it.crs4.seal.common.Utils.java Source code

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Here is the source code for it.crs4.seal.common.Utils.java

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// Copyright (C) 2011-2012 CRS4.
//
// This file is part of Seal.
//
// Seal is free software: you can redistribute it and/or modify it
// under the terms of the GNU General Public License as published by the Free
// Software Foundation, either version 3 of the License, or (at your option)
// any later version.
//
// Seal is distributed in the hope that it will be useful, but
// WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
// or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
// for more details.
//
// You should have received a copy of the GNU General Public License along
// with Seal.  If not, see <http://www.gnu.org/licenses/>.

package it.crs4.seal.common;

import org.apache.hadoop.conf.Configuration;
import org.apache.commons.logging.Log;

import org.apache.hadoop.mapreduce.TaskAttemptContext;
import org.apache.hadoop.mapreduce.TaskAttemptID;

public class Utils {
    /**
     * Offset by which Sanger-style ASCII-encoded quality scores are shifted.
     */
    public static final int SANGER_OFFSET = 33;

    /**
     * Maximum encodable quality score for Sanger Phred+33 encoded base qualities.
     */
    public static final int SANGER_MAX = 62;

    /**
     * Offset by which Illumina-style ASCII-encoded quality scores are shifted.
     */
    public static final int ILLUMINA_OFFSET = 64;

    /**
     * Maximum encodable quality score for Illumina Phred+64 encoded base qualities.
     */
    public static final int ILLUMINA_MAX = 62;

    private Utils() {
    } // no instantiation

    /**
     * Given a number of parameters, return the first that is not null.
     * If all parameters are null then the result is null.
     */
    @SuppressWarnings("unchecked")
    public static <T extends Object> T firstNonNull(T... objects) {
        for (T o : objects) {
            if (o != null)
                return o;
        }
        return null;
    }

    /**
     * Warn the user that he's using a deprecated property.
     * If newProperty is provided, the message will suggest to the user to substitute uses
     * of the deprecatedProperty with the new one.
     */
    public static void deprecationWarning(Log log, String deprecatedProperty, String newProperty) {
        log.warn("Your configuration is using the deprecated property " + deprecatedProperty);
        if (newProperty == null)
            log.warn("You should update your configuration to avoid using it.  See the documentation for details.");
        else
            log.warn("You should update your configuration to replace it with " + newProperty
                    + ". See the documentation for details.");
    }

    /**
     * Check whether a deprecated property is used, and if so emit a warning.
     * @param deprecatedProperty The name of the deprecated property.
     * @param newProperty The name of the property that replaces the deprecated one, if any,
     *        to write a suggestion to the user.
     */
    public static void checkDeprecatedProp(Configuration conf, Log log, String deprecatedProperty,
            String newProperty) {
        if (conf.get(deprecatedProperty) != null)
            deprecationWarning(log, deprecatedProperty, newProperty);
    }

    /**
     * Substitute any characters to be avoided in a file name with '_'.
     */
    public static String sanitizeFilename(String name) {
        if (name.isEmpty())
            throw new IllegalArgumentException("Empty file name!");
        // replace all non-word characters (a word character is: [a-zA-Z_0-9]) except '.' and '-'
        return name.replaceAll("[\\W&&[^.-]]", "_");
    }

    /**
     * Hide the version-agnostic way we instantiate a TaskAttemptContext.
     *
     * The shift from Hadoop 1 to Hadoop 2 has changed TaskAttemptContext from
     * a class to an interface.  This creates an issue for us as we'd like to
     * support both versions.  To support both versions, we instantiate a
     * TaskAttemptContext through reflection and hide the mess in this method.
     */
    public static TaskAttemptContext getTaskAttemptContext(Configuration conf) {
        final String[] knownImplementations = new String[] {
                "org.apache.hadoop.mapreduce.task.TaskAttemptContextImpl",
                "org.apache.hadoop.mapreduce.TaskAttemptContext" };

        for (String name : knownImplementations) {
            TaskAttemptContext tac = createTACImplementation(name, conf);
            if (tac != null)
                return tac;
            // else, try again
        }
        // If we're here, it means we couldn't instantiate a TaskAttemptContext.
        // Only only option now is to throw an exception
        throw new RuntimeException("It seems this software isn't compatible with your\n"
                + " version of Hadoop.  Please file a bug report.  Message:\n"
                + "Couldn't instantiate a TaskAttemptContext");
    }

    private static TaskAttemptContext createTACImplementation(String fullName, Configuration conf) {
        try {
            return (TaskAttemptContext) Class.forName(fullName)
                    .getConstructor(Configuration.class, TaskAttemptID.class)
                    .newInstance(conf, new TaskAttemptID());
        } catch (ClassNotFoundException e) {
        } catch (NoSuchMethodException e) {
        } catch (Exception e) {
            System.err
                    .println("WARNING! Couldn't instantiate " + fullName + " though we found it. Exception: " + e);
        }
        return null;
    }

}