[scholix] added step to create tar archive
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2aa16d0432
commit
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@ -5,13 +5,71 @@ import java.io.BufferedInputStream;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.Serializable;
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import java.util.Optional;
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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 MakeTarArchive implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(MakeTarArchive.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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MakeTarArchive.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/common/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("hdfsPath");
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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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final int gBperSplit = Optional
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.ofNullable(parser.get("splitSize"))
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.map(Integer::valueOf)
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.orElse(10);
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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, gBperSplit);
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}
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public static void makeTArArchive(FileSystem fileSystem, String inputPath, String outputPath, int gBperSplit)
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throws IOException {
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RemoteIterator<LocatedFileStatus> dirIterator = fileSystem.listLocatedStatus(new Path(inputPath));
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while (dirIterator.hasNext()) {
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LocatedFileStatus fileStatus = dirIterator.next();
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Path p = fileStatus.getPath();
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String pathString = p.toString();
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String entity = pathString.substring(pathString.lastIndexOf("/") + 1);
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MakeTarArchive.tarMaxSize(fileSystem, pathString, outputPath + "/" + entity, entity, gBperSplit);
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}
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}
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private static TarArchiveOutputStream getTar(FileSystem fileSystem, String outputPath) throws IOException {
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Path hdfsWritePath = new Path(outputPath);
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if (fileSystem.exists(hdfsWritePath)) {
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@ -21,7 +79,7 @@ public class MakeTarArchive implements Serializable {
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return new TarArchiveOutputStream(fileSystem.create(hdfsWritePath).getWrappedStream());
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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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private static void write(FileSystem fileSystem, String inputPath, String outputPath, String dirName)
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throws IOException {
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Path hdfsWritePath = new Path(outputPath);
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@ -37,7 +95,7 @@ public class MakeTarArchive implements Serializable {
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new Path(inputPath), true);
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while (iterator.hasNext()) {
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writeCurrentFile(fileSystem, dir_name, iterator, ar, 0);
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writeCurrentFile(fileSystem, dirName, iterator, ar, 0);
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}
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}
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@ -59,32 +117,30 @@ public class MakeTarArchive implements Serializable {
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new Path(inputPath), true);
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boolean next = fileStatusListIterator.hasNext();
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while (next) {
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TarArchiveOutputStream ar = getTar(fileSystem, outputPath + "_" + (partNum + 1) + ".tar");
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try (TarArchiveOutputStream ar = getTar(fileSystem, outputPath + "_" + (partNum + 1) + ".tar")) {
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long current_size = 0;
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while (next && current_size < bytesPerSplit) {
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current_size = writeCurrentFile(fileSystem, dir_name, fileStatusListIterator, ar, current_size);
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next = fileStatusListIterator.hasNext();
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long currentSize = 0;
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while (next && currentSize < bytesPerSplit) {
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currentSize = writeCurrentFile(fileSystem, dir_name, fileStatusListIterator, ar, currentSize);
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next = fileStatusListIterator.hasNext();
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}
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partNum += 1;
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}
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partNum += 1;
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ar.close();
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}
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}
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}
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private static long writeCurrentFile(FileSystem fileSystem, String dir_name,
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private static long writeCurrentFile(FileSystem fileSystem, String dirName,
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RemoteIterator<LocatedFileStatus> fileStatusListIterator,
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TarArchiveOutputStream ar, long current_size) throws IOException {
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TarArchiveOutputStream ar, long currentSize) throws IOException {
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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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String pString = p.toString();
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if (!pString.endsWith("_SUCCESS")) {
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String name = pString.substring(pString.lastIndexOf("/") + 1);
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if (name.startsWith("part-") & name.length() > 10) {
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String tmp = name.substring(0, 10);
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if (name.contains(".")) {
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@ -92,9 +148,9 @@ public class MakeTarArchive implements Serializable {
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}
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name = tmp;
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}
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TarArchiveEntry entry = new TarArchiveEntry(dir_name + "/" + name);
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TarArchiveEntry entry = new TarArchiveEntry(dirName + "/" + name);
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entry.setSize(fileStatus.getLen());
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current_size += fileStatus.getLen();
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currentSize += fileStatus.getLen();
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ar.putArchiveEntry(entry);
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InputStream is = fileSystem.open(fileStatus.getPath());
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@ -110,7 +166,7 @@ public class MakeTarArchive implements Serializable {
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ar.closeArchiveEntry();
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}
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return current_size;
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return currentSize;
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}
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}
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@ -0,0 +1,30 @@
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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 path of the sequencial file to read",
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"paramRequired": true
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},
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{
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"paramName": "hdp",
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"paramLongName": "hdfsPath",
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"paramDescription": "the path used to store the output archive",
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"paramRequired": true
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},
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{
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"paramName":"nn",
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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":"ss",
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"paramLongName":"splitSize",
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"paramDescription": "the maximum size of the archive",
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"paramRequired": false
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}
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]
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@ -140,11 +140,21 @@
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<arg>--objectType</arg><arg>scholix</arg>
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<arg>--maxPidNumberFilter</arg><arg>maxNumberOfPid</arg>
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</spark>
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<ok to="make_tar"/>
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<error to="Kill"/>
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</action>
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<action name="make_tar">
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<java>
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<main-class>eu.dnetlib.dhp.common.MakeTarArchive</main-class>
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<arg>--nameNode</arg><arg>${nameNode}</arg>
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<arg>--hdfsPath</arg><arg>${targetPath}/tar</arg>
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<arg>--sourcePath</arg><arg>${targetPath}/json</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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