Example usage for org.apache.hadoop.conf Configuration getBoolean

Introduction

In this page you can find the example usage for org.apache.hadoop.conf Configuration getBoolean.

Prototype

public boolean getBoolean(String name, boolean defaultValue) 

Source Link

Document

Get the value of the name property as a boolean.

Usage

From source file:it.crs4.pydoop.mapreduce.pipes.CommandLineParser.java

License:Apache License

/**
 * Check whether the job is using a Java Reducer.
 * @param conf the configuration to check
 * @return is it a Java Reducer?//from   ww  w  .ja  v  a 2  s . c  o  m
 */
public static boolean getIsJavaReducer(Configuration conf) {
    return conf.getBoolean(Submitter.IS_JAVA_REDUCE, false);
}

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From source file:it.crs4.pydoop.mapreduce.pipes.CommandLineParser.java

License:Apache License

/**
 * Will the reduce use a Java RecordWriter?
 * @param conf the configuration to check
 * @return true, if the output of the job will be written by Java
 *///from   w ww .j  a  v a 2s.c o  m
public static boolean getIsJavaRecordWriter(Configuration conf) {
    return conf.getBoolean(Submitter.IS_JAVA_RW, false);
}

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From source file:it.crs4.pydoop.mapreduce.pipes.CommandLineParser.java

License:Apache License

/**
 * Does the user want to keep the command file for debugging? If
 * this is true, pipes will write a copy of the command data to a
 * file in the task directory named "downlink.data", which may be
 * used to run the C++ program under the debugger. You probably also
 * want to set Configuration.setKeepFailedTaskFiles(true) to keep
 * the entire directory from being deleted.  To run using the data
 * file, set the environment variable "mapreduce.pipes.commandfile"
 * to point to the file./* w w  w  . j  a v  a  2 s.  com*/
 * @param conf the configuration to check
 * @return will the framework save the command file?
 */
public static boolean getKeepCommandFile(Configuration conf) {
    return conf.getBoolean(Submitter.PRESERVE_COMMANDFILE, false);
}

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From source file:it.crs4.seal.demux.DemuxReducer.java

License:Open Source License

public void setup(String localSampleSheetPath, Configuration conf) throws IOException {
    // load the sample sheet
    Path path = new Path(localSampleSheetPath).makeQualified(FileSystem.getLocal(conf));
    SampleSheet sampleSheet;//from w ww.ja v  a 2  s  .  c  o m
    try {
        sampleSheet = DemuxUtils.loadSampleSheet(path, conf);
    } catch (SampleSheet.FormatException e) {
        throw new RuntimeException("Error loading sample sheet.  Message: " + e.getMessage());
    }
    barcodeLookup = new BarcodeLookup(sampleSheet,
            conf.getInt(Demux.CONF_MAX_MISMATCHES, Demux.DEFAULT_MAX_MISMATCHES));

    expectIndexRead = !conf.getBoolean(Demux.CONF_NO_INDEX_READS, false);
    separatesReads = conf.getBoolean(Demux.CONF_SEPARATE_READS, false);
}

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From source file:it.crs4.seal.prq.PrqOptionParser.java

License:Open Source License

@Override
protected CommandLine parseOptions(Configuration conf, String[] args) throws IOException, ParseException {
    conf.setInt(MinBasesThresholdConfigName, DefaultMinBasesThreshold);
    conf.setBoolean(DropFailedFilterConfigName, DropFailedFilterDefault);
    conf.setBoolean(WarningOnlyIfUnpairedConfigName, WarningOnlyIfUnpairedDefault);
    conf.setInt(NumReadsExpectedConfigName, NumReadsExpectedDefault);

    CommandLine line = super.parseOptions(conf, args);

    /* **** handle deprected properties **** */
    if (conf.get(PrqOptionParser.OLD_INPUT_FORMAT_CONF) != null) {
        throw new ParseException("The property " + PrqOptionParser.OLD_INPUT_FORMAT_CONF
                + " is no longer supported.\n" + "Please use the command line option --input-format instead.");
    }/*  w ww.  j  a  v  a  2 s .co m*/

