com.intel.genomicsdb.GenomicsDBInputSplit.java Source code

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Here is the source code for com.intel.genomicsdb.GenomicsDBInputSplit.java

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/*
 * The MIT License (MIT)
 * Copyright (c) 2016 Intel Corporation
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy of
 * this software and associated documentation files (the "Software"), to deal in
 * the Software without restriction, including without limitation the rights to
 * use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
 * the Software, and to permit persons to whom the Software is furnished to do so,
 * subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in all
 * copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
 * FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
 * COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
 * IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
 * CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */

package com.intel.genomicsdb;

import org.apache.hadoop.io.Writable;
import org.apache.hadoop.mapreduce.InputSplit;
import org.apache.log4j.Logger;
import org.apache.spark.Partition;
import java.io.DataInput;
import java.io.DataOutput;
import java.io.IOException;
import java.net.InetAddress;

public class GenomicsDBInputSplit extends InputSplit implements Writable {

    // Note that for now the assumption is that there is
    // one GenomicsDB instance per node, hence one host
    // per split
    String[] hosts;
    long length = 0;

    Logger logger = Logger.getLogger(GenomicsDBInputSplit.class);

    /**
     * Default constructor
     */
    public GenomicsDBInputSplit() {
    }

    public GenomicsDBInputSplit(long length) {
        this.length = length;
    }

    public void write(DataOutput dataOutput) throws IOException {
        dataOutput.writeLong(this.length);
    }

    public void readFields(DataInput dataInput) throws IOException {
        hosts = null;
        length = dataInput.readLong();
    }

    public long getLength() throws IOException, InterruptedException {
        return this.length;
    }

    /**
     * Called from {@link org.apache.spark.rdd.NewHadoopRDD#getPreferredLocations(Partition)}
     *
     * @return locations  The values of locations or nodes are passed from host file
     *                   in GenomicsDBConfiguration or hadoopConfiguration in SparkContext
     */
    public String[] getLocations() throws IOException, InterruptedException {
        hosts = new String[1];
        hosts[0] = InetAddress.getLocalHost().getHostName();
        return hosts;
    }
}