org.apache.mahout.ga.watchmaker.cd.tool.CDInfosTool.java Source code

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/**
 * 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.mahout.ga.watchmaker.cd.tool;

import java.io.BufferedWriter;
import java.io.IOException;
import java.io.OutputStreamWriter;
import java.util.Collection;
import java.util.List;
import java.util.Locale;
import java.util.Scanner;

import com.google.common.base.Preconditions;
import com.google.common.collect.Lists;
import com.google.common.io.Closeables;
import org.apache.commons.cli2.CommandLine;
import org.apache.commons.cli2.Group;
import org.apache.commons.cli2.Option;
import org.apache.commons.cli2.OptionException;
import org.apache.commons.cli2.builder.GroupBuilder;
import org.apache.commons.cli2.commandline.Parser;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FSDataInputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.LongWritable;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.io.SequenceFile;
import org.apache.hadoop.io.Writable;
import org.apache.hadoop.mapreduce.Job;
import org.apache.hadoop.mapreduce.lib.input.FileInputFormat;
import org.apache.hadoop.mapreduce.lib.input.TextInputFormat;
import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat;
import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat;
import org.apache.mahout.common.CommandLineUtil;
import org.apache.mahout.common.commandline.DefaultOptionCreator;
import org.apache.mahout.common.iterator.sequencefile.SequenceFileValueIterable;
import org.apache.mahout.ga.watchmaker.OutputUtils;
import org.apache.mahout.ga.watchmaker.cd.FileInfoParser;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

/**
 * Gathers additional information about a given dataset. Takes a descriptor
 * about the attributes, and generates a description for each one.
 */
public final class CDInfosTool {

    private static final Logger log = LoggerFactory.getLogger(CDInfosTool.class);

    private CDInfosTool() {
    }

    /**
     * Uses Mahout to gather the information about a dataset.
     *
     * @param descriptors about the available attributes
     * @param inpath input path (the dataset)
     * @param descriptions {@code List<String>} that contains the
     *        generated descriptions for each non ignored attribute
     */
    public static void gatherInfos(Descriptors descriptors, Path inpath, Path output,
            Collection<String> descriptions) throws IOException, InterruptedException, ClassNotFoundException {
        Configuration conf = new Configuration();
        FileSystem fs = FileSystem.get(inpath.toUri(), conf);
        Preconditions.checkArgument(fs.exists(inpath) && fs.getFileStatus(inpath).isDir(), "%s is not a directory",
                inpath);

        Job job = new Job(conf);

        configureJob(job, descriptors, inpath, output);
        job.waitForCompletion(true);

        importDescriptions(fs, conf, output, descriptions);
    }

    /**
     * Configure the job
     *
     * @param descriptors attributes's descriptors
     * @param inpath input {@code Path}
     * @param outpath output {@code Path}
     */
    private static void configureJob(Job job, Descriptors descriptors, Path inpath, Path outpath)
            throws IOException {
        FileInputFormat.setInputPaths(job, inpath);
        FileOutputFormat.setOutputPath(job, outpath);

        job.setJarByClass(CDInfosTool.class);
        job.setOutputKeyClass(LongWritable.class);
        job.setOutputValueClass(Text.class);

        job.setMapperClass(ToolMapper.class);
        job.setCombinerClass(ToolCombiner.class);
        job.setReducerClass(ToolReducer.class);

        job.setInputFormatClass(TextInputFormat.class);
        job.setOutputFormatClass(SequenceFileOutputFormat.class);

        // store the stringified descriptors
        job.getConfiguration().set(ToolMapper.ATTRIBUTES, new String(descriptors.getChars()));
    }

    /**
     * Reads back the descriptions.
     *
     * @param fs file system
     * @param conf job configuration
     * @param outpath output {@code Path}
     * @param descriptions List of attribute's descriptions
     */
    private static void importDescriptions(FileSystem fs, Configuration conf, Path outpath,
            Collection<String> descriptions) throws IOException {
        SequenceFile.Sorter sorter = new SequenceFile.Sorter(fs, LongWritable.class, Text.class, conf);

