forked from D-Net/dnet-hadoop
[scholix] added step to create tar archive
This commit is contained in:
parent
2aa16d0432
commit
cb7c07c54e
|
|
@ -5,13 +5,71 @@ import java.io.BufferedInputStream;
|
|||
import java.io.IOException;
|
||||
import java.io.InputStream;
|
||||
import java.io.Serializable;
|
||||
import java.util.Optional;
|
||||
|
||||
import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
|
||||
import org.apache.commons.compress.archivers.tar.TarArchiveOutputStream;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.hadoop.conf.Configuration;
|
||||
import org.apache.hadoop.fs.*;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
|
||||
public class MakeTarArchive implements Serializable {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(MakeTarArchive.class);
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
String jsonConfiguration = IOUtils
|
||||
.toString(
|
||||
MakeTarArchive.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/common/input_maketar_parameters.json"));
|
||||
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
|
||||
parser.parseArgument(args);
|
||||
|
||||
final String outputPath = parser.get("hdfsPath");
|
||||
log.info("hdfsPath: {}", outputPath);
|
||||
|
||||
final String hdfsNameNode = parser.get("nameNode");
|
||||
log.info("nameNode: {}", hdfsNameNode);
|
||||
|
||||
final String inputPath = parser.get("sourcePath");
|
||||
log.info("input path : {}", inputPath);
|
||||
|
||||
final int gBperSplit = Optional
|
||||
.ofNullable(parser.get("splitSize"))
|
||||
.map(Integer::valueOf)
|
||||
.orElse(10);
|
||||
|
||||
Configuration conf = new Configuration();
|
||||
conf.set("fs.defaultFS", hdfsNameNode);
|
||||
|
||||
FileSystem fileSystem = FileSystem.get(conf);
|
||||
|
||||
makeTArArchive(fileSystem, inputPath, outputPath, gBperSplit);
|
||||
|
||||
}
|
||||
|
||||
public static void makeTArArchive(FileSystem fileSystem, String inputPath, String outputPath, int gBperSplit)
|
||||
throws IOException {
|
||||
|
||||
RemoteIterator<LocatedFileStatus> dirIterator = fileSystem.listLocatedStatus(new Path(inputPath));
|
||||
|
||||
while (dirIterator.hasNext()) {
|
||||
LocatedFileStatus fileStatus = dirIterator.next();
|
||||
|
||||
Path p = fileStatus.getPath();
|
||||
String pathString = p.toString();
|
||||
String entity = pathString.substring(pathString.lastIndexOf("/") + 1);
|
||||
|
||||
MakeTarArchive.tarMaxSize(fileSystem, pathString, outputPath + "/" + entity, entity, gBperSplit);
|
||||
}
|
||||
}
|
||||
|
||||
private static TarArchiveOutputStream getTar(FileSystem fileSystem, String outputPath) throws IOException {
|
||||
Path hdfsWritePath = new Path(outputPath);
|
||||
if (fileSystem.exists(hdfsWritePath)) {
|
||||
|
|
@ -21,7 +79,7 @@ public class MakeTarArchive implements Serializable {
|
|||
return new TarArchiveOutputStream(fileSystem.create(hdfsWritePath).getWrappedStream());
|
||||
}
|
||||
|
||||
private static void write(FileSystem fileSystem, String inputPath, String outputPath, String dir_name)
|
||||
private static void write(FileSystem fileSystem, String inputPath, String outputPath, String dirName)
|
||||
throws IOException {
|
||||
|
||||
Path hdfsWritePath = new Path(outputPath);
|
||||
|
|
@ -37,7 +95,7 @@ public class MakeTarArchive implements Serializable {
|
|||
new Path(inputPath), true);
|
||||
|
||||
while (iterator.hasNext()) {
|
||||
writeCurrentFile(fileSystem, dir_name, iterator, ar, 0);
|
||||
writeCurrentFile(fileSystem, dirName, iterator, ar, 0);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -59,32 +117,30 @@ public class MakeTarArchive implements Serializable {
|
|||
new Path(inputPath), true);
|
||||
boolean next = fileStatusListIterator.hasNext();
|
||||
while (next) {
|
||||
TarArchiveOutputStream ar = getTar(fileSystem, outputPath + "_" + (partNum + 1) + ".tar");
