/**
* (C) Copyright IBM Corp. 2010, 2015
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*/
package com.ibm.bi.dml.runtime.io;
import java.io.BufferedWriter;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.io.OutputStreamWriter;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileStatus;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.IOUtils;
import org.apache.hadoop.mapred.JobConf;
import com.ibm.bi.dml.conf.ConfigurationManager;
import com.ibm.bi.dml.runtime.DMLRuntimeException;
import com.ibm.bi.dml.runtime.DMLUnsupportedOperationException;
import com.ibm.bi.dml.runtime.matrix.CSVReblockMR;
import com.ibm.bi.dml.runtime.matrix.data.CSVFileFormatProperties;
import com.ibm.bi.dml.runtime.matrix.data.MatrixBlock;
import com.ibm.bi.dml.runtime.matrix.data.SparseRow;
import com.ibm.bi.dml.runtime.util.MapReduceTool;
/**
*
*/
public class WriterTextCSV extends MatrixWriter
{
//blocksize for string concatenation in order to prevent write OOM
//(can be set to very large value to disable blocking)
public static final int BLOCKSIZE_J = 32; //32 cells (typically ~512B, should be less than write buffer of 1KB)
protected CSVFileFormatProperties _props = null;
public WriterTextCSV( CSVFileFormatProperties props ) {
_props = props;
}
@Override
public void writeMatrixToHDFS(MatrixBlock src, String fname, long rlen, long clen, int brlen, int bclen, long nnz)
throws IOException, DMLRuntimeException, DMLUnsupportedOperationException
{
//validity check matrix dimensions
if( src.getNumRows() != rlen || src.getNumColumns() != clen ) {
throw new IOException("Matrix dimensions mismatch with metadata: "+src.getNumRows()+"x"+src.getNumColumns()+" vs "+rlen+"x"+clen+".");
}
//prepare file access
JobConf job = new JobConf(ConfigurationManager.getCachedJobConf());
Path path = new Path( fname );
//if the file already exists on HDFS, remove it.
MapReduceTool.deleteFileIfExistOnHDFS( fname );
//core write
writeCSVMatrixToHDFS(path, job, src, rlen, clen, nnz, _props);
}
@Override
public void writeEmptyMatrixToHDFS(String fname, long rlen, long clen, int brlen, int bclen)
throws IOException, DMLRuntimeException
{
JobConf job = new JobConf(ConfigurationManager.getCachedJobConf());
Path path = new Path( fname );
MatrixBlock src = new MatrixBlock((int)rlen, 1, true);
writeCSVMatrixToHDFS(path, job, src, brlen, clen, 0, _props);
}
/**
*
* @param fileName
* @param src
* @param rlen
* @param clen
* @param nnz
* @throws IOException
*/
protected void writeCSVMatrixToHDFS( Path path, JobConf job, MatrixBlock src, long rlen, long clen, long nnz, CSVFileFormatProperties props )
throws IOException
{
boolean sparse = src.isInSparseFormat();
FileSystem fs = FileSystem.get(job);
BufferedWriter br=new BufferedWriter(new OutputStreamWriter(fs.create(path,true)));
try
{
//for obj reuse and preventing repeated buffer re-allocations
StringBuilder sb = new StringBuilder();
props = (props==null)? new CSVFileFormatProperties() : props;
String delim = props.getDelim();
boolean csvsparse = props.isSparse();
// Write header line, if needed
if( props.hasHeader() )
{
//write row chunk-wise to prevent OOM on large number of columns
for( int bj=0; bj<clen; bj+=BLOCKSIZE_J )
{
for( int j=bj; j < Math.min(clen,bj+BLOCKSIZE_J); j++)
{
sb.append("C"+ (j+1));
if ( j < clen-1 )
sb.append(delim);
}
br.write( sb.toString() );
sb.setLength(0);
}
sb.append('\n');
br.write( sb.toString() );
sb.setLength(0);
}
// Write data lines
if( sparse ) //SPARSE
{
SparseRow[] sparseRows = src.getSparseRows();
for(int i=0; i < rlen; i++)
{
//write row chunk-wise to prevent OOM on large number of columns
int prev_jix = -1;
if( sparseRows!=null && i<sparseRows.length
&& sparseRows[i]!=null && !sparseRows[i].isEmpty() )
{
SparseRow arow = sparseRows[i];
int alen = arow.size();
int[] aix = arow.getIndexContainer();
double[] avals = arow.getValueContainer();
for(int j=0; j < alen; j++)
{
int jix = aix[j];
// output empty fields, if needed
for( int j2=prev_jix; j2<jix-1; j2++ ) {
if( !csvsparse )
sb.append('0');
sb.append(delim);
//flush buffered string
if( j2%BLOCKSIZE_J==0 ){
br.write( sb.toString() );
sb.setLength(0);
}
}
// output the value (non-zero)
sb.append( avals[j] );
if( jix < clen-1)
sb.append(delim);
br.write( sb.toString() );
sb.setLength(0);
//flush buffered string
if( jix%BLOCKSIZE_J==0 ){
br.write( sb.toString() );
sb.setLength(0);
}
prev_jix = jix;
}
}
// Output empty fields at the end of the row.
