first steps in the implementation of the integration of opencitations
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package eu.dnetlib.dhp.actionmanager.opencitations;
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import java.io.BufferedOutputStream;
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import java.net.URI;
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import java.util.zip.GZIPOutputStream;
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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.gzip.GzipCompressorInputStream;
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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.FSDataInputStream;
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import org.apache.hadoop.fs.FSDataOutputStream;
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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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public class ExtractOpenCitationRefs {
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public static void main(String[] args) throws Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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ExtractOpenCitationRefs.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/a/ccionmanager/opencitations/opencitations_parameters.json")));
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parser.parseArgument(args);
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final String hdfsServerUri = parser.get("hdfsServerUri");
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final String workingPath = hdfsServerUri.concat(parser.get("workingPath"));
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final String outputPath = parser.get("outputPath");
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final String opencitationFile = parser.get("opencitationFile");
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Path hdfsreadpath = new Path(workingPath.concat("/").concat(opencitationFile));
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Configuration conf = new Configuration();
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conf.set("fs.defaultFS", workingPath);
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conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName());
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conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName());
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FileSystem fs = FileSystem.get(URI.create(workingPath), conf);
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FSDataInputStream crossrefFileStream = fs.open(hdfsreadpath);
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try (TarArchiveInputStream tais = new TarArchiveInputStream(
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new GzipCompressorInputStream(crossrefFileStream))) {
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TarArchiveEntry entry = null;
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while ((entry = tais.getNextTarEntry()) != null) {
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if (!entry.isDirectory()) {
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try (
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FSDataOutputStream out = fs
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.create(new Path(outputPath.concat(entry.getName()).concat(".gz")));
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GZIPOutputStream gzipOs = new GZIPOutputStream(new BufferedOutputStream(out))) {
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IOUtils.copy(tais, gzipOs);
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}
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}
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}
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}
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Log.info("Crossref dump reading completed");
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}
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}
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package eu.dnetlib.dhp.actionmanager.opencitations;
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import java.io.*;
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import java.io.Serializable;
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import java.util.Objects;
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import java.util.zip.GZIPOutputStream;
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import java.util.zip.ZipEntry;
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import java.util.zip.ZipInputStream;
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import org.apache.commons.cli.ParseException;
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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.FSDataInputStream;
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import org.apache.hadoop.fs.FSDataOutputStream;
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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.application.ArgumentApplicationParser;
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public class GetOpenCitationsRefs implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(GetOpenCitationsRefs.class);
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public static void main(final String[] args) throws IOException, ParseException {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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Objects
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.requireNonNull(
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GetOpenCitationsRefs.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/actionmanager/opencitations/input_parameters.json"))));
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parser.parseArgument(args);
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final String inputFile = parser.get("inputFile");
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log.info("inputFile {}", inputFile);
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final String workingPath = parser.get("workingPath");
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log.info("workingPath {}", workingPath);
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final String hdfsNameNode = parser.get("hdfsNameNode");
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log.info("hdfsNameNode {}", hdfsNameNode);
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Configuration conf = new Configuration();
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conf.set("fs.defaultFS", hdfsNameNode);
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FileSystem fileSystem = FileSystem.get(conf);
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new GetOpenCitationsRefs().doExtract(inputFile, workingPath, fileSystem);
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}
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private void doExtract(String inputFile, String workingPath, FileSystem fileSystem)
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throws IOException {
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final Path path = new Path(inputFile);
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FSDataInputStream oc_zip = fileSystem.open(path);
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int count = 1;
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try (ZipInputStream zis = new ZipInputStream(oc_zip)) {
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ZipEntry entry = null;
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while ((entry = zis.getNextEntry()) != null) {
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if (!entry.isDirectory()) {
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String fileName = entry.getName();
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fileName = fileName.substring(0, fileName.indexOf("T")) + "_" + count;
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count++;
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try (
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FSDataOutputStream out = fileSystem
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.create(new Path(workingPath + "/COCI/" + fileName + ".gz"));
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GZIPOutputStream gzipOs = new GZIPOutputStream(new BufferedOutputStream(out))) {
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IOUtils.copy(zis, gzipOs);
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}
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}
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}
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}
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}
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}
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[
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{
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"paramName": "if",
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"paramLongName": "inputFile",
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"paramDescription": "the zipped opencitations file",
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"paramRequired": true
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},
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{
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"paramName": "wp",
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"paramLongName": "workingPath",
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"paramDescription": "the working path",
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"paramRequired": true
