Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/commons/core/utils/PipelineStepFTests.py @ 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 #!/usr/bin/env python
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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 (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
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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8 # 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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9 # 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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10 # 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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11 # "http://www.cecill.info".
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12 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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13 # 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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14 # 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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15 # 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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16 # 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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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
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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20 # 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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21 # 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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22 # 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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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
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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25 # 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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26 # 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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27 # 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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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
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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