added workflow upload on zenodo
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sandro
parent
fed711da80
commit
d58d02d448
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package eu.dnetlib.dhp.export.zenodo;
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import java.io.*;
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import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
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import org.apache.commons.compress.archivers.tar.TarArchiveOutputStream;
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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.*;
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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 MakeTar implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(MakeTar.class);
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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.toString(
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MakeTar.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/export/input_maketar_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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final String outputPath = parser.get("targetPath");
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log.info("hdfsPath: {}", outputPath);
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final String hdfsNameNode = parser.get("nameNode");
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log.info("nameNode: {}", hdfsNameNode);
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final String inputPath = parser.get("sourcePath");
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log.info("input path : {}", inputPath);
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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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makeTArArchive(fileSystem, inputPath, outputPath);
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}
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public static void makeTArArchive(FileSystem fileSystem, String inputPath, String outputPath) throws IOException {
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RemoteIterator<LocatedFileStatus> dir_iterator = fileSystem.listLocatedStatus(new Path(inputPath));
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while (dir_iterator.hasNext()) {
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LocatedFileStatus fileStatus = dir_iterator.next();
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Path p = fileStatus.getPath();
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String p_string = p.toString();
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String entity = p_string.substring(p_string.lastIndexOf("/") + 1);
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write(fileSystem, p_string, outputPath + "/" + entity + ".tar", entity);
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}
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}
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private static void write(FileSystem fileSystem, String inputPath, String outputPath, String dir_name)
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throws IOException {
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Path hdfsWritePath = new Path(outputPath);
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FSDataOutputStream fsDataOutputStream = null;
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if (fileSystem.exists(hdfsWritePath)) {
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fileSystem.delete(hdfsWritePath, true);
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}
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fsDataOutputStream = fileSystem.create(hdfsWritePath);
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TarArchiveOutputStream ar = new TarArchiveOutputStream(fsDataOutputStream.getWrappedStream());
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RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
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.listFiles(
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new Path(inputPath), true);
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while (fileStatusListIterator.hasNext()) {
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LocatedFileStatus fileStatus = fileStatusListIterator.next();
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Path p = fileStatus.getPath();
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String p_string = p.toString();
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if (!p_string.endsWith("_SUCCESS")) {
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String name = p_string.substring(p_string.lastIndexOf("/") + 1);
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TarArchiveEntry entry = new TarArchiveEntry(dir_name + "/" + name + ".json.gz");
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entry.setSize(fileStatus.getLen());
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ar.putArchiveEntry(entry);
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InputStream is = fileSystem.open(fileStatus.getPath());
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BufferedInputStream bis = new BufferedInputStream(is);
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int count;
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byte data[] = new byte[1024];
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while ((count = bis.read(data, 0, data.length)) != -1) {
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ar.write(data, 0, count);
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}
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bis.close();
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ar.closeArchiveEntry();
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}
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}
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ar.close();
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}
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}
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@ -0,0 +1,20 @@
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[
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{
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"paramName": "n",
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"paramLongName": "nameNode",
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"paramDescription": "the Name Node",
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"paramRequired": true
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},
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{
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"paramName": "s",
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"paramLongName": "sourcePath",
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"paramDescription": "the source path",
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"paramRequired": true
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},
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{
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"paramName": "t",
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"paramLongName": "targetPath",
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"paramDescription": "the target path",
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"paramRequired": true
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}
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]
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@ -0,0 +1,42 @@
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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>oozie.wf.rerun.failnodes</name>
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<value>false</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>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>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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</configuration>
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@ -0,0 +1,33 @@
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<workflow-app name="Send Dump to Zenodo" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>sourcePath</name>
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<description>the source path</description>
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</property>
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<property>
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<name>targetPath</name>
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<description>the target path</description>
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</property>
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</parameters>
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<start to="MakeTar"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="MakeTar">
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<java>
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<main-class>eu.dnetlib.dhp.export.zenodo.MakeTar</main-class>
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<arg>-t</arg><arg>${targetPath}</arg>
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<arg>-n</arg><arg>${nameNode}</arg>
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<arg>-s</arg><arg>${sourcePath}</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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