Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/utils/PipelineStepFTests.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 #!/usr/bin/env python |
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2 |
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3 # Copyright INRA (Institut National de la Recherche Agronomique) |
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4 # http://www.inra.fr |
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5 # http://urgi.versailles.inra.fr |
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6 # |
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7 # This software is governed by the CeCILL license under French law and |
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8 # abiding by the rules of distribution of free software. You can use, |
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9 # modify and/ or redistribute the software under the terms of the CeCILL |
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10 # license as circulated by CEA, CNRS and INRIA at the following URL |
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11 # "http://www.cecill.info". |
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12 # |
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13 # As a counterpart to the access to the source code and rights to copy, |
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14 # modify and redistribute granted by the license, users are provided only |
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15 # with a limited warranty and the software's author, the holder of the |
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16 # economic rights, and the successive licensors have only limited |
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17 # liability. |
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18 # |
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19 # In this respect, the user's attention is drawn to the risks associated |
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20 # with loading, using, modifying and/or developing or reproducing the |
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21 # software by the user in light of its specific status of free software, |
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22 # that may mean that it is complicated to manipulate, and that also |
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23 # therefore means that it is reserved for developers and experienced |
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24 # professionals having in-depth computer knowledge. Users are therefore |
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25 # encouraged to load and test the software's suitability as regards their |
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26 # requirements in conditions enabling the security of their systems and/or |
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27 # data to be ensured and, more generally, to use and operate it in the |
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28 # same conditions as regards security. |
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29 # |
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30 # The fact that you are presently reading this means that you have had |
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31 # knowledge of the CeCILL license and that you accept its terms. |
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32 |
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33 import sys |
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34 import os |
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35 import shutil |
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36 from commons.core.utils.FileUtils import FileUtils |
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37 |
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38 class PipelineStepFTests(object): |
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39 |
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40 def __init__(self, pipelineName, packageDir, workingDir, projectName, config = "", clean = True): |
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41 self._pipelineName = pipelineName |
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42 self._packageDir = packageDir |
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43 self._workingDir = workingDir |
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44 self._projectName = projectName |
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45 self._clean = clean |
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46 self._configFileName = config |
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47 |
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48 def run(self): |
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49 self.launchStep() |
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50 self.assertStep() |
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51 |
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52 # def replaceInFile(self, fileName, oldPattern, newPattern, newFileName = ""): |
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53 # if newFileName == "": |
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54 # newFileName = "%s.new" % fileName |
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55 # f = open(newFileName, "w") |
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56 # for line in fileinput.input(fileName, inplace=1): |
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57 # newLine = line.replace(oldPattern, newPattern) |
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58 # f.write(newLine) |
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59 # f.close() |
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60 # fileinput.close() |
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61 |
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62 def _checkIfFileExist(self, fileName): |
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63 if not FileUtils.isRessourceExists(fileName): |
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64 print "%s do not exists\n" % fileName |
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65 return False |
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66 return True |
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67 |
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68 def _printMessageAndClean(self, msg): |
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69 print "%s in %s functional test\n" % (msg, self._pipelineName) |
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70 sys.stdout.flush() |
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71 os.chdir("../") |
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72 if self._clean: |
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73 shutil.rmtree(self._workingDir) |
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74 |
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75 def _areTwoFilesIdenticalByScript( self, expFileName, obsFileName, scriptName): |
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76 cmd = "%s -v 1 -r %s -t %s 2>/dev/null" % (scriptName, expFileName, obsFileName) |
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77 log = os.system(cmd) |
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78 print |
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79 sys.stdout.flush() |
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80 if log != 0: |
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81 return False |
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82 else: |
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83 return True |