org.icgc.dcc.release.job.annotate.snpeff.SnpEffProcess.java Source code

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Here is the source code for org.icgc.dcc.release.job.annotate.snpeff.SnpEffProcess.java

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/*
 * Copyright (c) 2014 The Ontario Institute for Cancer Research. All rights reserved.                             
 *                                                                                                               
 * This program and the accompanying materials are made available under the terms of the GNU Public License v3.0.
 * You should have received a copy of the GNU General Public License along with                                  
 * this program. If not, see <http://www.gnu.org/licenses/>.                                                     
 *                                                                                                               
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY                           
 * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES                          
 * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT                           
 * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,                                
 * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED                          
 * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;                               
 * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER                              
 * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN                         
 * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */
package org.icgc.dcc.release.job.annotate.snpeff;

import static com.google.common.base.Charsets.UTF_8;
import static com.google.common.io.Resources.getResource;

import java.io.File;

import lombok.NonNull;
import lombok.SneakyThrows;
import lombok.val;
import lombok.experimental.Delegate;
import lombok.extern.slf4j.Slf4j;

import com.google.common.io.Files;
import com.google.common.io.Resources;

/**
 * Abstraction that manages the creating of the forked SnpEff process.
 */
@Slf4j
public class SnpEffProcess extends Process {

    /**
     * Configuration.
     */
    private final File jar;
    private final File java;
    private final File dataDir;
    private final String databaseVersion;

    /**
     * State.
     */
    @Delegate
    private final Process delegate;

    public SnpEffProcess(@NonNull File jar, @NonNull File java, @NonNull File dataDir,
            @NonNull String databaseVersion) {
        this.jar = jar;
        this.java = java;
        this.dataDir = dataDir;
        this.databaseVersion = databaseVersion;
        this.delegate = createProcess();
    }

    @SneakyThrows
    private Process createProcess() {
        val builder = new ProcessBuilder(getJavaPath(), "-Xmx4g", "-cp", getClassPath(), getMainClass(), "eff",
                "-cancer", "-v", "-geneId", "-sequenceOntology", "-noStats", "-noLog", "-c", getConfigFile(),
                databaseVersion);

        log.error("Process command: {}", builder.command());
        return builder.start();
    }

    @SneakyThrows
    private String getConfigFile() {
        // Template
        val contents = Resources.toString(getResource("snpEff.config"), UTF_8).replace("${dataDir}",
                dataDir.getAbsolutePath());

        val configFile = File.createTempFile("snpEff", ".config");

        log.info("Creating temporary configuration file at '{}'...", configFile);
        Files.write(contents, configFile, UTF_8);

        return configFile.getAbsolutePath();
    }

    private String getJavaPath() {
        return java.getAbsolutePath();
    }

    private String getMainClass() {
        // This cannot use SnpEff.class.getName() since we are not running Java 7 yet.
        // TODO: Use SnpEff.class.getName()
        return "ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff";
    }

    private String getClassPath() {
        return jar.getAbsolutePath();
    }

}