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1 import os
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2 import unittest
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3 from commons.pyRepetUnit.hmmer.LaunchPreProcessHmmpfamPostProcessNotInParallel import *
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4 from pyRepet.util.file.FileUtils import *
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5 import ConfigParser
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6
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7 if (not os.environ.has_key("REPET_PATH")):
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8 print "*** Error: no environment variable REPET_PATH"
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9 exit =1
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10
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11 if (not os.environ.has_key("PYTHONPATH")):
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12 print "*** Error: no environment variable PYTHONPATH"
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13 exit =1
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14
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15 if (exit == 1):
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16 sys.exit(1)
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17
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18 CONFIG_FILE = "datas/configTestLaunchPreProcessHmmpfamPostProcessNotInParallel.cfg"
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19 CURRENT_DIR = os.getcwd()
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20
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21 class TestLaunchPreProcessHmmpfamPostProcessNotInParallel(unittest.TestCase):
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22
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23 def setUp( self ):
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24 os.chdir(CURRENT_DIR)
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25 self._LaunchPreProcessHmmpfamPostProcess = LaunchPreProcessHmmpfamPostProcessNotInParallel()
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26 self._configFile = CONFIG_FILE
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27 config = ConfigParser.ConfigParser()
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28 config.readfp(open(self._configFile))
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29 self._InputFile = config.get("hmmer_config", "input_file")
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30 self._OutputFile = config.get("hmmer_config", "output_file")
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31 self.fileUtils = FileUtils()
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32
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33 def testRun(self):
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34 #Normal launch
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35 self._LaunchPreProcessHmmpfamPostProcess.setInputFile( self._InputFile )
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36 self._LaunchPreProcessHmmpfamPostProcess.setOutputFile( self._OutputFile )
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37 self._LaunchPreProcessHmmpfamPostProcess.setConfigFile( self._configFile )
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38 self._LaunchPreProcessHmmpfamPostProcess.run()
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39 self.assertTrue(self.fileUtils.isRessourceExists(self._OutputFile))
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40 self.assertFalse(self.fileUtils.isFileEmpty(self._OutputFile))
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41 os.system("rm " + self._OutputFile)
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42 #without config file
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43 configFile = "/workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas/configdummy.cfg"
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44 self._LaunchPreProcessHmmpfamPostProcess.setConfigFile( configFile )
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45 self._LaunchPreProcessHmmpfamPostProcess.run()
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46 self.assertFalse(self.fileUtils.isRessourceExists(self._OutputFile))
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47 #without input file
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48 InputFile = ""
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49 self._LaunchPreProcessHmmpfamPostProcess.setInputFile( InputFile )
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50 self._LaunchPreProcessHmmpfamPostProcess.run()
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51 self.assertFalse(self.fileUtils.isRessourceExists(self._OutputFile))
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52 #without output file
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53 self._LaunchPreProcessHmmpfamPostProcess.setConfigFile( self._configFile )
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54 self._LaunchPreProcessHmmpfamPostProcess.setInputFile( self._InputFile )
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55 OutputFile = ""
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56 self._LaunchPreProcessHmmpfamPostProcess.setOutputFile( OutputFile )
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57 self._LaunchPreProcessHmmpfamPostProcess.run()
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58 self.assertFalse(self.fileUtils.isRessourceExists(self._OutputFile))
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59
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60
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61
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62 if __name__ == "__main__":
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63 unittest.main()
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