Java tutorial
/* * Cloud9: A MapReduce Library for Hadoop * * 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 cc.slda; import java.io.IOException; import java.util.HashMap; import java.util.Iterator; import java.util.Map; import java.util.StringTokenizer; import org.apache.commons.cli.CommandLine; import org.apache.commons.cli.CommandLineParser; import org.apache.commons.cli.GnuParser; import org.apache.commons.cli.HelpFormatter; import org.apache.commons.cli.OptionBuilder; import org.apache.commons.cli.Options; import org.apache.commons.cli.ParseException; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.conf.Configured; import org.apache.hadoop.filecache.DistributedCache; import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; import org.apache.hadoop.io.IOUtils; import org.apache.hadoop.io.IntWritable; import org.apache.hadoop.io.SequenceFile; import org.apache.hadoop.io.Text; import org.apache.hadoop.mapreduce.Job; import org.apache.hadoop.mapreduce.Mapper; import org.apache.hadoop.mapreduce.Reducer; import org.apache.hadoop.mapreduce.lib.input.FileInputFormat; import org.apache.hadoop.mapreduce.lib.input.SequenceFileInputFormat; import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat; import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat; import org.apache.hadoop.util.Tool; import org.apache.hadoop.util.ToolRunner; import org.apache.log4j.Logger; import com.google.common.base.Preconditions; import cern.colt.Arrays; import edu.umd.cloud9.io.array.ArrayListOfDoublesWritable; import edu.umd.cloud9.io.map.HMapIVW; import edu.umd.cloud9.io.map.HMapSIW; import edu.umd.cloud9.io.map.HashMapWritable; import edu.umd.cloud9.io.pair.PairOfInts; /** * Annotate documents with output from LDA * * @author Khoa Doan */ public class AnnotateDocuments extends Configured implements Tool { private static final Logger LOG = Logger.getLogger(AnnotateDocuments.class); public static final String TERM = "term"; public static final String TITLE = "title"; // Mapper: emits (token, 1) for every word occurrence. private static class MyMapper extends Mapper<IntWritable, HMapIVW<ArrayListOfDoublesWritable>, Text, HMapSIW> { // Reuse objects to save overhead of object creation. private static Map<Integer, String> termIndex = null; private static Map<Integer, String> titleIndex = null; private static Text title = new Text(); private static HMapSIW labels = new HMapSIW(); private static double labelCutoff; @Override public void setup(Context context) throws InterruptedException { SequenceFile.Reader sequenceFileReader = null; try { Configuration conf = context.getConfiguration(); Path[] inputFiles = DistributedCache.getLocalCacheFiles(conf); labelCutoff = Math.log(conf.getFloat(PCUTOFF, 0.9f)); // Read term and title index if (inputFiles != null) { for (Path path : inputFiles) { try { sequenceFileReader = new SequenceFile.Reader(FileSystem.getLocal(conf), path, conf); if (path.getName().startsWith(TERM)) { Preconditions.checkArgument(termIndex == null, "Term index was initialized already..."); termIndex = AnnotateDocuments.importParameter(sequenceFileReader); } else if (path.getName().startsWith(TITLE)) { Preconditions.checkArgument(titleIndex == null, "Title index was initialized already..."); titleIndex = AnnotateDocuments.importParameter(sequenceFileReader); } else { throw new IllegalArgumentException( "Unexpected file in distributed cache: " + path.getName()); } } catch (IllegalArgumentException iae) { iae.printStackTrace(); } catch (IOException ioe) { ioe.printStackTrace(); } } } } catch (IOException ioe) { ioe.printStackTrace(); } finally { IOUtils.closeStream(sequenceFileReader); } } @Override public void map(IntWritable key, HMapIVW<ArrayListOfDoublesWritable> value, Context context) throws IOException, InterruptedException { title.set(titleIndex.get(key.get())); labels.clear(); for (Integer termId : value.keySet()) { //Determine the label ArrayListOfDoublesWritable phi = value.get(termId); for (int i = 0; i < phi.size(); i++) { //Label the term only when its assignment prob to a topic is greater than the cutoff if (phi.get(i) >= labelCutoff) { labels.put(termIndex.get(termId), i + 1); break; } else { //No label labels.put(termIndex.get(termId), 0); } } } context.write(title, labels); } } /** * Creates an instance of this tool. */ public AnnotateDocuments() { } private