AlignmentRegionCoverageHBaseDataWriterTest.java

/*
 * Copyright 2015-2016 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */

package org.opencb.opencga.storage.alignment;

import org.apache.hadoop.hbase.HBaseConfiguration;
import org.junit.Test;
import org.opencb.commons.bioformats.alignment.AlignmentRegion;
import org.opencb.commons.bioformats.alignment.io.readers.AlignmentDataReader;
import org.opencb.commons.bioformats.alignment.io.readers.AlignmentRegionDataReader;
import org.opencb.commons.bioformats.alignment.sam.io.AlignmentSamDataReader;
import org.opencb.commons.bioformats.alignment.tasks.AlignmentCoverageCalculatorTask;
import org.opencb.commons.io.DataWriter;
import org.opencb.commons.run.Runner;
import org.opencb.commons.run.Task;
import org.opencb.commons.test.GenericTest;
import org.opencb.opencga.core.auth.IllegalOpenCGACredentialsException;
import org.opencb.opencga.core.auth.MonbaseCredentials;
import org.opencb.opencga.storage.alignment.hbase.AlignmentRegionCoverageHBaseDataWriter;

import java.io.IOException;
import java.util.LinkedList;
import java.util.List;

/**
 * Created with IntelliJ IDEA.
 * User: jcoll
 * Date: 2/20/14
 * Time: 7:12 PM
 * To change this template use File | Settings | File Templates.
 */
public class AlignmentRegionCoverageHBaseDataWriterTest extends GenericTest {

    String shortSam = getClass().getResource("/alignments_small.sam").getFile();
    String longBam = "/home/jcoll/Documents/HG00096.chrom20.ILLUMINA.bwa.GBR.low_coverage.20120522.bam";

    String usedFile = longBam;

    @Test
        public void openClose_Test(){
        String tableName = "coverage_test_jj";
        MonbaseCredentials credentials = null;
        org.apache.hadoop.conf.Configuration config;

        // Credentials for the query builder
        try {
            credentials = new MonbaseCredentials("172.24.79.30", 60010, "172.24.79.30", 2181, "localhost", 9999, tableName, "cgonzalez", "cgonzalez");
        } catch (IllegalOpenCGACredentialsException e) {
            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
        }


        // HBase configuration with the active credentials
        config = HBaseConfiguration.create();
        config.set("hbase.master", credentials.getHbaseMasterHost() + ":" + credentials.getHbaseMasterPort());
        config.set("hbase.zookeeper.quorum", credentials.getHbaseZookeeperQuorum());
        config.set("hbase.zookeeper.property.clientPort", String.valueOf(credentials.getHbaseZookeeperClientPort()));



        AlignmentRegionCoverageHBaseDataWriter alignmentRegionCoverageHBaseDataWriter =
                new AlignmentRegionCoverageHBaseDataWriter(config, tableName);

        alignmentRegionCoverageHBaseDataWriter.open();
        alignmentRegionCoverageHBaseDataWriter.pre();

        alignmentRegionCoverageHBaseDataWriter.post();
        alignmentRegionCoverageHBaseDataWriter.close();



    }

    @Test
    public void AlignmentRegionCoverageHBaseDataWriterTest_1(){
        System.out.println("Iniciamos");
        //Reader
        AlignmentDataReader alignmentDataReader = new AlignmentSamDataReader(usedFile);
        AlignmentRegionDataReader alignmentRegionDataReader = new AlignmentRegionDataReader(alignmentDataReader,20000);


        //Task
        List<Task<AlignmentRegion>> tasks = new LinkedList<>();
        AlignmentCoverageCalculatorTask alignmentCoverageCalculatorTask =
                new AlignmentCoverageCalculatorTask();
       // alignmentCoverageCalculatorTask.addMeanCoverageCalculator(10   ,"010");
        //alignmentCoverageCalculatorTask.addMeanCoverageCalculator(100  ,"100");
        alignmentCoverageCalculatorTask.addMeanCoverageCalculator(1000 ,"1K");
        alignmentCoverageCalculatorTask.addMeanCoverageCalculator(10000,"10K");
        tasks.add(alignmentCoverageCalculatorTask);
        //Writer
        List<DataWriter<AlignmentRegion>> writers = new LinkedList<>();
        // HBase configuration with the active credentials
        String tableName = "coverage_test_2_jj";
        MonbaseCredentials credentials = null;
        org.apache.hadoop.conf.Configuration config;


        // Credentials for the query builder
        try {
            credentials = new MonbaseCredentials("172.24.79.30", 60010, "172.24.79.30", 2181, "localhost", 9999, tableName, "jcoll", "jcoll");
        } catch (IllegalOpenCGACredentialsException e) {
            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
        }

        // HBase configuration with the active credentials
        config = HBaseConfiguration.create();
        config.set("hbase.master", credentials.getHbaseMasterHost() + ":" + credentials.getHbaseMasterPort());
        config.set("hbase.zookeeper.quorum", credentials.getHbaseZookeeperQuorum());
        config.set("hbase.zookeeper.property.clientPort", String.valueOf(credentials.getHbaseZookeeperClientPort()));



        AlignmentRegionCoverageHBaseDataWriter alignmentRegionCoverageHBaseDataWriter =
                new AlignmentRegionCoverageHBaseDataWriter(config, tableName);
        alignmentRegionCoverageHBaseDataWriter.setSample("Sample1");
        alignmentRegionCoverageHBaseDataWriter.setColumnFamilyName("Family1");


        writers.add(alignmentRegionCoverageHBaseDataWriter);

        Runner<AlignmentRegion> runner = new Runner<>(alignmentRegionDataReader,writers,tasks);
        runner.setBatchSize(1);

        System.out.println("runner.run()");

        try {
            runner.run();
        } catch (IOException e) {
            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
        }
        System.out.println("fin");

    }
}