Examples with CommandLineParser org.apache.commons.cli.CommandLineParser used on opensource projects

Example 71 with CommandLineParser

use of org.apache.commons.cli.CommandLineParser in project Cloud9 by lintool.

the class WikipediaDocnoMappingBuilder method run.

@SuppressWarnings("static-access")
@Override
public int run(String[] args) throws Exception {
    Options options = new Options();
    options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("XML dump file").create(INPUT_OPTION));
    options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("output file").create(OUTPUT_FILE_OPTION));
    options.addOption(OptionBuilder.withArgName("en|sv|de|cs|es|zh|ar|tr").hasArg().withDescription("two-letter language code").create(LANGUAGE_OPTION));
    options.addOption(KEEP_ALL_OPTION, false, "keep all pages");
    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_OPTION) || !cmdline.hasOption(OUTPUT_FILE_OPTION)) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(this.getClass().getName(), options);
        ToolRunner.printGenericCommandUsage(System.out);
        return -1;
    }
    String language = null;
    if (cmdline.hasOption(LANGUAGE_OPTION)) {
        language = cmdline.getOptionValue(LANGUAGE_OPTION);
        if (language.length() != 2) {
            System.err.println("Error: \"" + language + "\" unknown language!");
            return -1;
        }
    }
    String inputPath = cmdline.getOptionValue(INPUT_OPTION);
    String outputFile = cmdline.getOptionValue(OUTPUT_FILE_OPTION);
    boolean keepAll = cmdline.hasOption(KEEP_ALL_OPTION);
    String tmpPath = "tmp-" + WikipediaDocnoMappingBuilder.class.getSimpleName() + "-" + RANDOM.nextInt(10000);
    LOG.info("Tool name: " + this.getClass().getName());
    LOG.info(" - input: " + inputPath);
    LOG.info(" - output file: " + outputFile);
    LOG.info(" - keep all pages: " + keepAll);
    LOG.info(" - language: " + language);
    Job job = Job.getInstance(getConf());
    job.setJarByClass(WikipediaDocnoMappingBuilder.class);
    job.setJobName(String.format("BuildWikipediaDocnoMapping[%s: %s, %s: %s, %s: %s]", INPUT_OPTION, inputPath, OUTPUT_FILE_OPTION, outputFile, LANGUAGE_OPTION, language));
    job.getConfiguration().setBoolean(KEEP_ALL_OPTION, keepAll);
    if (language != null) {
        job.getConfiguration().set("wiki.language", language);
    }
    job.setNumReduceTasks(1);
    FileInputFormat.setInputPaths(job, new Path(inputPath));
    FileOutputFormat.setOutputPath(job, new Path(tmpPath));
    FileOutputFormat.setCompressOutput(job, false);
    job.setOutputKeyClass(IntWritable.class);
    job.setOutputValueClass(IntWritable.class);
    job.setInputFormatClass(WikipediaPageInputFormat.class);
    job.setOutputFormatClass(TextOutputFormat.class);
    job.setMapperClass(MyMapper.class);
    job.setReducerClass(MyReducer.class);
    // Delete the output directory if it exists already.
    FileSystem.get(getConf()).delete(new Path(tmpPath), true);
    job.waitForCompletion(true);
    long cnt = keepAll ? job.getCounters().findCounter(PageTypes.TOTAL).getValue() : job.getCounters().findCounter(PageTypes.ARTICLE).getValue();
    WikipediaDocnoMapping.writeDocnoMappingData(FileSystem.get(getConf()), tmpPath + "/part-r-00000", (int) cnt, outputFile);
    FileSystem.get(getConf()).delete(new Path(tmpPath), true);
    return 0;
}

Example 72 with CommandLineParser

use of org.apache.commons.cli.CommandLineParser in project Cloud9 by lintool.

the class TrecForwardIndexBuilder method run.

