Java tutorial
/** * (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"); } } }