Mercurial > repos > yufei-luo > s_mart
view smart_toolShed/SMART/Java/PythonProgramFinder.java @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
---|---|
date | Thu, 17 Jan 2013 10:52:14 -0500 |
parents | |
children |
line wrap: on
line source
/** * * Copyright INRA-URGI 2009-2010 * * This software is governed by the CeCILL license under French law and * abiding by the rules of distribution of free software. You can use, * modify and/ or redistribute the software under the terms of the CeCILL * license as circulated by CEA, CNRS and INRIA at the following URL * "http://www.cecill.info". * * As a counterpart to the access to the source code and rights to copy, * modify and redistribute granted by the license, users are provided only * with a limited warranty and the software's author, the holder of the * economic rights, and the successive licensors have only limited * liability. * * In this respect, the user's attention is drawn to the risks associated * with loading, using, modifying and/or developing or reproducing the * software by the user in light of its specific status of free software, * that may mean that it is complicated to manipulate, and that also * therefore means that it is reserved for developers and experienced * professionals having in-depth computer knowledge. Users are therefore * encouraged to load and test the software's suitability as regards their * requirements in conditions enabling the security of their systems and/or * data to be ensured and, more generally, to use and operate it in the * same conditions as regards security. * * The fact that you are presently reading this means that you have had * knowledge of the CeCILL license and that you accept its terms. * */ import java.io.*; import java.util.*; public class PythonProgramFinder { String dirName; Vector < Program > programs; public PythonProgramFinder(String dirName) { this.dirName = dirName; } public String findPrograms() { java.io.File directory = new java.io.File(this.dirName); String[] files = directory.list(new FilenameFilter() {public boolean accept(java.io.File dir, String name) {return ((! name.startsWith(".")) && (! name.startsWith("test")) && ((new java.io.File(dir, name)).isFile()) && (name.endsWith(".py")) && (name.compareToIgnoreCase("__init__.py") != 0));}}); this.programs = new Vector < Program > (); for (int i = 0; i < files.length; i++) { String[] commandList = {Global.pythonCommand, "Python" + java.io.File.separator + files[i], "-h"}; String command = ""; for (int j = 0; j < commandList.length; j++) { command += commandList[j] + " "; } ProcessBuilder pb = new ProcessBuilder(commandList); pb = pb.redirectErrorStream(true); Map<String, String> env = pb.environment(); env.put("PYTHONPATH", System.getProperty("user.dir") + java.io.File.separator + "Python"); env.put("SMARTPATH", System.getProperty("user.dir") + java.io.File.separator + "Python"); env.put("SMARTMYSQLPATH", Global.mysqlCommand); env.put("SMARTRPATH", Global.rCommand); PythonHelperReader helperReader = new PythonHelperReader(files[i]); try { final Process process = pb.start(); InputStream is = process.getInputStream(); InputStreamReader isr = new InputStreamReader(is); BufferedReader br = new BufferedReader(isr); helperReader.setReader(br); helperReader.run(); } catch (IOException e) { final Writer result = new StringWriter(); final PrintWriter printWriter = new PrintWriter(result); e.printStackTrace(printWriter); return "Command '" + command + "' failed (I/O error)...\n" + result.toString(); } String comments = helperReader.getMessage(); if (comments != null) return comments; Program program = helperReader.getProgram(); if (("Personnal".compareToIgnoreCase(program.getSection()) != 0) && ("Personal".compareToIgnoreCase(program.getSection()) != 0)) { this.programs.add(program); } } return null; } public Vector <Program> getPrograms () { return this.programs; } }