        // merge and sort the outputs
        Path[] outfiles = OutputUtils.listOutputFiles(fs, outpath);
        Path output = new Path(outpath, "output.sorted");
        sorter.merge(outfiles, output);

        // import the descriptions
        for (Writable value : new SequenceFileValueIterable<Writable>(output, true, conf)) {
            descriptions.add(value.toString());
        }
    }

    /**
     * Load the dataset's attributes descriptors from an .info file
     * 
     * @param inpath dataset path
     */
    private static Descriptors loadDescriptors(FileSystem fs, Path inpath) throws IOException {
        // TODO should become part of FileInfoParser

        Path infpath = FileInfoParser.getInfoFile(fs, inpath);

        FSDataInputStream input = fs.open(infpath);
        Scanner reader = new Scanner(input);

        List<Character> descriptors = Lists.newArrayList();

        while (reader.hasNextLine()) {
            String c = reader.nextLine();
            descriptors.add(c.toUpperCase(Locale.ENGLISH).charAt(0));
        }

        if (descriptors.isEmpty()) {
            throw new IllegalArgumentException("Infos file is empty");
        }

        char[] desc = new char[descriptors.size()];
        for (int index = 0; index < descriptors.size(); index++) {
            desc[index] = descriptors.get(index);
        }

        return new Descriptors(desc);
    }

    private static void storeDescriptions(FileSystem fs, Path inpath, Descriptors descriptors,
            List<String> descriptions) throws IOException {
        // TODO should become part of FileInfoParser

        Path infpath = FileInfoParser.getInfoFile(fs, inpath);

        BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(fs.create(infpath)));
        try {
            int aindex = 0;
            for (int index = 0; index < descriptors.size(); index++) {
                if (descriptors.isLabel(index)) {
                    writer.write(FileInfoParser.LABEL_TOKEN + ", ");
                    writer.write(descriptions.get(aindex++));
                } else if (descriptors.isNumerical(index)) {
                    writer.write(FileInfoParser.NUMERICAL_TOKEN + ", ");
                    writer.write(descriptions.get(aindex++));
                } else if (descriptors.isNominal(index)) {
                    writer.write(FileInfoParser.NOMINAL_TOKEN + ", ");
                    writer.write(descriptions.get(aindex++));
                } else {
                    writer.write(FileInfoParser.IGNORED_TOKEN);
                }

                writer.newLine();
            }
        } finally {
            Closeables.closeQuietly(writer);
        }
    }

    public static void main(String[] args) throws IOException, InterruptedException, ClassNotFoundException {
        GroupBuilder gbuilder = new GroupBuilder();

        Option inputOpt = DefaultOptionCreator.inputOption().create();

        Option helpOpt = DefaultOptionCreator.helpOption();

        Group group = gbuilder.withName("Options").withOption(inputOpt).withOption(helpOpt).create();

        Parser parser = new Parser();
        parser.setGroup(group);
        try {
            CommandLine cmdLine = parser.parse(args);

            if (cmdLine.hasOption(helpOpt)) {
                CommandLineUtil.printHelp(group);
                return;
            }

            Path input = new Path(cmdLine.getValue(inputOpt).toString());
            Path output = new Path("output"); // TODO surely this should be configurable?

            FileSystem fs = FileSystem.get(input.toUri(), new Configuration());

            log.info("Loading Descriptors...");
            Descriptors descriptors = loadDescriptors(fs, input);

            log.info("Gathering informations...");
            List<String> descriptions = Lists.newArrayList();
            gatherInfos(descriptors, input, output, descriptions);

            log.info("Storing Descriptions...");
            storeDescriptions(fs, input, descriptors, descriptions);
        } catch (OptionException e) {
            log.error("Error while parsing options", e);
            CommandLineUtil.printHelp(group);
        }
    }
}