// In case of an empty row, output (clen-1) empty fields
for( int bj=prev_jix+1; bj<clen; bj+=BLOCKSIZE_J )
{
for( int j = bj; j < Math.min(clen,bj+BLOCKSIZE_J); j++) {
if( !csvsparse )
sb.append('0');
if( j < clen-1 )
sb.append(delim);
}
br.write( sb.toString() );
sb.setLength(0);
}
sb.append('\n');
br.write( sb.toString() );
sb.setLength(0);
}
}
else //DENSE
{
for( int i=0; i<rlen; i++ )
{
//write row chunk-wise to prevent OOM on large number of columns
for( int bj=0; bj<clen; bj+=BLOCKSIZE_J )
{
for( int j=bj; j<Math.min(clen,bj+BLOCKSIZE_J); j++ )
{
double lvalue = src.getValueDenseUnsafe(i, j);
if( lvalue != 0 ) //for nnz
sb.append(lvalue);
else if( !csvsparse )
sb.append('0');
if( j != clen-1 )
sb.append(delim);
}
br.write( sb.toString() );
sb.setLength(0);
}
sb.append('\n');
br.write( sb.toString() ); //same as append
sb.setLength(0);
}
}
}
finally
{
IOUtilFunctions.closeSilently(br);
}
}
/**
* Method to merge multiple CSV part files on HDFS into a single CSV file on HDFS.
* The part files are created by CSV_WRITE MR job.
*
* This method is invoked from CP-write instruction.
*
* @param srcFileName
* @param destFileName
* @param csvprop
* @param rlen
* @param clen
* @throws IOException
*/
public void mergeCSVPartFiles(String srcFileName, String destFileName, CSVFileFormatProperties csvprop, long rlen, long clen)
throws IOException
{
Configuration conf = new Configuration(ConfigurationManager.getCachedJobConf());
Path srcFilePath = new Path(srcFileName);
Path mergedFilePath = new Path(destFileName);
FileSystem hdfs = FileSystem.get(conf);
if (hdfs.exists(mergedFilePath)) {
hdfs.delete(mergedFilePath, true);
}
OutputStream out = hdfs.create(mergedFilePath, true);
// write out the header, if needed
if (csvprop.hasHeader()) {
StringBuilder sb = new StringBuilder();
for (int i = 0; i < clen; i++) {
sb.append("C" + (i + 1));
if (i < clen - 1)
sb.append(csvprop.getDelim());
}
sb.append('\n');
out.write(sb.toString().getBytes());
sb.setLength(0);
}
// if the source is a directory
if (hdfs.isDirectory(srcFilePath)) {
try {
FileStatus[] contents = hdfs.listStatus(srcFilePath);
Path[] partPaths = new Path[contents.length];
int numPartFiles = 0;
for (int i = 0; i < contents.length; i++) {
if (!contents[i].isDirectory()) {
partPaths[i] = contents[i].getPath();
numPartFiles++;
}
}
Arrays.sort(partPaths);
for (int i = 0; i < numPartFiles; i++) {
InputStream in = hdfs.open(partPaths[i]);
try {
IOUtils.copyBytes(in, out, conf, false);
if(i<numPartFiles-1)
out.write('\n');
}
finally {
IOUtilFunctions.closeSilently(in);
}
}
} finally {
IOUtilFunctions.closeSilently(out);
}
} else if (hdfs.isFile(srcFilePath)) {
InputStream in = null;
try {
in = hdfs.open(srcFilePath);
IOUtils.copyBytes(in, out, conf, true);
} finally {
IOUtilFunctions.closeSilently(in);
IOUtilFunctions.closeSilently(out);
}
} else {
throw new IOException(srcFilePath.toString()
+ ": No such file or directory");
}
}
/**
*
* @param srcFileName
* @param destFileName
* @param csvprop
* @param rlen
* @param clen
* @throws IOException
*/
@SuppressWarnings("unchecked")
public void addHeaderToCSV(String srcFileName, String destFileName, long rlen, long clen)
throws IOException
{
Configuration conf = new Configuration(ConfigurationManager.getCachedJobConf());
Path srcFilePath = new Path(srcFileName);
Path destFilePath = new Path(destFileName);
FileSystem hdfs = FileSystem.get(conf);
if ( !_props.hasHeader() ) {
// simply move srcFile to destFile
/*
* TODO: Remove this roundabout way!
