forked from D-Net/dnet-hadoop
code formatting
This commit is contained in:
parent
f5f346dd2b
commit
4625b7486e
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@ -1,119 +1,117 @@
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package eu.dnetlib.dhp.common;
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import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
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package eu.dnetlib.dhp.common;
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import org.apache.commons.compress.archivers.tar.TarArchiveOutputStream;
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import org.apache.hadoop.fs.*;
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import java.io.BufferedInputStream;
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import java.io.BufferedInputStream;
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import java.io.IOException;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.InputStream;
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import java.io.Serializable;
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import java.io.Serializable;
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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.hadoop.fs.*;
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public class MakeTarArchive implements Serializable {
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public class MakeTarArchive implements Serializable {
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private static TarArchiveOutputStream getTar(FileSystem fileSystem, String outputPath) throws IOException {
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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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Path hdfsWritePath = new Path(outputPath);
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FSDataOutputStream fsDataOutputStream = null;
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FSDataOutputStream fsDataOutputStream = null;
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if (fileSystem.exists(hdfsWritePath)) {
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if (fileSystem.exists(hdfsWritePath)) {
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fileSystem.delete(hdfsWritePath, true);
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fileSystem.delete(hdfsWritePath, true);
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}
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}
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fsDataOutputStream = fileSystem.create(hdfsWritePath);
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fsDataOutputStream = fileSystem.create(hdfsWritePath);
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return new TarArchiveOutputStream(fsDataOutputStream.getWrappedStream());
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return new TarArchiveOutputStream(fsDataOutputStream.getWrappedStream());
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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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private static void write(FileSystem fileSystem, String inputPath, String outputPath, String dir_name)
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throws IOException {
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throws IOException {
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Path hdfsWritePath = new Path(outputPath);
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Path hdfsWritePath = new Path(outputPath);
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FSDataOutputStream fsDataOutputStream = null;
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FSDataOutputStream fsDataOutputStream = null;
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if (fileSystem.exists(hdfsWritePath)) {
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if (fileSystem.exists(hdfsWritePath)) {
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fileSystem.delete(hdfsWritePath, true);
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fileSystem.delete(hdfsWritePath, true);
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}
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}
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fsDataOutputStream = fileSystem.create(hdfsWritePath);
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fsDataOutputStream = fileSystem.create(hdfsWritePath);
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TarArchiveOutputStream ar = new TarArchiveOutputStream(fsDataOutputStream.getWrappedStream());
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TarArchiveOutputStream ar = new TarArchiveOutputStream(fsDataOutputStream.getWrappedStream());
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RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
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RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
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.listFiles(
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.listFiles(
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new Path(inputPath), true);
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new Path(inputPath), true);
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while (fileStatusListIterator.hasNext()) {
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while (fileStatusListIterator.hasNext()) {
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writeCurrentFile(fileSystem, dir_name, fileStatusListIterator, ar, 0);
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writeCurrentFile(fileSystem, dir_name, fileStatusListIterator, ar, 0);
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}
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}
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ar.close();
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ar.close();
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}
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}
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public static void tarMaxSize(FileSystem fileSystem, String inputPath, String outputPath, String dir_name,
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public static void tarMaxSize(FileSystem fileSystem, String inputPath, String outputPath, String dir_name,
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int gBperSplit) throws IOException {
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int gBperSplit) throws IOException {
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final long bytesPerSplit = 1024L * 1024L * 1024L * gBperSplit;
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final long bytesPerSplit = 1024L * 1024L * 1024L * gBperSplit;
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long sourceSize = fileSystem.getContentSummary(new Path(inputPath)).getSpaceConsumed();
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long sourceSize = fileSystem.getContentSummary(new Path(inputPath)).getSpaceConsumed();
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if (sourceSize < bytesPerSplit) {
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if (sourceSize < bytesPerSplit) {
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write(fileSystem, inputPath, outputPath + ".tar", dir_name);
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write(fileSystem, inputPath, outputPath + ".tar", dir_name);
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} else {
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} else {
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int partNum = 0;
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int partNum = 0;
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RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
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RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
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.listFiles(
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.listFiles(
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new Path(inputPath), true);
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new Path(inputPath), true);
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boolean next = fileStatusListIterator.hasNext();
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boolean next = fileStatusListIterator.hasNext();
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while (next) {
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while (next) {
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TarArchiveOutputStream ar = getTar(fileSystem, outputPath + "_" + (partNum + 1) + ".tar");
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TarArchiveOutputStream ar = getTar(fileSystem, outputPath + "_" + (partNum + 1) + ".tar");
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long current_size = 0;
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long current_size = 0;
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while (next && current_size < bytesPerSplit) {
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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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current_size = writeCurrentFile(fileSystem, dir_name, fileStatusListIterator, ar, current_size);
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next = fileStatusListIterator.hasNext();
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next = fileStatusListIterator.hasNext();
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}
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}
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partNum += 1;
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partNum += 1;
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ar.close();
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ar.close();
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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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private static long writeCurrentFile(FileSystem fileSystem, String dir_name,
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private static long writeCurrentFile(FileSystem fileSystem, String dir_name,
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RemoteIterator<LocatedFileStatus> fileStatusListIterator,
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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 current_size) throws IOException {
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LocatedFileStatus fileStatus = fileStatusListIterator.next();
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LocatedFileStatus fileStatus = fileStatusListIterator.next();
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Path p = fileStatus.getPath();
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Path p = fileStatus.getPath();
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String p_string = p.toString();
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String p_string = p.toString();
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if (!p_string.endsWith("_SUCCESS")) {
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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 name = p_string.substring(p_string.lastIndexOf("/") + 1);
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if (name.trim().equalsIgnoreCase("communities_infrastructures")) {
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if (name.trim().equalsIgnoreCase("communities_infrastructures")) {
