Mercurial > repos > yufei-luo > s_mart
view commons/pyRepetUnit/hmmer/tests/TestLaunchPreProcessHmmpfamPostProcessNotInParallel.py @ 18:94ab73e8a190
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author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:20:15 -0400 |
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import os import unittest from commons.pyRepetUnit.hmmer.LaunchPreProcessHmmpfamPostProcessNotInParallel import * from pyRepet.util.file.FileUtils import * import ConfigParser if (not os.environ.has_key("REPET_PATH")): print "*** Error: no environment variable REPET_PATH" exit =1 if (not os.environ.has_key("PYTHONPATH")): print "*** Error: no environment variable PYTHONPATH" exit =1 if (exit == 1): sys.exit(1) CONFIG_FILE = "datas/configTestLaunchPreProcessHmmpfamPostProcessNotInParallel.cfg" CURRENT_DIR = os.getcwd() class TestLaunchPreProcessHmmpfamPostProcessNotInParallel(unittest.TestCase): def setUp( self ): os.chdir(CURRENT_DIR) self._LaunchPreProcessHmmpfamPostProcess = LaunchPreProcessHmmpfamPostProcessNotInParallel() self._configFile = CONFIG_FILE config = ConfigParser.ConfigParser() config.readfp(open(self._configFile)) self._InputFile = config.get("hmmer_config", "input_file") self._OutputFile = config.get("hmmer_config", "output_file") self.fileUtils = FileUtils() def testRun(self): #Normal launch self._LaunchPreProcessHmmpfamPostProcess.setInputFile( self._InputFile ) self._LaunchPreProcessHmmpfamPostProcess.setOutputFile( self._OutputFile ) self._LaunchPreProcessHmmpfamPostProcess.setConfigFile( self._configFile ) self._LaunchPreProcessHmmpfamPostProcess.run() self.assertTrue(self.fileUtils.isRessourceExists(self._OutputFile)) self.assertFalse(self.fileUtils.isFileEmpty(self._OutputFile)) os.system("rm " + self._OutputFile) #without config file configFile = "/workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas/configdummy.cfg" self._LaunchPreProcessHmmpfamPostProcess.setConfigFile( configFile ) self._LaunchPreProcessHmmpfamPostProcess.run() self.assertFalse(self.fileUtils.isRessourceExists(self._OutputFile)) #without input file InputFile = "" self._LaunchPreProcessHmmpfamPostProcess.setInputFile( InputFile ) self._LaunchPreProcessHmmpfamPostProcess.run() self.assertFalse(self.fileUtils.isRessourceExists(self._OutputFile)) #without output file self._LaunchPreProcessHmmpfamPostProcess.setConfigFile( self._configFile ) self._LaunchPreProcessHmmpfamPostProcess.setInputFile( self._InputFile ) OutputFile = "" self._LaunchPreProcessHmmpfamPostProcess.setOutputFile( OutputFile ) self._LaunchPreProcessHmmpfamPostProcess.run() self.assertFalse(self.fileUtils.isRessourceExists(self._OutputFile)) if __name__ == "__main__": unittest.main()