org.cbioportal.database.DatabaseAnnotator.java Source code

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Here is the source code for org.cbioportal.database.DatabaseAnnotator.java

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/*
 * Copyright (c) 2017 Memorial Sloan-Kettering Cancer Center.
 *
 * This library 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. The software and documentation provided hereunder
 * is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no
 * obligations to provide maintenance, support, updates, enhancements or
 * modifications. In no event shall Memorial Sloan-Kettering Cancer Center be
 * liable to any party for direct, indirect, special, incidental or
 * consequential damages, including lost profits, arising out of the use of this
 * software and its documentation, even if Memorial Sloan-Kettering Cancer
 * Center has been advised of the possibility of such damage.
 */

/*
 * This file is part of cBioPortal CMO-Pipelines.
 *
 * cBioPortal is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Affero General Public License as
 * published by the Free Software Foundation, either version 3 of the
 * License.
 *
 * This program 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 Affero General Public License for more details.
 *
 * You should have received a copy of the GNU Affero General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
*/

package org.cbioportal.database;

import org.cbioportal.database.annotator.BatchConfiguration;
import org.apache.commons.cli.*;
import org.apache.commons.cli.Options;
import org.springframework.boot.SpringApplication;
import org.springframework.boot.autoconfigure.SpringBootApplication;
import org.springframework.context.ConfigurableApplicationContext;
import org.springframework.batch.core.*;
import org.springframework.batch.core.launch.JobLauncher;
import org.apache.log4j.Logger;

/**
 *
 * @author heinsz
 */

@SpringBootApplication
public class DatabaseAnnotator {

    private static Logger log = Logger.getLogger(DatabaseAnnotator.class);

    private static Options getOptions(String[] args) {
        Options gnuOptions = new Options();
        gnuOptions.addOption("h", "help", false, "shows this help document and quits.");
        gnuOptions.addOption("i", "isoform", true, "Isoform desired for annotation. mskcc or uniprot");
        gnuOptions.addOption("s", "studies", true, "Colon (:) delimited studies)");
        return gnuOptions;
    }

    private static void help(Options gnuOptions, int exitStatus) {
        HelpFormatter helpFormatter = new HelpFormatter();
        helpFormatter.printHelp("Darwin Pipeline", gnuOptions);
        System.exit(exitStatus);
    }

    private static void launchJob(String[] args, String isoform, String studies) throws Exception {
        SpringApplication app = new SpringApplication(DatabaseAnnotator.class);

        ConfigurableApplicationContext ctx = app.run(args);
        JobLauncher jobLauncher = ctx.getBean(JobLauncher.class);
        JobParameters jobParameters = new JobParametersBuilder().addString("isoform", isoform)
                .addString("studies", studies).toJobParameters();
        Job databaseAnnotatorJob = ctx.getBean(BatchConfiguration.DATABASE_ANNOTATOR_JOB, Job.class);
        JobExecution jobExecution = jobLauncher.run(databaseAnnotatorJob, jobParameters);
        ctx.close();
    }

    public static void main(String[] args) throws Exception {
        Options gnuOptions = DatabaseAnnotator.getOptions(args);
        CommandLineParser parser = new GnuParser();
        CommandLine commandLine = parser.parse(gnuOptions, args);
        if (commandLine.hasOption("h") || !commandLine.hasOption("i")) {
            help(gnuOptions, 0);
        }

        launchJob(args, commandLine.getOptionValue("isoform"), commandLine.getOptionValue("studies"));
    }
}