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name = "communities_infrastructures.json";
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name = "communities_infrastructures.json";
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}
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}
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TarArchiveEntry entry = new TarArchiveEntry(dir_name + "/" + name);
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TarArchiveEntry entry = new TarArchiveEntry(dir_name + "/" + name);
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entry.setSize(fileStatus.getLen());
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entry.setSize(fileStatus.getLen());
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current_size += fileStatus.getLen();
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current_size += fileStatus.getLen();
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ar.putArchiveEntry(entry);
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ar.putArchiveEntry(entry);
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InputStream is = fileSystem.open(fileStatus.getPath());
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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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return current_size;
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}
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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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return current_size;
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}
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}
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}
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@ -109,20 +109,20 @@ public class CleaningFunctions {
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}
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}
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if (Objects.nonNull(r.getPid())) {
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if (Objects.nonNull(r.getPid())) {
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r
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r
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.setPid(
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.setPid(
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r
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r
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.getPid()
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.getPid()
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.stream()
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.stream()
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.filter(Objects::nonNull)
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.filter(Objects::nonNull)
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.filter(sp -> StringUtils.isNotBlank(StringUtils.trim(sp.getValue())))
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.filter(sp -> StringUtils.isNotBlank(StringUtils.trim(sp.getValue())))
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.filter(sp -> NONE.equalsIgnoreCase(sp.getValue()))
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.filter(sp -> NONE.equalsIgnoreCase(sp.getValue()))
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.filter(sp -> Objects.nonNull(sp.getQualifier()))
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.filter(sp -> Objects.nonNull(sp.getQualifier()))
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.filter(sp -> StringUtils.isNotBlank(sp.getQualifier().getClassid()))
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.filter(sp -> StringUtils.isNotBlank(sp.getQualifier().getClassid()))
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.map(sp -> {
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.map(sp -> {
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sp.setValue(StringUtils.trim(sp.getValue()));
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sp.setValue(StringUtils.trim(sp.getValue()));
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return sp;
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return sp;
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})
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})
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.collect(Collectors.toList()));
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.collect(Collectors.toList()));
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}
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}
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if (Objects.isNull(r.getResourcetype()) || StringUtils.isBlank(r.getResourcetype().getClassid())) {
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if (Objects.isNull(r.getResourcetype()) || StringUtils.isBlank(r.getResourcetype().getClassid())) {
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r
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r
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@ -4,7 +4,6 @@ package eu.dnetlib.dhp.oa.graph.dump;
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import java.io.*;
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import java.io.*;
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import java.util.Optional;
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import java.util.Optional;
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import eu.dnetlib.dhp.common.MakeTarArchive;
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import org.apache.commons.compress.archivers.ar.ArArchiveEntry;
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import org.apache.commons.compress.archivers.ar.ArArchiveEntry;
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import org.apache.commons.compress.archivers.ar.ArArchiveOutputStream;
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import org.apache.commons.compress.archivers.ar.ArArchiveOutputStream;
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import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
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import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
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import org.slf4j.LoggerFactory;
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import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.common.MakeTarArchive;
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import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
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import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
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public class MakeTar implements Serializable {
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public class MakeTar implements Serializable {
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final String inputPath = parser.get("sourcePath");
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final String inputPath = parser.get("sourcePath");
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log.info("input path : {}", inputPath);
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log.info("input path : {}", inputPath);
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final int gBperSplit = Optional.ofNullable(parser.get("splitSize"))
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final int gBperSplit = Optional
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.map(Integer::valueOf)
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.ofNullable(parser.get("splitSize"))
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.orElse(10);
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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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Configuration conf = new Configuration();
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conf.set("fs.defaultFS", hdfsNameNode);
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conf.set("fs.defaultFS", hdfsNameNode);
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}
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}
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public static void makeTArArchive(FileSystem fileSystem, String inputPath, String outputPath, int gBperSplit) throws IOException {
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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> dir_iterator = fileSystem.listLocatedStatus(new Path(inputPath));
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RemoteIterator<LocatedFileStatus> dir_iterator = fileSystem.listLocatedStatus(new Path(inputPath));
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@ -70,5 +72,4 @@ public class MakeTar implements Serializable {
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}
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}
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}
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}
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import java.io.IOException;
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import java.io.IOException;
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import java.io.InputStreamReader;
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import java.io.InputStreamReader;
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import org.apache.hadoop.fs.FileSystem;
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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.apache.hadoop.fs.Path;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SparkSession;
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import org.apache.spark.sql.SparkSession;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.google.gson.Gson;
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import com.google.gson.Gson;
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import eu.dnetlib.dhp.common.HdfsSupport;
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import eu.dnetlib.dhp.common.HdfsSupport;
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import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
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import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
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import eu.dnetlib.dhp.oa.graph.dump.graph.Constants;
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import eu.dnetlib.dhp.oa.graph.dump.graph.Constants;
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import eu.dnetlib.dhp.utils.DHPUtils;
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import eu.dnetlib.dhp.utils.DHPUtils;
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import eu.dnetlib.dhp.utils.ISLookupClientFactory;
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import eu.dnetlib.dhp.utils.ISLookupClientFactory;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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@ -74,5 +71,4 @@ public class Utils {
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return new Gson().fromJson(sb.toString(), CommunityMap.class);
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return new Gson().fromJson(sb.toString(), CommunityMap.class);
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}
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}
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}
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}
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