|
||||
try (TarArchiveOutputStream ar = getTar(fileSystem, outputPath + "_" + (partNum + 1) + ".tar")) {
|
||||
|
||||
long current_size = 0;
|
||||
while (next && current_size < bytesPerSplit) {
|
||||
current_size = writeCurrentFile(fileSystem, dir_name, fileStatusListIterator, ar, current_size);
|
||||
next = fileStatusListIterator.hasNext();
|
||||
long currentSize = 0;
|
||||
while (next && currentSize < bytesPerSplit) {
|
||||
currentSize = writeCurrentFile(fileSystem, dir_name, fileStatusListIterator, ar, currentSize);
|
||||
next = fileStatusListIterator.hasNext();
|
||||
|
||||
}
|
||||
|
||||
partNum += 1;
|
||||
}
|
||||
|
||||
partNum += 1;
|
||||
ar.close();
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
private static long writeCurrentFile(FileSystem fileSystem, String dir_name,
|
||||
private static long writeCurrentFile(FileSystem fileSystem, String dirName,
|
||||
RemoteIterator<LocatedFileStatus> fileStatusListIterator,
|
||||
TarArchiveOutputStream ar, long current_size) throws IOException {
|
||||
TarArchiveOutputStream ar, long currentSize) throws IOException {
|
||||
LocatedFileStatus fileStatus = fileStatusListIterator.next();
|
||||
|
||||
Path p = fileStatus.getPath();
|
||||
String p_string = p.toString();
|
||||
if (!p_string.endsWith("_SUCCESS")) {
|
||||
String name = p_string.substring(p_string.lastIndexOf("/") + 1);
|
||||
String pString = p.toString();
|
||||
if (!pString.endsWith("_SUCCESS")) {
|
||||
String name = pString.substring(pString.lastIndexOf("/") + 1);
|
||||
if (name.startsWith("part-") & name.length() > 10) {
|
||||
String tmp = name.substring(0, 10);
|
||||
if (name.contains(".")) {
|
||||
|
|
@ -92,9 +148,9 @@ public class MakeTarArchive implements Serializable {
|
|||
}
|
||||
name = tmp;
|
||||
}
|
||||
TarArchiveEntry entry = new TarArchiveEntry(dir_name + "/" + name);
|
||||
TarArchiveEntry entry = new TarArchiveEntry(dirName + "/" + name);
|
||||
entry.setSize(fileStatus.getLen());
|
||||
current_size += fileStatus.getLen();
|
||||
currentSize += fileStatus.getLen();
|
||||
ar.putArchiveEntry(entry);
|
||||
|
||||
InputStream is = fileSystem.open(fileStatus.getPath());
|
||||
|
|
@ -110,7 +166,7 @@ public class MakeTarArchive implements Serializable {
|
|||
ar.closeArchiveEntry();
|
||||
|
||||
}
|
||||
return current_size;
|
||||
return currentSize;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -0,0 +1,30 @@
|
|||
[
|
||||
|
||||
{
|
||||
"paramName":"s",
|
||||
"paramLongName":"sourcePath",
|
||||
"paramDescription": "the path of the sequencial file to read",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "hdp",
|
||||
"paramLongName": "hdfsPath",
|
||||
"paramDescription": "the path used to store the output archive",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName":"nn",
|
||||
"paramLongName":"nameNode",
|
||||
"paramDescription": "the name node",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName":"ss",
|
||||
"paramLongName":"splitSize",
|
||||
"paramDescription": "the maximum size of the archive",
|
||||
"paramRequired": false
|
||||
}
|
||||
]
|
||||
|
||||
|
||||
|
||||
|
|
@ -140,11 +140,21 @@
|
|||
<arg>--objectType</arg><arg>scholix</arg>
|
||||
<arg>--maxPidNumberFilter</arg><arg>maxNumberOfPid</arg>
|
||||
</spark>
|
||||
<ok to="make_tar"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="make_tar">
|
||||
<java>
|
||||
<main-class>eu.dnetlib.dhp.common.MakeTarArchive</main-class>
|
||||
<arg>--nameNode</arg><arg>${nameNode}</arg>
|
||||
<arg>--hdfsPath</arg><arg>${targetPath}/tar</arg>
|
||||
<arg>--sourcePath</arg><arg>${targetPath}/json</arg>
|
||||
</java>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
|
||||
|
||||
<end name="End"/>
|
||||
|
||||
</workflow-app>
|
||||
Loading…
Reference in New Issue