
<value>true</value>
|
||||||
|
</property>
|
||||||
|
</configuration>
|
||||||
|
</global>
|
||||||
|
|
||||||
|
<start to="ResetWorkingPath"/>
|
||||||
|
|
||||||
|
|
||||||
|
<kill name="Kill">
|
||||||
|
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||||
|
</kill>
|
||||||
|
|
||||||
|
<action name="ResetWorkingPath">
|
||||||
|
<fs>
|
||||||
|
<delete path='${workingPath}/xml/works'/>
|
||||||
|
<mkdir path='${workingPath}/xml/works'/>
|
||||||
|
</fs>
|
||||||
|
<ok to="fork_node"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<fork name = "fork_node">
|
||||||
|
<path start = "ExtractXMLWorkActivities_0"/>
|
||||||
|
<path start = "ExtractXMLWorkActivities_1"/>
|
||||||
|
<path start = "ExtractXMLWorkActivities_2"/>
|
||||||
|
<path start = "ExtractXMLWorkActivities_3"/>
|
||||||
|
<path start = "ExtractXMLWorkActivities_4"/>
|
||||||
|
<path start = "ExtractXMLWorkActivities_5"/>
|
||||||
|
<path start = "ExtractXMLWorkActivities_6"/>
|
||||||
|
<path start = "ExtractXMLWorkActivities_7"/>
|
||||||
|
<path start = "ExtractXMLWorkActivities_8"/>
|
||||||
|
<path start = "ExtractXMLWorkActivities_9"/>
|
||||||
|
<path start = "ExtractXMLWorkActivities_X"/>
|
||||||
|
</fork>
|
||||||
|
|
||||||
|
<action name="ExtractXMLWorkActivities_0">
|
||||||
|
<java>
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<main-class>eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData</main-class>
|
||||||
|
<arg>-w</arg><arg>${workingPath}/</arg>
|
||||||
|
<arg>-n</arg><arg>${nameNode}</arg>
|
||||||
|
<arg>-f</arg><arg>ORCID_2020_10_activites_0.tar.gz</arg>
|
||||||
|
<arg>-ow</arg><arg>xml/works/xml_works_0.seq</arg>
|
||||||
|
<arg>-oew</arg><arg>---</arg>
|
||||||
|
</java>
|
||||||
|
<ok to="join_node"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="ExtractXMLWorkActivities_1">
|
||||||
|
<java>
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<main-class>eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData</main-class>
|
||||||
|
<arg>-w</arg><arg>${workingPath}/</arg>
|
||||||
|
<arg>-n</arg><arg>${nameNode}</arg>
|
||||||
|
<arg>-f</arg><arg>ORCID_2020_10_activites_1.tar.gz</arg>
|
||||||
|
<arg>-ow</arg><arg>xml/works/xml_works_1.seq</arg>
|
||||||
|
<arg>-oew</arg><arg>---</arg>
|
||||||
|
</java>
|
||||||
|
<ok to="join_node"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="ExtractXMLWorkActivities_2">
|
||||||
|
<java>
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<main-class>eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData</main-class>
|
||||||
|
<arg>-w</arg><arg>${workingPath}/</arg>
|
||||||
|
<arg>-n</arg><arg>${nameNode}</arg>
|
||||||
|
<arg>-f</arg><arg>ORCID_2020_10_activites_2.tar.gz</arg>
|
||||||
|
<arg>-ow</arg><arg>xml/works/xml_works_2.seq</arg>
|
||||||
|
<arg>-oew</arg><arg>---</arg>
|
||||||
|
</java>
|
||||||
|
<ok to="join_node"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="ExtractXMLWorkActivities_3">
|
||||||
|
<java>
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<main-class>eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData</main-class>
|
||||||
|
<arg>-w</arg><arg>${workingPath}/</arg>
|
||||||
|
<arg>-n</arg><arg>${nameNode}</arg>
|
||||||
|
<arg>-f</arg><arg>ORCID_2020_10_activites_3.tar.gz</arg>
|
||||||
|
<arg>-ow</arg><arg>xml/works/xml_works_3.seq</arg>
|
||||||
|
<arg>-oew</arg><arg>---</arg>
|
||||||
|
</java>
|
||||||
|
<ok to="join_node"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="ExtractXMLWorkActivities_4">
|
||||||
|
<java>
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<main-class>eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData</main-class>
|
||||||
|
<arg>-w</arg><arg>${workingPath}/</arg>
|
||||||
|
<arg>-n</arg><arg>${nameNode}</arg>
|
||||||
|
<arg>-f</arg><arg>ORCID_2020_10_activites_4.tar.gz</arg>
|
||||||
|
<arg>-ow</arg><arg>xml/works/xml_works_4.seq</arg>
|
||||||
|
<arg>-oew</arg><arg>---</arg>
|
||||||
|
</java>
|
||||||
|
