com.intel.genomicsdb.GenomicsDBConfiguration.java Source code

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Here is the source code for com.intel.genomicsdb.GenomicsDBConfiguration.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.conf.Configuration;

import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.LinkedList;
import java.util.List;
import java.util.Scanner;

/**
 * The configuration class enables users to use Java/Scala
 * to populate the input parameters of GenomicsDB. The first
 * version of the input format are JSON files. Through this
 * class, we provide a programmable interface. Note, that once
 * fully coded, this configuration object can be directly
 * passed from GATK4.0
 */
public class GenomicsDBConfiguration extends Configuration implements Serializable {

    public static final String LOADERJSON = "genomicsdb.input.loaderjsonfile";
    public static final String QUERYJSON = "genomicsdb.input.queryjsonfile";
    public static final String MPIHOSTFILE = "genomicsdb.input.mpi.hostfile";
    public static final String PARTITION_STRATEGY = "genomicsdb.partition.strategy";

    private Boolean produceCombinedVCF = false;
    private Boolean produceTileDBArray = false;
    private Integer segmentSize = 1000;
    private Integer nCellsPerTile = 1000;

    private LinkedList<GenomicsDBPartitionInfo> partitionInfoList = null;

    public GenomicsDBConfiguration(Configuration configuration) throws FileNotFoundException {
        super(configuration);
    }

    /**
     * Constructor with partition information
     * @param configuration  Existing configuration object (can contain Hadoop config values)
     * @param list  Contains partition information
     * @throws FileNotFoundException thrown when loader file not found
     */
    public GenomicsDBConfiguration(Configuration configuration, List<GenomicsDBPartitionInfo> list)
            throws FileNotFoundException {
        super(configuration);
        for (GenomicsDBPartitionInfo info : list) {
            addPartitions(info);
        }
    }

    // <String> left for backward compatibility to Java 7
    private ArrayList<String> hosts = new ArrayList<>();

    public GenomicsDBConfiguration setLoaderJsonFile(String path) {
        set(LOADERJSON, path);
        return this;
    }

    public GenomicsDBConfiguration setQueryJsonFile(String path) {
        set(QUERYJSON, path);
        return this;
    }

    /**
     * Host file contains the hosts where GenomicsDB instances reside.
     * This file can be a replica of the slaves file. For now, we have
     * kept it separate, can be merged later
     *
     * @param path  Full path of the host file
     * @return  GenomicsDBConfiguration object
     * @throws FileNotFoundException  If file not found, throw exception
     */
    public GenomicsDBConfiguration setHostFile(String path) throws FileNotFoundException {
        set(MPIHOSTFILE, path);

        Scanner scanner = new Scanner(new FileInputStream(path));
        while (scanner.hasNextLine()) {
            String host = scanner.nextLine();
            hosts.add(host);
        }
        return this;
    }

    List<String> getHosts() {
        return hosts;
    }

    /**
     * Set the partition strategy for underlying TileDB storage manager
     *
     * @param isRowPartitioned If true, data is partitioned as row major (ROW_MAJOR),
     *                         COL_MAJOR otherwise
     */
    void setPartitionStrategy(Boolean isRowPartitioned) {

        if (isRowPartitioned) {
            set(PARTITION_STRATEGY, String.valueOf(GenomicsDBPartitionStrategy.ROW_MAJOR()));
        } else {
            set(PARTITION_STRATEGY, String.valueOf(GenomicsDBPartitionStrategy.COL_MAJOR()));
        }
    }

    /**
     * Set the partition strategy for underlying TileDB storage manager
     *
     * @param partitionStrategy Partition strategy can be either column major
     *                           (COL_MAJOR) or row major (ROW_MAJOR)
     */
    void setPartitionStrategy(String partitionStrategy) {
        if (partitionStrategy.equals("ROW_MAJOR")) {
            set(PARTITION_STRATEGY, String.valueOf(GenomicsDBPartitionStrategy.ROW_MAJOR()));
        } else if (partitionStrategy.equals("COL_MAJOR")) {
            set(PARTITION_STRATEGY, String.valueOf(GenomicsDBPartitionStrategy.COL_MAJOR()));
        }
    }

    private void addPartitions(GenomicsDBPartitionInfo genomicsDBPartitionInfo) {
        if (partitionInfoList == null) {
            partitionInfoList = new LinkedList<>();
        }
        partitionInfoList.push(genomicsDBPartitionInfo);
    }
}