    Utils.checkDeprecatedProp(conf, LOG, MinBasesThresholdConfigName_deprecated, MinBasesThresholdConfigName);
    Utils.checkDeprecatedProp(conf, LOG, DropFailedFilterConfigName_deprecated, DropFailedFilterConfigName);
    Utils.checkDeprecatedProp(conf, LOG, WarningOnlyIfUnpairedConfigName_deprecated,
            WarningOnlyIfUnpairedConfigName);

    // Let the deprecated properties override the new ones, unless the new ones have a non-default value.
    // If the new property has a non-default value, it must have been set by the user.
    // If, on the other hand, the deprecated property has a value, it must have been set by the user since
    // we're not setting them here.
    if (conf.get(MinBasesThresholdConfigName_deprecated) != null
            && conf.getInt(MinBasesThresholdConfigName, DefaultMinBasesThreshold) == DefaultMinBasesThreshold) {
        conf.setInt(MinBasesThresholdConfigName,
                conf.getInt(MinBasesThresholdConfigName_deprecated, DefaultMinBasesThreshold));
    }

    if (conf.get(DropFailedFilterConfigName_deprecated) != null && conf.getBoolean(DropFailedFilterConfigName,
            DropFailedFilterDefault) == DropFailedFilterDefault) {
        conf.setBoolean(DropFailedFilterConfigName,
                conf.getBoolean(DropFailedFilterConfigName_deprecated, DropFailedFilterDefault));
    }

    if (conf.get(WarningOnlyIfUnpairedConfigName_deprecated) != null
            && conf.getBoolean(WarningOnlyIfUnpairedConfigName,
                    WarningOnlyIfUnpairedDefault) == WarningOnlyIfUnpairedDefault) {
        conf.setBoolean(WarningOnlyIfUnpairedConfigName,
                conf.getBoolean(WarningOnlyIfUnpairedConfigName_deprecated, WarningOnlyIfUnpairedDefault));
    }

    /* **** end handle deprecated properties **** */

    if (line.hasOption(opt_traditionalIds.getOpt()))
        conf.setBoolean(PairReadsQSeq.PRQ_CONF_TRADITIONAL_IDS, true);

    if (line.hasOption(opt_numReads.getOpt())) {
        int numReads;
        try {
            numReads = Integer.valueOf(line.getOptionValue(opt_numReads.getOpt()));
            if (numReads <= 0)
                throw new ParseException("Number of reads per fragment must be >= 0 (got " + numReads + ")");
            if (numReads > 2) {
                throw new ParseException(
                        "Working with more than two reads per template is not supported at the moment.\n"
                                + "If you're interested in seeing this feature implemented contact the Seal developers.");
            }
        } catch (NumberFormatException e) {
            throw new ParseException(e.getMessage());
        }
        conf.setInt(NumReadsExpectedConfigName, numReads);
    }

    // set number of reduce tasks to use
    conf.set(ClusterUtils.NUM_RED_TASKS_PROPERTY, String.valueOf(getNReduceTasks()));
    return line;
}

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From source file:it.crs4.seal.recab.RecabTableMapper.java

License:Open Source License

public void setup(VariantReader reader, IMRContext<Text, ObservationCount> context, Configuration conf)
        throws IOException {
    this.context = context;
    snps = new ArrayVariantTable();
    LOG.info("Using " + snps.getClass().getName() + " snp table implementation.");
    LOG.info("loading known variation sites.");
    snps.load(reader);/*from ww  w .j a v a  2s.  c  o  m*/
    if (LOG.isInfoEnabled())
        LOG.info("loaded " + snps.size() + " known variation sites.");

    referenceCoordinates = new ArrayList<Integer>(200);
    referenceMatches = new ArrayList<Boolean>(200);

    // TODO:  make it configurable
    covariateList = new ArrayList<Covariate>(5);
    covariateList.add(new ReadGroupCovariate(conf));
    covariateList.add(new QualityCovariate());
    covariateList.add(new CycleCovariate());
    covariateList.add(new DinucCovariate());