static final String INPUT = "input"; private static final String OUTPUT = "output"; private static final String NUM_REDUCERS = "numReducers"; private static final String PCUTOFF = "probCutoff"; private static final String INDEX = "index"; /** * Runs this tool. */ @SuppressWarnings({ "static-access" }) public int run(String[] args) throws Exception { Options options = new Options(); options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("input path").create(INPUT)); options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("output path").create(OUTPUT)); options.addOption(OptionBuilder.withArgName("num").hasArg().withDescription("number of reducers") .create(NUM_REDUCERS)); options.addOption(OptionBuilder.withArgName(PCUTOFF).hasArg() .withDescription("probability of topic assignment").create(PCUTOFF)); options.addOption(OptionBuilder.withArgName(INDEX).hasArg() .withDescription("path to data directory containing term and title indices").create(INDEX)); CommandLine cmdline; CommandLineParser parser = new GnuParser(); try { cmdline = parser.parse(options, args); } catch (ParseException exp) { System.err.println("Error parsing command line: " + exp.getMessage()); return -1; } if (!cmdline.hasOption(INPUT) || !cmdline.hasOption(OUTPUT) || !cmdline.hasOption(INDEX)) { System.out.println("args: " + Arrays.toString(args)); HelpFormatter formatter = new HelpFormatter(); formatter.setWidth(120); formatter.printHelp(this.getClass().getName(), options); ToolRunner.printGenericCommandUsage(System.out); return -1; } String indexPath = cmdline.getOptionValue(INDEX); String inputPath = cmdline.getOptionValue(INPUT); String outputPath = cmdline.getOptionValue(OUTPUT); int reduceTasks = cmdline.hasOption(NUM_REDUCERS) ? Integer.parseInt(cmdline.getOptionValue(NUM_REDUCERS)) : 1; float cutoff = 0.9f; if (cmdline.hasOption(PCUTOFF)) { cutoff = Float.parseFloat(cmdline.getOptionValue(PCUTOFF)); } LOG.info("Tool: " + AnnotateDocuments.class.getSimpleName()); LOG.info(" - indices path: " + indexPath); LOG.info(" - input path: " + inputPath); LOG.info(" - output path: " + outputPath); LOG.info(" - number of reducers: " + reduceTasks); LOG.info(" - log(probCutoff): " + Math.log(cutoff)); Configuration conf = getConf(); FileSystem fs = FileSystem.get(conf); Job job = Job.getInstance(conf); job.setJobName(AnnotateDocuments.class.getSimpleName()); job.setJarByClass(AnnotateDocuments.class); String termIndex = indexPath + Path.SEPARATOR + TERM; String titleIndex = indexPath + Path.SEPARATOR + TITLE; Path termIndexPath = new Path(termIndex); Path titleIndexPath = new Path(titleIndex); Preconditions.checkArgument(fs.exists(termIndexPath), "Missing term index files... " + termIndexPath); DistributedCache.addCacheFile(termIndexPath.toUri(), job.getConfiguration()); Preconditions.checkArgument(fs.exists(titleIndexPath), "Missing title index files... " + titleIndexPath); DistributedCache.addCacheFile(titleIndexPath.toUri(), job.getConfiguration()); job.setNumReduceTasks(reduceTasks); conf.setFloat(PCUTOFF, cutoff); job.setInputFormatClass(SequenceFileInputFormat.class); job.setOutputFormatClass(SequenceFileOutputFormat.class); FileInputFormat.setInputPaths(job, new Path(inputPath)); FileOutputFormat.setOutputPath(job, new Path(outputPath)); job.setMapOutputKeyClass(Text.class); job.setMapOutputValueClass(HMapSIW.class); job.setOutputKeyClass(Text.class); job.setOutputValueClass(HMapSIW.class); job.setMapperClass(MyMapper.class); // Delete the output directory if it exists already. Path outputDir = new Path(outputPath); FileSystem.get(conf).delete(outputDir, true); long startTime = System.currentTimeMillis(); job.waitForCompletion(true); LOG.info("Job Finished in " + (System.currentTimeMillis() - startTime) / 1000.0 + " seconds"); return 0; } public static Map<Integer, String> importParameter(SequenceFile.Reader sequenceFileReader) throws IOException { Map<Integer, String> hashMap = new HashMap<Integer, String>(); IntWritable intWritable = new IntWritable(); Text text = new Text(); while (sequenceFileReader.next(intWritable, text)) { hashMap.put(intWritable.get(), text.toString()); } return hashMap; } /** * Dispatches command-line arguments to the tool via the {@code ToolRunner}. */ public static void main(String[] args) throws Exception { ToolRunner.run(new AnnotateDocuments(), args); } }