/**
   * Runs this tool.
   */
@SuppressWarnings("static-access")
public int run(String[] args) throws Exception {
    Options options = new Options();
    options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("(required) collection path").create(COLLECTION_OPTION));
    options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("(required) output index path").create(INDEX_OPTION));
    options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("(required) DocnoMapping data").create(MAPPING_OPTION));
    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(COLLECTION_OPTION) || !cmdline.hasOption(INDEX_OPTION) || !cmdline.hasOption(MAPPING_OPTION)) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(this.getClass().getName(), options);
        ToolRunner.printGenericCommandUsage(System.out);
        return -1;
    }
    String collectionPath = cmdline.getOptionValue(COLLECTION_OPTION);
    String indexFile = cmdline.getOptionValue(INDEX_OPTION);
    String mappingFile = cmdline.getOptionValue(MAPPING_OPTION);
    String tmpDir = "tmp-" + TrecForwardIndexBuilder.class.getSimpleName() + "-" + random.nextInt(10000);
    Job job = new Job(getConf(), TrecForwardIndexBuilder.class.getSimpleName() + ":" + collectionPath);
    job.setJarByClass(TrecForwardIndexBuilder.class);
    FileSystem fs = FileSystem.get(getConf());
    LOG.info("Tool name: " + TrecForwardIndexBuilder.class.getSimpleName());
    LOG.info(" - collection path: " + collectionPath);
    LOG.info(" - index file: " + indexFile);
    LOG.info(" - DocnoMapping file: " + mappingFile);
    LOG.info(" - temp output directory: " + tmpDir);
    job.setNumReduceTasks(1);
    if (job.getConfiguration().get("mapred.job.tracker").equals("local")) {
        job.getConfiguration().set(DOCNO_MAPPING_FILE_PROPERTY, mappingFile);
    } else {
        DistributedCache.addCacheFile(new URI(mappingFile), job.getConfiguration());
    }
    FileInputFormat.setInputPaths(job, new Path(collectionPath));
    FileOutputFormat.setOutputPath(job, new Path(tmpDir));
    FileOutputFormat.setCompressOutput(job, false);
    job.setInputFormatClass(TrecDocumentInputFormat.class);
    job.setOutputKeyClass(IntWritable.class);
    job.setOutputValueClass(Text.class);
    job.setMapperClass(MyMapper.class);
    // delete the output directory if it exists already
    FileSystem.get(getConf()).delete(new Path(tmpDir), true);
    job.waitForCompletion(true);
    Counters counters = job.getCounters();
    int numDocs = (int) counters.findCounter(Count.DOCS).getValue();
    String inputFile = tmpDir + "/" + "part-r-00000";
    LOG.info("Writing " + numDocs + " doc offseta to " + indexFile);
    LineReader reader = new LineReader(fs.open(new Path(inputFile)));
    FSDataOutputStream writer = fs.create(new Path(indexFile), true);
    writer.writeUTF(edu.umd.cloud9.collection.trec.TrecForwardIndex.class.getCanonicalName());
    writer.writeUTF(collectionPath);
    writer.writeInt(numDocs);
    int cnt = 0;
    Text line = new Text();
    while (reader.readLine(line) > 0) {
        String[] arr = line.toString().split("\\t");
        long offset = Long.parseLong(arr[1]);
        int len = Integer.parseInt(arr[2]);
        writer.writeLong(offset);
        writer.writeInt(len);
        cnt++;
        if (cnt % 100000 == 0) {
            LOG.info(cnt + " docs");
        }
    }
    reader.close();
    writer.close();
    LOG.info(cnt + " docs total. Done!");
    if (numDocs != cnt) {
        throw new RuntimeException("Unexpected number of documents in building forward index!");
    }
    fs.delete(new Path(tmpDir), true);
    return 0;
}

Example 73 with CommandLineParser

use of org.apache.commons.cli.CommandLineParser in project Cloud9 by lintool.

the class CountMedlineCitations method run.