    // set counters
    for (BaseCounters c : BaseCounters.class.getEnumConstants())
        context.increment(c, 0);

    for (ReadCounters c : ReadCounters.class.getEnumConstants())
        context.increment(c, 0);

    skipKnownVariantPositions = conf.getBoolean(CONF_SKIP_KNOWN_VAR_SITES, true);
    if (!skipKnownVariantPositions)
        LOG.warn("Not skipping known variant sites.  This is not recommended for regular usage.");
}

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From source file:kdp.jobcontrol.ControlledJob.java

License:Apache License

/**
 * Submit this job to mapred. The state becomes RUNNING if submission is
 * successful, FAILED otherwise./* w ww  . j av  a 2  s.c o  m*/
 */
protected synchronized void submit() {
    try {
        Configuration conf = job.getConfiguration();
        if (conf.getBoolean(CREATE_DIR, false)) {
            FileSystem fs = FileSystem.get(conf);
            Path inputPaths[] = FileInputFormat.getInputPaths(job);
            for (int i = 0; i < inputPaths.length; i++) {
                if (!fs.exists(inputPaths[i])) {
                    try {
                        fs.mkdirs(inputPaths[i]);
                    } catch (IOException e) {

                    }
                }
            }
        }
        if (requiredCounters != null) {
            for (RequiredCounter counter : requiredCounters) {
                conf.set(counter.getPropertyName(), Long.toString(counter.getCounter()));
            }
        }
        job.submit();
        this.state = State.RUNNING;
    } catch (Exception ioe) {
        this.state = State.FAILED;
        this.message = StringUtils.stringifyException(ioe);
    }
}

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From source file:kogiri.common.hadoop.io.format.fasta.FastaReadDescriptionInputFormat.java

License:Open Source License

public static boolean isSplitable(Configuration conf) {
    return conf.getBoolean(CONF_SPLITABLE, true);
}

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From source file:ldbc.snb.datagen.generator.CommentGenerator.java

public CommentGenerator(TextGenerator generator, LikeGenerator likeGenerator, Configuration conf) {
    this.generator = generator;
    this.likeGenerator_ = likeGenerator;
    this.comment_ = new Comment();
    this.richRdf = conf.getBoolean("ldbc.snb.datagen.generator.richRdf", false);
}

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From source file:ldbc.snb.datagen.generator.DatagenParams.java

License:Open Source License

public static void readConf(Configuration conf) {
    try {//from w  ww.  j a va  2 s .co  m

        ParameterNames values[] = ParameterNames.values();
        for (int i = 0; i < values.length; ++i) {
            if (conf.get(values[i].toString()) == null) {
                throw new IllegalStateException("Missing " + values[i].toString() + " parameter");
            }
        }

