org.mskcc.cbio.importer.util.Shell.java Source code

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Here is the source code for org.mskcc.cbio.importer.util.Shell.java

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/** Copyright (c) 2012 Memorial Sloan-Kettering Cancer Center.
**
** This library is free software; you can redistribute it and/or modify it
** under the terms of the GNU Lesser General Public License as published
** by the Free Software Foundation; either version 2.1 of the License, or
** any later version.
**
** 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.  See
** the GNU Lesser General Public License for more details.
**
** You should have received a copy of the GNU Lesser General Public License
** along with this library; if not, write to the Free Software Foundation,
** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
**/

// package
package org.mskcc.cbio.importer.util;

// imports
import org.mskcc.cbio.importer.Fetcher;
import org.mskcc.cbio.importer.Importer;
import org.mskcc.cbio.importer.model.ReferenceMetadata;

import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

import java.io.File;
import java.util.List;
import java.util.ArrayList;

import java.lang.reflect.Method;

/**
 * Class which provides commandline execution.
 */
public class Shell {

    // our logger
    private static Log LOG = LogFactory.getLog(Shell.class);

    /**
     * Function which executes either a fetcher or importer based on caller.  Class args are
     * required if we are instantiating an instance of a class that implements Fetcher or Importer interface.
     *
     * @param referenceMetadata ReferenceMetadata
     * @param caller Object
     * @param classArgs Object[] 
     * @param workingDirectory String
     * @return boolean
     */
    public static boolean exec(ReferenceMetadata referenceMetadata, Object caller, Object[] classArgs,
            String workingDirectory) {

        String command = null;
        List<String> commandArgs = null;
        if (caller instanceof Fetcher) {
            command = referenceMetadata.getFetcherName();
            commandArgs = referenceMetadata.getFetcherArgs();
        } else if (caller instanceof Importer) {
            command = referenceMetadata.getImporterName();
            commandArgs = referenceMetadata.getImporterArgs();
        } else {
            if (LOG.isInfoEnabled()) {
                LOG.info("exec() unrecognized caller type:" + caller.getClass().getName() + ", exiting...");
            }
            return false;
        }

        // sanity check
        if (command == null || commandArgs == null) {
            if (LOG.isInfoEnabled()) {
                LOG.info("exec(), invalid command or command args, exiting...");
            }
            return false;
        } else if (LOG.isInfoEnabled()) {
            LOG.info("exec(), command: " + command);
            LOG.info("exec(), commandArgs: " + commandArgs);
        }

        boolean toReturn = false;
        try {
            if (command.contains("org.mskcc.cbio")) {
                // we are either going to use a cgds package importer which has a main method
                // or one of our own classes which implements the Importer interface.
                // Check for a main method, if found, use it, otherwise assume we have a class
                // that implements the Importer interface.
                Method mainMethod = ClassLoader.getMethod(command, "main");
                if (mainMethod != null) {
                    mainMethod.invoke(null, (Object) commandArgs.toArray(new String[0]));
                } else {
                    Importer importer = (Importer) ClassLoader.getInstance(command, classArgs);
                    importer.importReferenceData(referenceMetadata);
                }
                toReturn = true;
            }
            // some type of script
            else {
                List<String> commandList = new ArrayList<String>();
                commandList.add(command);
                commandList.addAll(commandArgs);
                toReturn = Shell.exec(commandList, workingDirectory);
            }
        } catch (Exception e) {
            if (LOG.isInfoEnabled()) {
                LOG.info(e.toString() + " thrown during shell command: " + e.getMessage() + ", aborting...");
            }
        }

        // should not get here
        return toReturn;
    }

    /**
     * Executes the given command via java ProcessBuilder.
     *
     * @param command List<String>
     * @param workingDirectory String
     * @return boolean
     */
    public static boolean exec(List<String> command, String workingDirectory) {

        if (LOG.isInfoEnabled()) {
            LOG.info("exec():, command: " + command);
            LOG.info("exec():, workingDirectory: " + workingDirectory);
        }

        try {
            ProcessBuilder processBuilder = new ProcessBuilder(command);
            processBuilder.directory(new File(workingDirectory));
            Process process = processBuilder.start();
            StreamSink stdoutSink = new StreamSink(process.getInputStream());
            StreamSink stderrSink = new StreamSink(process.getErrorStream());
            stdoutSink.start();
            stderrSink.start();
            process.waitFor();
            return process.exitValue() == 0;
        } catch (Exception e) {
            if (LOG.isInfoEnabled()) {
                LOG.info(e.toString() + " thrown during shell command: " + command);
            }
            return false;
        }
    }
}