@SuppressWarnings("static-access")
public int run(String[] args) throws Exception {
    Options options = new Options();
    options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("(required) collection path").create(COLLECTION_OPTION));
    options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("(required) output path").create(OUTPUT_OPTION));
    options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("(required) DocnoMapping data").create(MAPPING_OPTION));
    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(COLLECTION_OPTION) || !cmdline.hasOption(OUTPUT_OPTION) || !cmdline.hasOption(MAPPING_OPTION)) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(this.getClass().getName(), options);
        ToolRunner.printGenericCommandUsage(System.out);
        return -1;
    }
    String inputPath = cmdline.getOptionValue(COLLECTION_OPTION);
    String outputPath = cmdline.getOptionValue(OUTPUT_OPTION);
    String mappingFile = cmdline.getOptionValue(MAPPING_OPTION);
    LOG.info("Tool: " + CountMedlineCitations.class.getSimpleName());
    LOG.info(" - input: " + inputPath);
    LOG.info(" - output dir: " + outputPath);
    LOG.info(" - docno mapping file: " + mappingFile);
    Job job = new Job(getConf(), CountMedlineCitations.class.getSimpleName() + ":" + inputPath);
    job.setJarByClass(CountMedlineCitations.class);
    job.setNumReduceTasks(0);
    // Pass in the class name as a String; this is makes the mapper general in being able to load
    // any collection of Indexable objects that has docid/docno mapping specified by a DocnoMapping
    // object.
    job.getConfiguration().set("DocnoMappingClass", MedlineDocnoMapping.class.getCanonicalName());
    // Put the mapping file in the distributed cache so each map worker will have it.
    DistributedCache.addCacheFile(new URI(mappingFile), job.getConfiguration());
    FileInputFormat.setInputPaths(job, new Path(inputPath));
    FileOutputFormat.setOutputPath(job, new Path(outputPath));
    FileOutputFormat.setCompressOutput(job, false);
    job.setInputFormatClass(MedlineCitationInputFormat.class);
    job.setOutputKeyClass(Text.class);
    job.setOutputValueClass(IntWritable.class);
    job.setMapperClass(MyMapper.class);
    // Delete the output directory if it exists already.
    FileSystem.get(job.getConfiguration()).delete(new Path(outputPath), true);
    job.waitForCompletion(true);
    Counters counters = job.getCounters();
    int numDocs = (int) counters.findCounter(Count.DOCS).getValue();
    LOG.info("Read " + numDocs + " docs.");
    return numDocs;
}

Example 74 with CommandLineParser

use of org.apache.commons.cli.CommandLineParser in project Cloud9 by lintool.

the class DocumentForwardIndexHttpServer method run.

@SuppressWarnings("static-access")
public int run(String[] args) throws Exception {
    Options options = new Options();
    options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("(required) forward index path").create(INDEX_OPTION));
    options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("(required) DocnoMapping data path").create(MAPPING_OPTION));
    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(INDEX_OPTION) || !cmdline.hasOption(MAPPING_OPTION)) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(this.getClass().getName(), options);
        ToolRunner.printGenericCommandUsage(System.out);
        return -1;
    }
    String indexFile = cmdline.getOptionValue(INDEX_OPTION);
    String mappingFile = cmdline.getOptionValue(MAPPING_OPTION);
    LOG.info("Launching DocumentForwardIndexHttpServer");
    LOG.info(" - index file: " + indexFile);
    LOG.info(" - docno mapping data file: " + mappingFile);
    Configuration conf = getConf();
    FileSystem fs = FileSystem.get(conf);
    Random rand = new Random();
    int r = rand.nextInt();
    // This tmp file as a rendezvous point.
    Path tmpPath = new Path("/tmp/" + r);
    if (fs.exists(tmpPath)) {
        fs.delete(tmpPath, true);
    }
    Job job = new Job(conf, DocumentForwardIndexHttpServer.class.getSimpleName());
    job.setJarByClass(DocumentForwardIndexHttpServer.class);
    job.getConfiguration().set("mapred.child.java.opts", "-Xmx1024m");
    job.getConfiguration().set(INDEX_KEY, indexFile);
    job.getConfiguration().set(DOCNO_MAPPING_KEY, mappingFile);
    job.getConfiguration().set(TMP_KEY, tmpPath.toString());
    job.setNumReduceTasks(0);
    job.setInputFormatClass(NullInputFormat.class);
    job.setOutputFormatClass(NullOutputFormat.class);
    job.setMapperClass(MyMapper.class);
    job.submit();
    LOG.info("Waiting for server to start up...");
    while (!fs.exists(tmpPath)) {
        Thread.sleep(50000);
        LOG.info("...");
    }
    FSDataInputStream in = fs.open(tmpPath);
    String host = in.readUTF();
    in.close();
    LOG.info("host: " + host);
    LOG.info("port: 8888");
    return 0;
}

Example 75 with CommandLineParser

use of org.apache.commons.cli.CommandLineParser in project Cloud9 by lintool.

the class HadoopAlign method main.