        cellSize = Short.parseShort(conf.get(ParameterNames.CELL_SIZE.toString()));
        numberOfCellPerWindow = Integer.parseInt(conf.get(ParameterNames.NUM_CELL_WINDOW.toString()));
        minNumFriends = Integer.parseInt(conf.get(ParameterNames.MIN_FRIENDS.toString()));
        maxNumFriends = Integer.parseInt(conf.get(ParameterNames.MAX_FRIENDS.toString()));
        friendRejectRatio = Double.parseDouble(conf.get(ParameterNames.FRIEND_REJECT.toString()));
        friendReApproveRatio = Double.parseDouble(conf.get(ParameterNames.FRIEND_REACCEPT.toString()));
        minNumTagsPerUser = Integer.parseInt(conf.get(ParameterNames.USER_MIN_TAGS.toString()));
        maxNumTagsPerUser = Integer.parseInt(conf.get(ParameterNames.USER_MAX_TAGS.toString()));
        maxNumPostPerMonth = Integer.parseInt(conf.get(ParameterNames.USER_MAX_POST_MONTH.toString()));
        maxNumComments = Integer.parseInt(conf.get(ParameterNames.MAX_COMMENT_POST.toString()));
        limitProCorrelated = Double.parseDouble(conf.get(ParameterNames.LIMIT_CORRELATED.toString()));
        baseProbCorrelated = Double.parseDouble(conf.get(ParameterNames.BASE_CORRELATED.toString()));
        maxEmails = Integer.parseInt(conf.get(ParameterNames.MAX_EMAIL.toString()));
        maxCompanies = Integer.parseInt(conf.get(ParameterNames.MAX_EMAIL.toString()));
        probEnglish = Double.parseDouble(conf.get(ParameterNames.MAX_EMAIL.toString()));
        probSecondLang = Double.parseDouble(conf.get(ParameterNames.MAX_EMAIL.toString()));
        probAnotherBrowser = Double.parseDouble(conf.get(ParameterNames.OTHER_BROWSER_RATIO.toString()));
        minTextSize = Integer.parseInt(conf.get(ParameterNames.MIN_TEXT_SIZE.toString()));
        maxTextSize = Integer.parseInt(conf.get(ParameterNames.MAX_TEXT_SIZE.toString()));
        minCommentSize = Integer.parseInt(conf.get(ParameterNames.MIN_COMMENT_SIZE.toString()));
        maxCommentSize = Integer.parseInt(conf.get(ParameterNames.MAX_COMMENT_SIZE.toString()));
        ratioReduceText = Double.parseDouble(conf.get(ParameterNames.REDUCE_TEXT_RATIO.toString()));
        minLargePostSize = Integer.parseInt(conf.get(ParameterNames.MIN_LARGE_POST_SIZE.toString()));
        maxLargePostSize = Integer.parseInt(conf.get(ParameterNames.MAX_LARGE_POST_SIZE.toString()));
        minLargeCommentSize = Integer.parseInt(conf.get(ParameterNames.MIN_LARGE_COMMENT_SIZE.toString()));
        maxLargeCommentSize = Integer.parseInt(conf.get(ParameterNames.MAX_LARGE_COMMENT_SIZE.toString()));
        ratioLargePost = Double.parseDouble(conf.get(ParameterNames.LARGE_POST_RATIO.toString()));
        ratioLargeComment = Double.parseDouble(conf.get(ParameterNames.LARGE_COMMENT_RATIO.toString()));
        maxNumLike = Integer.parseInt(conf.get(ParameterNames.MAX_NUM_LIKE.toString()));
        maxNumPhotoAlbumsPerMonth = Integer.parseInt(conf.get(ParameterNames.MAX_PHOTOALBUM.toString()));
        maxNumPhotoPerAlbums = Integer.parseInt(conf.get(ParameterNames.MAX_PHOTO_PER_ALBUM.toString()));
        maxNumGroupCreatedPerUser = Integer.parseInt(conf.get(ParameterNames.USER_MAX_GROUP.toString()));
        maxNumMemberGroup = Integer.parseInt(conf.get(ParameterNames.MAX_GROUP_MEMBERS.toString()));
        groupModeratorProb = Double.parseDouble(conf.get(ParameterNames.GROUP_MODERATOR_RATIO.toString()));
        maxNumGroupPostPerMonth = Integer.parseInt(conf.get(ParameterNames.GROUP_MAX_POST_MONTH.toString()));
        missingRatio = Double.parseDouble(conf.get(ParameterNames.MISSING_RATIO.toString()));
        missingStatusRatio = Double.parseDouble(conf.get(ParameterNames.STATUS_MISSING_RATIO.toString()));
        probSingleStatus = Double.parseDouble(conf.get(ParameterNames.STATUS_SINGLE_RATIO.toString()));
        probDiffIPinTravelSeason = Double
                .parseDouble(conf.get(ParameterNames.DIFFERENT_IP_IN_TRAVEL_RATIO.toString()));
        probDiffIPnotTravelSeason = Double
                .parseDouble(conf.get(ParameterNames.DIFFERENT_IP_NOT_TRAVEL_RATIO.toString()));
        probUnCorrelatedCompany = Double
                .parseDouble(conf.get(ParameterNames.COMPANY_UNCORRELATED_RATIO.toString()));
        probUnCorrelatedOrganization = Double
                .parseDouble(conf.get(ParameterNames.UNIVERSITY_UNCORRELATED_RATIO.toString()));
        probTopUniv = Double.parseDouble(conf.get(ParameterNames.BEST_UNIVERSTY_RATIO.toString()));
        maxNumPopularPlaces = Integer.parseInt(conf.get(ParameterNames.MAX_POPULAR_PLACES.toString()));
        probPopularPlaces = Double.parseDouble(conf.get(ParameterNames.POPULAR_PLACE_RATIO.toString()));
        tagCountryCorrProb = Double.parseDouble(conf.get(ParameterNames.TAG_UNCORRELATED_COUNTRY.toString()));
        flashmobTagsPerMonth = Integer.parseInt(conf.get(ParameterNames.FLASHMOB_TAGS_PER_MONTH.toString()));
        probInterestFlashmobTag = Double
                .parseDouble(conf.get(ParameterNames.PROB_INTEREST_FLASHMOB_TAG.toString()));
        probRandomPerLevel = Double.parseDouble(conf.get(ParameterNames.PROB_RANDOM_PER_LEVEL.toString()));
        maxNumFlashmobPostPerMonth = Integer
                .parseInt(conf.get(ParameterNames.MAX_NUM_FLASHMOB_POST_PER_MONTH.toString()));
        maxNumGroupFlashmobPostPerMonth = Integer
                .parseInt(conf.get(ParameterNames.MAX_NUM_GROUP_FLASHMOB_POST_PER_MONTH.toString()));
        maxNumTagPerFlashmobPost = Integer
                .parseInt(conf.get(ParameterNames.MAX_NUM_TAG_PER_FLASHMOB_POST.toString()));
        flashmobTagMinLevel = Double.parseDouble(conf.get(ParameterNames.FLASHMOB_TAG_MIN_LEVEL.toString()));
        flashmobTagMaxLevel = Double.parseDouble(conf.get(ParameterNames.FLASHMOB_TAG_MAX_LEVEL.toString()));
        flashmobTagDistExp = Double.parseDouble(conf.get(ParameterNames.FLASHMOB_TAG_DIST_EXP.toString()));
        updatePortion = Double.parseDouble(conf.get(ParameterNames.UPDATE_PORTION.toString()));
        blockSize = Integer.parseInt(conf.get(ParameterNames.BLOCK_SIZE.toString()));
    } catch (Exception e) {
        System.out.println("Error reading scale factors");
        System.err.println(e.getMessage());
        System.exit(-1);
    }