<ok to="join_node"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="ExtractXMLWorkActivities_5">
|
||||||
|
<java>
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<main-class>eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData</main-class>
|
||||||
|
<arg>-w</arg><arg>${workingPath}/</arg>
|
||||||
|
<arg>-n</arg><arg>${nameNode}</arg>
|
||||||
|
<arg>-f</arg><arg>ORCID_2020_10_activites_5.tar.gz</arg>
|
||||||
|
<arg>-ow</arg><arg>xml/works/xml_works_5.seq</arg>
|
||||||
|
<arg>-oew</arg><arg>---</arg>
|
||||||
|
</java>
|
||||||
|
<ok to="join_node"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
|
||||||
|
<action name="ExtractXMLWorkActivities_6">
|
||||||
|
<java>
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<main-class>eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData</main-class>
|
||||||
|
<arg>-w</arg><arg>${workingPath}/</arg>
|
||||||
|
<arg>-n</arg><arg>${nameNode}</arg>
|
||||||
|
<arg>-f</arg><arg>ORCID_2020_10_activites_6.tar.gz</arg>
|
||||||
|
<arg>-ow</arg><arg>xml/works/xml_works_6.seq</arg>
|
||||||
|
<arg>-oew</arg><arg>---</arg>
|
||||||
|
</java>
|
||||||
|
<ok to="join_node"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="ExtractXMLWorkActivities_7">
|
||||||
|
<java>
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<main-class>eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData</main-class>
|
||||||
|
<arg>-w</arg><arg>${workingPath}/</arg>
|
||||||
|
<arg>-n</arg><arg>${nameNode}</arg>
|
||||||
|
<arg>-f</arg><arg>ORCID_2020_10_activites_7.tar.gz</arg>
|
||||||
|
<arg>-ow</arg><arg>xml/works/xml_works_7.seq</arg>
|
||||||
|
<arg>-oew</arg><arg>---</arg>
|
||||||
|
</java>
|
||||||
|
<ok to="join_node"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
|
||||||
|
<action name="ExtractXMLWorkActivities_8">
|
||||||
|
<java>
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<main-class>eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData</main-class>
|
||||||
|
<arg>-w</arg><arg>${workingPath}/</arg>
|
||||||
|
<arg>-n</arg><arg>${nameNode}</arg>
|
||||||
|
<arg>-f</arg><arg>ORCID_2020_10_activites_8.tar.gz</arg>
|
||||||
|
<arg>-ow</arg><arg>xml/works/xml_works_8.seq</arg>
|
||||||
|
<arg>-oew</arg><arg>---</arg>
|
||||||
|
</java>
|
||||||
|
<ok to="join_node"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="ExtractXMLWorkActivities_9">
|
||||||
|
<java>
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<main-class>eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData</main-class>
|
||||||
|
<arg>-w</arg><arg>${workingPath}/</arg>
|
||||||
|
<arg>-n</arg><arg>${nameNode}</arg>
|
||||||
|
<arg>-f</arg><arg>ORCID_2020_10_activites_9.tar.gz</arg>
|
||||||
|
<arg>-ow</arg><arg>xml/works/xml_works_9.seq</arg>
|
||||||
|
<arg>-oew</arg><arg>---</arg>
|
||||||
|
</java>
|
||||||
|
<ok to="join_node"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="ExtractXMLWorkActivities_X">
|
||||||
|
<java>
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<main-class>eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData</main-class>
|
||||||
|
<arg>-w</arg><arg>${workingPath}/</arg>
|
||||||
|
<arg>-n</arg><arg>${nameNode}</arg>
|
||||||
|
<arg>-f</arg><arg>ORCID_2020_10_activites_X.tar.gz</arg>
|
||||||
|
<arg>-ow</arg><arg>xml/works/xml_works_X.seq</arg>
|
||||||
|
<arg>-oew</arg><arg>---</arg>
|
||||||
|
</java>
|
||||||
|
<ok to="join_node"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<join name = "join_node" to = "End"/>
|
||||||
|
|
||||||
|
<end name="End"/>
|
||||||
|
</workflow-app>
|
||||||
|
|
@ -0,0 +1,26 @@
|
||||||
|
<configuration>
|
||||||
|
<property>
|
||||||
|
<name>jobTracker</name>
|
||||||
|
<value>yarnRM</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>nameNode</name>
|
||||||
|
<value>hdfs://nameservice1</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>oozie.use.system.libpath</name>
|
||||||
|
<value>true</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>oozie.action.sharelib.for.spark</name>
|
||||||
|