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},
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{
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"paramName": "hnn",
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"paramLongName": "hdfsNameNode",
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"paramDescription": "the hdfs name node",
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"paramRequired": true
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}
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]
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<configuration>
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<property>
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<name>jobTracker</name>
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<value>yarnRM</value>
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</property>
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<property>
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<name>nameNode</name>
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<value>hdfs://nameservice1</value>
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</property>
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<property>
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<name>oozie.use.system.libpath</name>
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<value>true</value>
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</property>
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<property>
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<name>oozie.action.sharelib.for.spark</name>
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<value>spark2</value>
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</property>
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<property>
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<name>hive_metastore_uris</name>
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<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
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</property>
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<property>
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<name>spark2YarnHistoryServerAddress</name>
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<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
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</property>
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<property>
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<name>spark2ExtraListeners</name>
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<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
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</property>
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<property>
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<name>spark2SqlQueryExecutionListeners</name>
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<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
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</property>
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<property>
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<name>oozie.launcher.mapreduce.user.classpath.first</name>
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<value>true</value>
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</property>
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<property>
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<name>sparkExecutorNumber</name>
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<value>4</value>
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</property>
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<property>
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<name>spark2EventLogDir</name>
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<value>/user/spark/spark2ApplicationHistory</value>
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</property>
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<property>
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<name>sparkDriverMemory</name>
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<value>15G</value>
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</property>
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<property>
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<name>sparkExecutorMemory</name>
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<value>6G</value>
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</property>
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<property>
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<name>sparkExecutorCores</name>
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<value>1</value>
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</property>
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</configuration>
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#!/bin/bash
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wget -i $1
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<workflow-app name="OpenCitations Integration" xmlns="uri:oozie:workflow:0.5">
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<global>
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<configuration>
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<property>
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<name>mapreduce.job.queuename</name>
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<value>${queueName}</value>
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</property>
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<property>
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<name>oozie.launcher.mapred.job.queue.name</name>
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<value>${oozieLauncherQueueName}</value>
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</property>
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<property>
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<name>oozie.action.sharelib.for.spark</name>
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<value>${oozieActionShareLibForSpark2}</value>
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</property>
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</configuration>
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</global>
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<start to="download"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="download">
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<shell xmlns="uri:oozie:shell-action:0.2">
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<configuration>
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<property>
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<name>mapred.job.queue.name</name>
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<value>${queueName}</value>
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</property>
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</configuration>
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<exec>download.sh</exec>
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<argument>${url}</argument>
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<argument>${crossrefDumpPath}</argument>
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<argument>${crossrefdumpfilename}</argument>
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<argument>${crossrefdumptoken}</argument>
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<env-var>HADOOP_USER_NAME=${wf:user()}</env-var>
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<file>download.sh</file>
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<capture-output/>
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</shell>
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<ok to="ImportCrossRef"/>
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<error to="Kill"/>
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</action>
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<action name="extract">
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<java>
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<main-class>eu.dnetlib.dhp.actionmanager.opencitations.GetOpenCitationsRefs</main-class>
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<arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
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<arg>--inputFile</arg><arg>${inputFile}</arg>
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<arg>--workingPath</arg><arg>${workingDir}/OpenCitations</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 +1,8 @@
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[
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{"paramName":"n", "paramLongName":"hdfsServerUri", "paramDescription": "the server uri", "paramRequired": true},
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{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the default work path", "paramRequired": true},
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{"paramName":"f", "paramLongName":"opencitationFile", "paramDescription": "the name of the file", "paramRequired": true},
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{"paramName":"issm", "paramLongName":"isSparkSessionManaged", "paramDescription": "the name of the activities orcid file", "paramRequired": false},
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{"paramName":"o", "paramLongName":"outputPath", "paramDescription": "the name of the activities orcid file", "paramRequired": true}
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]
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