@SuppressWarnings("static-access")
public static void main(String[] args) throws IOException {
    options = new Options();
    options.addOption(OptionBuilder.withDescription("path to XML-formatted parallel corpus").withArgName("path").hasArg().isRequired().create(INPUT_OPTION));
    options.addOption(OptionBuilder.withDescription("path to work/output directory on HDFS").withArgName("path").hasArg().isRequired().create(WORK_OPTION));
    options.addOption(OptionBuilder.withDescription("two-letter collection language code").withArgName("en|de|fr|zh|es|ar|tr").hasArg().isRequired().create(FLANG_OPTION));
    options.addOption(OptionBuilder.withDescription("two-letter collection language code").withArgName("en|de|fr|zh|es|ar|tr").hasArg().isRequired().create(ELANG_OPTION));
    options.addOption(OptionBuilder.withDescription("number of IBM Model 1 iterations").withArgName("positive integer").hasArg().create(MODEL1_OPTION));
    options.addOption(OptionBuilder.withDescription("number of HMM iterations").withArgName("positive integer").hasArg().create(HMM_OPTION));
    options.addOption(OptionBuilder.withDescription("truncate/stem text or not").create(TRUNCATE_OPTION));
    options.addOption(OptionBuilder.withDescription("number of reducers").withArgName("positive integer").hasArg().create(REDUCE_OPTION));
    options.addOption(OptionBuilder.withDescription("Hadoop option to load external jars").withArgName("jar packages").hasArg().create(LIBJARS_OPTION));
    CommandLine cmdline;
    CommandLineParser parser = new GnuParser();
    try {
        cmdline = parser.parse(options, args);
    } catch (ParseException exp) {
        printUsage();
        System.err.println("Error parsing command line: " + exp.getMessage());
        return;
    }
    String bitextPath = cmdline.getOptionValue(INPUT_OPTION);
    String workDir = cmdline.getOptionValue(WORK_OPTION);
    String srcLang = cmdline.getOptionValue(FLANG_OPTION);
    String trgLang = cmdline.getOptionValue(ELANG_OPTION);
    int model1Iters = cmdline.hasOption(MODEL1_OPTION) ? Integer.parseInt(cmdline.getOptionValue(MODEL1_OPTION)) : 0;
    int hmmIters = cmdline.hasOption(HMM_OPTION) ? Integer.parseInt(cmdline.getOptionValue(HMM_OPTION)) : 0;
    if (model1Iters + hmmIters == 0) {
        System.err.println("Please enter a positive number of iterations for either Model 1 or HMM");
        printUsage();
        return;
    }
    boolean isTruncate = cmdline.hasOption(TRUNCATE_OPTION) ? true : false;
    int numReducers = cmdline.hasOption(REDUCE_OPTION) ? Integer.parseInt(cmdline.getOptionValue(REDUCE_OPTION)) : 50;
    HadoopAlignConfig hac = new HadoopAlignConfig(workDir, trgLang, srcLang, bitextPath, model1Iters, hmmIters, // use null word
    true, // use variational bayes
    false, // use word truncation
    isTruncate, // alpha
    0.00f);
    hac.setHMMHomogeneous(false);
    hac.set("mapreduce.map.memory.mb", "2048");
    hac.set("mapreduce.map.java.opts", "-Xmx2048m");
    hac.set("mapreduce.reduce.memory.mb", "2048");
    hac.set("mapreduce.reduce.java.opts", "-Xmx2048m");
    hac.setHMMp0(0.2);
    hac.setMaxSentLen(15);
    doAlignment(50, numReducers, hac);
}