<value>spark2</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>oozie.launcher.mapreduce.user.classpath.first</name>
|
||||||
|
<value>true</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>oozie.launcher.mapreduce.map.java.opts</name>
|
||||||
|
<value>-Xmx8g</value>
|
||||||
|
</property>
|
||||||
|
</configuration>
|
||||||
|
|
@ -0,0 +1,40 @@
|
||||||
|
<workflow-app name="Extract Orcid XML Authors From Summaries" xmlns="uri:oozie:workflow:0.5">
|
||||||
|
<parameters>
|
||||||
|
<property>
|
||||||
|
<name>workingPath</name>
|
||||||
|
<description>the working dir base path</description>
|
||||||
|
</property>
|
||||||
|
</parameters>
|
||||||
|
|
||||||
|
<start to="ResetWorkingPath"/>
|
||||||
|
|
||||||
|
|
||||||
|
<kill name="Kill">
|
||||||
|
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||||
|
</kill>
|
||||||
|
|
||||||
|
<action name="ResetWorkingPath">
|
||||||
|
<fs>
|
||||||
|
<delete path='${workingPath}/xml/authors'/>
|
||||||
|
<mkdir path='${workingPath}/xml/authors'/>
|
||||||
|
</fs>
|
||||||
|
<ok to="ExtractXMLAuthorsSummaries"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="ExtractXMLAuthorsSummaries">
|
||||||
|
<java>
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<main-class>eu.dnetlib.doiboost.orcid.ExtractXMLSummariesData</main-class>
|
||||||
|
<arg>-w</arg><arg>${workingPath}/</arg>
|
||||||
|
<arg>-n</arg><arg>${nameNode}</arg>
|
||||||
|
<arg>-f</arg><arg>ORCID_2020_10_summaries.tar.gz</arg>
|
||||||
|
<arg>-o</arg><arg>xml/authors/</arg>
|
||||||
|
</java>
|
||||||
|
<ok to="End"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<end name="End"/>
|
||||||
|
</workflow-app>
|
||||||
|
|
@ -0,0 +1,64 @@
|
||||||
|
<workflow-app name="Orcid Updates Download" xmlns="uri:oozie:workflow:0.5">
|
||||||
|
<parameters>
|
||||||
|
<property>
|
||||||
|
<name>workingPath</name>
|
||||||
|
<description>the working dir base path</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>token</name>
|
||||||
|
<description>access token</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>shell_cmd</name>
|
||||||
|
<value>wget -O /tmp/last_modified.csv.tar http://74804fb637bd8e2fba5b-e0a029c2f87486cddec3b416996a6057.r3.cf1.rackcdn.com/last_modified.csv.tar ; hdfs dfs -copyFromLocal /tmp/last_modified.csv.tar /data/orcid_activities_2020/last_modified.csv.tar ; rm -f /tmp/last_modified.csv.tar
|
||||||
|
</value>
|
||||||
|
<description>the shell command that downloads the lambda file from orcid containing last orcid update informations</description>
|
||||||
|
</property>
|
||||||
|
</parameters>
|
||||||
|
|
||||||
|
<start to="ResetWorkingPath"/>
|
||||||
|
|
||||||
|
|
||||||
|
<kill name="Kill">
|
||||||
|
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||||
|
</kill>
|
||||||
|
|
||||||
|
<action name="ResetWorkingPath">
|
||||||
|
<fs>
|
||||||
|
<delete path='${workingPath}/downloads'/>
|
||||||
|
<mkdir path='${workingPath}/downloads'/>
|
||||||
|
</fs>
|
||||||
|
<ok to="DownloadLambdaFile"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="DownloadLambdaFile">
|
||||||
|
<shell xmlns="uri:oozie:shell-action:0.1">
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<exec>bash</exec>
|
||||||
|
<argument>-c</argument>
|
||||||
|
<argument>${shell_cmd}</argument>
|
||||||
|
<capture-output/>
|
||||||
|
</shell>
|
||||||
|
<ok to="End"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="DownloadOrcidData">
|
||||||
|
<java>
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<main-class>eu.dnetlib.doiboost.orcid.OrcidDownloader</main-class>
|
||||||
|
<arg>-d</arg><arg>${workingPathOrcid}/</arg>
|
||||||
|
<arg>-n</arg><arg>${nameNode}</arg>
|
||||||
|
<arg>-f</arg><arg>last_modified.csv</arg>
|
||||||
|
<arg>-o</arg><arg>download/</arg>
|
||||||
|
<arg>-t</arg><arg>${token}</arg>
|
||||||
|
</java>
|
||||||
|
<ok to="End"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<end name="End"/>
|
||||||
|
</workflow-app>
|
||||||
Loading…
Reference in New Issue