94 lines
3.4 KiB
Java
94 lines
3.4 KiB
Java
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/*
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* The Broad Institute
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* SOFTWARE COPYRIGHT NOTICE AGREEMENT
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* This software and its documentation are copyright 2009 by the
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* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
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*
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* This software is supplied without any warranty or guaranteed support whatsoever. Neither
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* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
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*/
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package edu.mit.broad.picard.util;
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import java.io.File;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.OutputStream;
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import edu.mit.broad.picard.PicardException;
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import edu.mit.broad.picard.io.IoUtil;
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/**
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* Util class for executing R scripts.
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*
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* @author Doug Voet
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*/
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public class RExecutor {
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private static final String R_EXE = "Rscript";
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/**
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* Executes the given R script that is stored in a file on the classpath. The script file
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* is read from the classpath and written to a temp file then executed by a call to Rscript.
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* Blocks until the R script is complete.
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*
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* @param rScriptName the fully qualified name of the classpath resource of the script
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* @param arguments any arguments required by the script
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* @return the return code of the R process
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*/
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public static int executeFromClasspath(String rScriptName, String... arguments) {
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File scriptFile = writeScriptFile(rScriptName);
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int returnCode = executeFromFile(scriptFile, arguments);
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scriptFile.delete();
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return returnCode;
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}
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/**
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* Executes the given R script that is stored in a file by a call to Rscript.
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* Blocks until the R script is complete.
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*
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* @param scriptFile the file object for the script
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* @param arguments any arguments required by the script
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* @return the return code of the R process
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*/
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public static int executeFromFile(File scriptFile, String... arguments) {
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String[] command = new String[arguments.length + 2];
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command[0] = R_EXE;
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command[1] = scriptFile.getAbsolutePath();
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System.arraycopy(arguments, 0, command, 2, arguments.length);
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return ProcessExecutor.execute(command);
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}
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/**
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* Writes the classpath resource named by rScriptName to the temp dir.
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*/
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private static File writeScriptFile(String rScriptName) {
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InputStream scriptStream = null;
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OutputStream scriptFileStream = null;
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try {
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scriptStream = RExecutor.class.getClassLoader().getResourceAsStream(rScriptName);
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if (scriptStream == null) {
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throw new IllegalArgumentException("Script [" + rScriptName + "] not found in classpath");
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}
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File scriptFile = File.createTempFile("script", ".R");
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scriptFileStream = IoUtil.openFileForWriting(scriptFile);
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IoUtil.copyStream(scriptStream, scriptFileStream);
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return scriptFile;
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} catch (IOException e) {
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throw new PicardException("Unexpected exception creating R script file", e);
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} finally {
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if (scriptStream != null) {
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try {
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scriptStream.close();
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} catch (IOException e) {
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}
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}
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if (scriptFileStream != null) {
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try {
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scriptFileStream.close();
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} catch (IOException e) {
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}
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}
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}
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}
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}
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