src/main/java/org/apache/sysds/runtime/io/WriterMatrixMarket.java

/*
 * Licensed to the Apache Software Foundation (ASF) under one
 * or more contributor license agreements.  See the NOTICE file
 * distributed with this work for additional information
 * regarding copyright ownership.  The ASF licenses this file
 * to you 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 org.apache.sysds.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.Iterator;

import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FSDataOutputStream;
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 org.apache.sysds.conf.ConfigurationManager;
import org.apache.sysds.runtime.DMLRuntimeException;
import org.apache.sysds.runtime.matrix.data.IJV;
import org.apache.sysds.runtime.matrix.data.MatrixBlock;
import org.apache.sysds.runtime.util.HDFSTool;

public class WriterMatrixMarket extends MatrixWriter
{
	@Override
	public final void writeMatrixToHDFS(MatrixBlock src, String fname, long rlen, long clen, int blen, long nnz, boolean diag) 
		throws IOException, DMLRuntimeException 
	{
		//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 );
		FileSystem fs = IOUtilFunctions.getFileSystem(path, job);
		
		//if the file already exists on HDFS, remove it.
		HDFSTool.deleteFileIfExistOnHDFS( fname );
			
		//core write
		writeMatrixMarketMatrixToHDFS(path, job, fs, src);

		IOUtilFunctions.deleteCrcFilesFromLocalFileSystem(fs, path);
	}

	@Override
	public final void writeEmptyMatrixToHDFS(String fname, long rlen, long clen, int blen) 
		throws IOException, DMLRuntimeException 
	{
		Path path = new Path( fname );
		FileSystem fs = IOUtilFunctions.getFileSystem(path);
		
		FSDataOutputStream writer = null;
		try {
			writer = fs.create(path);
			writer.writeBytes(IOUtilFunctions.EMPTY_TEXT_LINE);
		}
		finally {
			IOUtilFunctions.closeSilently(writer);
		}
		IOUtilFunctions.deleteCrcFilesFromLocalFileSystem(fs, path);
	}

	protected void writeMatrixMarketMatrixToHDFS( Path path, JobConf job, FileSystem fs, MatrixBlock src )
		throws IOException
	{
		//sequential write
		writeMatrixMarketMatrixToFile(path, job, fs, src, 0, src.getNumRows());
	}

	protected static void writeMatrixMarketMatrixToFile( Path path, JobConf job, FileSystem fs, MatrixBlock src, int rl, int ru )
		throws IOException
	{
		boolean sparse = src.isInSparseFormat();
		int rlen = src.getNumRows();
		int clen = src.getNumColumns();
		long nnz = src.getNonZeros();
		
		BufferedWriter br=new BufferedWriter(new OutputStreamWriter(fs.create(path,true)));		

		try
		{
			//for obj reuse and preventing repeated buffer re-allocations
			StringBuilder sb = new StringBuilder();
			
			if( rl == 0 ) {
				// First output MM header
				sb.append ("%%MatrixMarket matrix coordinate real general\n");
			
				// output number of rows, number of columns and number of nnz
				sb.append (rlen + " " + clen + " " + nnz + "\n");
				br.write( sb.toString());
				sb.setLength(0);
			}
			 
            // output matrix cell
			if( sparse ) //SPARSE
			{			   
				Iterator<IJV> iter = src.getSparseBlockIterator(rl, ru);
				while( iter.hasNext() )
				{
					IJV cell = iter.next();

					sb.append(cell.getI()+1);
					sb.append(' ');
					sb.append(cell.getJ()+1);
					sb.append(' ');
					sb.append(cell.getV());
					sb.append('\n');
					br.write( sb.toString() ); //same as append
					sb.setLength(0); 
				}
			}
			else //DENSE
			{
				for( int i=rl; i<ru; i++ )
				{
					String rowIndex = Integer.toString(i+1);					
					for( int j=0; j<clen; j++ )
					{
						double lvalue = src.getValueDenseUnsafe(i, j);
						if( lvalue != 0 ) //for nnz
						{
							sb.append(rowIndex);
							sb.append(' ');
							sb.append(j+1);
							sb.append(' ');
							sb.append(lvalue);
							sb.append('\n');
							br.write( sb.toString() ); //same as append
							sb.setLength(0); 
						}
					}
				}
			}
	
			//handle empty result
			if ( src.isEmptyBlock(false) && rl==0 )
				br.write(IOUtilFunctions.EMPTY_TEXT_LINE);
		}
		finally {
			IOUtilFunctions.closeSilently(br);
		}
	}

	public static void mergeTextcellToMatrixMarket( String srcFileName, String fileName, long rlen, long clen, long nnz )
		throws IOException
	{
		  Configuration conf = new Configuration(ConfigurationManager.getCachedJobConf());
		
		  Path src = new Path (srcFileName);
	      Path merge = new Path (fileName);
	      FileSystem fs = IOUtilFunctions.getFileSystem(src, conf);
			
	      if (fs.exists (merge)) {
	    	fs.delete(merge, true);
	      }
        
	      OutputStream out = fs.create(merge, true);

	      // write out the header first 
	      StringBuilder  sb = new StringBuilder();
	      sb.append ("%%MatrixMarket matrix coordinate real general\n");
	    
	      // output number of rows, number of columns and number of nnz
	 	  sb.append (rlen + " " + clen + " " + nnz + "\n");
	      out.write (sb.toString().getBytes());

	      // if the source is a directory
	      if (fs.getFileStatus(src).isDirectory()) {
	        try {
	          FileStatus[] contents = fs.listStatus(src);
	          for (int i = 0; i < contents.length; i++) {
	            if (!contents[i].isDirectory()) {
	               InputStream in = fs.open (contents[i].getPath());
	               try {
	                 IOUtils.copyBytes (in, out, conf, false);
	               }  finally {
	                  IOUtilFunctions.closeSilently(in);
	               }
	             }
	           }
	         } finally {
	        	 IOUtilFunctions.closeSilently(out);
	         }
	      } else if (fs.isFile(src))  {
	        InputStream in = null;
	        try {
   	          in = fs.open (src);
	          IOUtils.copyBytes (in, out, conf, true);
	        } 
	        finally {
	        	IOUtilFunctions.closeSilently(in);
	        	IOUtilFunctions.closeSilently(out);
	        }
	      } else {
	        throw new IOException(src.toString() + ": No such file or directory");
	      }
	}
}