Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/SMART/Java/PythonProgramFinder.java @ 0:e0f8dcca02ed

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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
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 /**
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 *
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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3 * Copyright INRA-URGI 2009-2010
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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4 *
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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5 * This software is governed by the CeCILL license under French law and
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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6 * abiding by the rules of distribution of free software. You can use,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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7 * modify and/ or redistribute the software under the terms of the CeCILL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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8 * license as circulated by CEA, CNRS and INRIA at the following URL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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9 * "http://www.cecill.info".
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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10 *
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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11 * As a counterpart to the access to the source code and rights to copy,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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12 * modify and redistribute granted by the license, users are provided only
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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13 * with a limited warranty and the software's author, the holder of the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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14 * economic rights, and the successive licensors have only limited
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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15 * liability.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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16 *
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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17 * In this respect, the user's attention is drawn to the risks associated
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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18 * with loading, using, modifying and/or developing or reproducing the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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19 * software by the user in light of its specific status of free software,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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20 * that may mean that it is complicated to manipulate, and that also
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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21 * therefore means that it is reserved for developers and experienced
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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22 * professionals having in-depth computer knowledge. Users are therefore
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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23 * encouraged to load and test the software's suitability as regards their
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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24 * requirements in conditions enabling the security of their systems and/or
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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25 * data to be ensured and, more generally, to use and operate it in the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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26 * same conditions as regards security.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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27 *
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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28 * The fact that you are presently reading this means that you have had
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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29 * knowledge of the CeCILL license and that you accept its terms.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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30 *
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31 */
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32 import java.io.*;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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33 import java.util.*;
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34
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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35 public class PythonProgramFinder {
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36
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37 String dirName;
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38 Vector < Program > programs;
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39
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40 public PythonProgramFinder(String dirName) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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41 this.dirName = dirName;
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42 }
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43
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44 public String findPrograms() {
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45 java.io.File directory = new java.io.File(this.dirName);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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")) && (name.compareToIgnoreCase("__init__.py") != 0));}});
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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47 this.programs = new Vector < Program > ();
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48
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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49 for (int i = 0; i < files.length; i++) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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50 String[] commandList = {Global.pythonCommand, "Python" + java.io.File.separator + files[i], "-h"};
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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51 String command = "";
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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52 for (int j = 0; j < commandList.length; j++) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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53 command += commandList[j] + " ";
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54 }
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55 ProcessBuilder pb = new ProcessBuilder(commandList);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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56 pb = pb.redirectErrorStream(true);
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57 Map<String, String> env = pb.environment();
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58 env.put("PYTHONPATH", System.getProperty("user.dir") + java.io.File.separator + "Python");
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59 env.put("SMARTPATH", System.getProperty("user.dir") + java.io.File.separator + "Python");
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60 env.put("SMARTMYSQLPATH", Global.mysqlCommand);
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61 env.put("SMARTRPATH", Global.rCommand);
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62
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63 PythonHelperReader helperReader = new PythonHelperReader(files[i]);
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64 try {
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65 final Process process = pb.start();
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66 InputStream is = process.getInputStream();
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67 InputStreamReader isr = new InputStreamReader(is);
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68 BufferedReader br = new BufferedReader(isr);
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69 helperReader.setReader(br);
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70 helperReader.run();
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71 }
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72 catch (IOException e) {
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73 final Writer result = new StringWriter();
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74 final PrintWriter printWriter = new PrintWriter(result);
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75 e.printStackTrace(printWriter);
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76 return "Command '" + command + "' failed (I/O error)...\n" + result.toString();
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77 }
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78 String comments = helperReader.getMessage();
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79 if (comments != null) return comments;
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80 Program program = helperReader.getProgram();
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81 if (("Personnal".compareToIgnoreCase(program.getSection()) != 0) && ("Personal".compareToIgnoreCase(program.getSection()) != 0)) {
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82 this.programs.add(program);
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83 }
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84 }
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85 return null;
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86 }
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87
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88 public Vector <Program> getPrograms () {
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89 return this.programs;
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90 }
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91 }
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92