    try {
        numPersons = Integer.parseInt(conf.get("ldbc.snb.datagen.generator.numPersons"));
        startYear = Integer.parseInt(conf.get("ldbc.snb.datagen.generator.startYear"));
        numYears = Integer.parseInt(conf.get("ldbc.snb.datagen.generator.numYears"));
        endYear = startYear + numYears;
        compressed = conf.getBoolean("ldbc.snb.datagen.serializer.compressed", false);
        numThreads = conf.getInt("ldbc.snb.datagen.generator.numThreads", 1);
        updateStreams = conf.getBoolean("ldbc.snb.datagen.serializer.updateStreams", false);
        numPartitions = conf.getInt("ldbc.snb.datagen.serializer.numPartitions", 1);
        numUpdatePartitions = conf.getInt("ldbc.snb.datagen.serializer.numUpdatePartitions", 1);
        deltaTime = conf.getInt("ldbc.snb.datagen.generator.deltaTime", 10000);
        outputDir = conf.get("ldbc.snb.datagen.serializer.outputDir");
        hadoopDir = outputDir + "/hadoop";
        socialNetworkDir = outputDir + "social_network";
        System.out.println(" ... Num Persons " + numPersons);
        System.out.println(" ... Start Year " + startYear);
        System.out.println(" ... Num Years " + numYears);
    } catch (Exception e) {
        System.err.println(e.getMessage());
        System.exit(-1);
    }
}

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