/*
* The MIT License
*
* Copyright (c) 2009 The Broad Institute
*
* 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 picard.util;
import htsjdk.samtools.util.CollectionUtil;
import htsjdk.samtools.util.IOUtil;
import htsjdk.samtools.util.Log;
import htsjdk.samtools.util.ProcessExecutor;
import picard.PicardException;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.util.Arrays;
/**
* Util class for executing R scripts.
*
* @author Doug Voet (dvoet at broadinstitute dot org)
*/
public class RExecutor {
private static final Log LOG = Log.getInstance(RExecutor.class);
private static final String R_EXE = "Rscript";
/**
* Executes the given R script that is stored in a file on the classpath. The script file
* is read from the classpath and written to a temp file then executed by a call to Rscript.
* Blocks until the R script is complete.
*
* @param rScriptName the fully qualified name of the classpath resource of the script
* @param arguments any arguments required by the script
* @return the return code of the R process
*/
public static int executeFromClasspath(final String rScriptName, final String... arguments) {
final File scriptFile = writeScriptFile(rScriptName);
final int returnCode = executeFromFile(scriptFile, arguments);
htsjdk.samtools.util.IOUtil.deleteFiles(scriptFile);
return returnCode;
}
/**
* Executes the given R script that is stored in a file by a call to Rscript.
* Blocks until the R script is complete.
*
* @param scriptFile the file object for the script
* @param arguments any arguments required by the script
* @return the return code of the R process
*/
public static int executeFromFile(final File scriptFile, final String... arguments) {
final String[] command = new String[arguments.length + 2];
command[0] = R_EXE;
command[1] = scriptFile.getAbsolutePath();
System.arraycopy(arguments, 0, command, 2, arguments.length);
LOG.info(String.format("Executing R script via command: %s", CollectionUtil.join(Arrays.asList(command), " ")));
return ProcessExecutor.execute(command);
}
/**
* Writes the classpath resource named by rScriptName to the temp dir.
*/
private static File writeScriptFile(final String rScriptName) {
InputStream scriptStream = null;
OutputStream scriptFileStream = null;
try {
scriptStream = RExecutor.class.getClassLoader().getResourceAsStream(rScriptName);
if (scriptStream == null) {
throw new IllegalArgumentException("Script [" + rScriptName + "] not found in classpath");
}
final File scriptFile = File.createTempFile("script", ".R");
scriptFileStream = IOUtil.openFileForWriting(scriptFile);
IOUtil.copyStream(scriptStream, scriptFileStream);
return scriptFile;
} catch (IOException e) {
throw new PicardException("Unexpected exception creating R script file", e);
} finally {
if (scriptStream != null) {
try {
scriptStream.close();
} catch (IOException ignored) {
}
}
if (scriptFileStream != null) {
try {
scriptFileStream.close();
} catch (IOException ignored) {
}
}
}
}
}