* For example: destFilePath = /user/biadmin/csv/temp/out/file.csv
* & the only path that exists already on HDFS is /user/biadmin/csv/.
* In this case: the directory structure /user/biadmin/csv/temp/out must be created.
* Simple hdfs.rename() does not seem to create this directory structure.
*/
// delete the destination file, if exists already
//boolean ret1 =
hdfs.delete(destFilePath, true);
// Create /user/biadmin/csv/temp/out/file.csv so that ..../temp/out/ is created.
//boolean ret2 =
hdfs.createNewFile(destFilePath);
// delete the file "file.csv" but preserve the directory structure /user/biadmin/csv/temp/out/
//boolean ret3 =
hdfs.delete(destFilePath, true);
// finally, move the data to destFilePath = /user/biadmin/csv/temp/out/file.csv
//boolean ret4 =
hdfs.rename(srcFilePath, destFilePath);
//System.out.println("Return values = del:" + ret1 + ", createNew:" + ret2 + ", del:" + ret3 + ", rename:" + ret4);
return;
}
// construct the header line
StringBuilder sb = new StringBuilder();
for (int i = 0; i < clen; i++) {
sb.append("C" + (i + 1));
if (i < clen - 1)
sb.append(_props.getDelim());
}
sb.append('\n');
if (hdfs.isDirectory(srcFilePath)) {
// compute sorted order among part files
ArrayList<Path> files=new ArrayList<Path>();
for(FileStatus stat: hdfs.listStatus(srcFilePath, CSVReblockMR.hiddenFileFilter))
files.add(stat.getPath());
Collections.sort(files);
// first part file path
Path firstpart = files.get(0);
// create a temp file, and add header and contents of first part
Path tmp = new Path(firstpart.toString() + ".tmp");
OutputStream out = hdfs.create(tmp, true);
out.write(sb.toString().getBytes());
sb.setLength(0);
// copy rest of the data from firstpart
InputStream in = null;
try {
in = hdfs.open(firstpart);
IOUtils.copyBytes(in, out, conf, true);
} finally {
IOUtilFunctions.closeSilently(in);
IOUtilFunctions.closeSilently(out);
}
// rename tmp to firstpart
hdfs.delete(firstpart, true);
hdfs.rename(tmp, firstpart);
// rename srcfile to destFile
hdfs.delete(destFilePath, true);
hdfs.createNewFile(destFilePath); // force the creation of directory structure
hdfs.delete(destFilePath, true); // delete the file, but preserve the directory structure
hdfs.rename(srcFilePath, destFilePath); // move the data
} else if (hdfs.isFile(srcFilePath)) {
// create destination file
OutputStream out = hdfs.create(destFilePath, true);
// write header
out.write(sb.toString().getBytes());
sb.setLength(0);
// copy the data from srcFile
InputStream in = null;
try {
in = hdfs.open(srcFilePath);
IOUtils.copyBytes(in, out, conf, true);
}
finally {
IOUtilFunctions.closeSilently(in);
IOUtilFunctions.closeSilently(out);
}
} else {
throw new IOException(srcFilePath.toString() + ": No such file or directory");
}
}
}