Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/SMART/Java/Sav/PythonProgramFinder.java @ 2:7c697a8bde9f
Deleted selected files
| author | yufei-luo | 
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| date | Thu, 17 Jan 2013 11:02:49 -0500 | 
| parents | e0f8dcca02ed | 
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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changeset | 1 /** | 
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changeset | 2 * | 
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changeset | 3 * Copyright INRA-URGI 2009-2010 | 
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changeset | 4 * | 
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changeset | 5 * This software is governed by the CeCILL license under French law and | 
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changeset | 6 * abiding by the rules of distribution of free software. You can use, | 
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changeset | 7 * modify and/ or redistribute the software under the terms of the CeCILL | 
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changeset | 8 * license as circulated by CEA, CNRS and INRIA at the following URL | 
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changeset | 9 * "http://www.cecill.info". | 
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changeset | 10 * | 
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changeset | 11 * As a counterpart to the access to the source code and rights to copy, | 
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changeset | 12 * modify and redistribute granted by the license, users are provided only | 
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changeset | 13 * with a limited warranty and the software's author, the holder of the | 
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changeset | 14 * economic rights, and the successive licensors have only limited | 
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changeset | 15 * liability. | 
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changeset | 16 * | 
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changeset | 17 * In this respect, the user's attention is drawn to the risks associated | 
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changeset | 18 * with loading, using, modifying and/or developing or reproducing the | 
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changeset | 19 * software by the user in light of its specific status of free software, | 
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changeset | 20 * that may mean that it is complicated to manipulate, and that also | 
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changeset | 21 * therefore means that it is reserved for developers and experienced | 
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changeset | 22 * professionals having in-depth computer knowledge. Users are therefore | 
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changeset | 23 * encouraged to load and test the software's suitability as regards their | 
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changeset | 24 * requirements in conditions enabling the security of their systems and/or | 
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changeset | 25 * data to be ensured and, more generally, to use and operate it in the | 
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changeset | 26 * same conditions as regards security. | 
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changeset | 27 * | 
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changeset | 28 * The fact that you are presently reading this means that you have had | 
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changeset | 29 * knowledge of the CeCILL license and that you accept its terms. | 
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changeset | 30 * | 
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changeset | 31 */ | 
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changeset | 32 import java.io.*; | 
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changeset | 33 import java.util.*; | 
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changeset | 34 | 
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changeset | 35 public class PythonProgramFinder { | 
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changeset | 36 | 
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changeset | 37 String dirName; | 
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changeset | 38 Vector < Program > programs; | 
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changeset | 39 | 
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changeset | 40 public PythonProgramFinder(String dirName) { | 
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changeset | 41 this.dirName = dirName; | 
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changeset | 42 } | 
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changeset | 43 | 
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changeset | 44 public String findPrograms() { | 
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changeset | 45 java.io.File directory = new java.io.File(this.dirName); | 
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changeset | 46 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")));}}); | 
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changeset | 47 this.programs = new Vector < Program > (); | 
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changeset | 48 | 
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changeset | 49 for (int i = 0; i < files.length; i++) { | 
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changeset | 50 String[] commandList = {Global.pythonCommand, "Python" + java.io.File.separator + files[i], "-h"}; | 
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changeset | 51 String command = ""; | 
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changeset | 52 for (int j = 0; j < commandList.length; j++) { | 
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changeset | 53 command += commandList[j] + " "; | 
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changeset | 54 } | 
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changeset | 55 ProcessBuilder pb = new ProcessBuilder(commandList); | 
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changeset | 56 pb = pb.redirectErrorStream(true); | 
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changeset | 57 Map<String, String> env = pb.environment(); | 
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changeset | 58 env.put("PYTHONPATH", System.getProperty("user.dir") + java.io.File.separator + "Python"); | 
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changeset | 59 env.put("SMARTPATH", System.getProperty("user.dir") + java.io.File.separator + "Python"); | 
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changeset | 60 env.put("SMARTMYSQLPATH", Global.mysqlCommand); | 
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changeset | 61 env.put("SMARTRPATH", Global.rCommand); | 
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changeset | 62 | 
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changeset | 63 PythonHelperReader helperReader = new PythonHelperReader(files[i]); | 
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changeset | 64 try { | 
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changeset | 65 final Process process = pb.start(); | 
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changeset | 66 InputStream is = process.getInputStream(); | 
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changeset | 67 InputStreamReader isr = new InputStreamReader(is); | 
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changeset | 68 BufferedReader br = new BufferedReader(isr); | 
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changeset | 69 helperReader.setReader(br); | 
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changeset | 70 helperReader.run(); | 
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changeset | 71 } | 
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changeset | 72 catch (IOException e) { | 
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changeset | 73 e.printStackTrace(); | 
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changeset | 74 return "Command '" + command + "' failed (I/O error)...\n"; | 
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changeset | 75 } | 
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changeset | 76 String comments = helperReader.getMessage(); | 
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changeset | 77 if (comments != null) return comments; | 
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changeset | 78 Program program = helperReader.getProgram(); | 
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changeset | 79 if ("Personnal".compareToIgnoreCase(program.getSection()) != 0) { | 
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changeset | 80 this.programs.add(program); | 
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changeset | 81 } | 
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changeset | 82 } | 
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changeset | 83 return null; | 
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changeset | 84 } | 
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changeset | 85 | 
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changeset | 86 public Vector <Program> getPrograms () { | 
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changeset | 87 return this.programs; | 
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changeset | 88 } | 
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changeset | 89 } | 
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changeset | 90 | 
