diff commons/pyRepetUnit/hmmer/tests/TestLaunchPreProcessHmmpfamPostProcessNotInParallel.py @ 31:0ab839023fe4

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/pyRepetUnit/hmmer/tests/TestLaunchPreProcessHmmpfamPostProcessNotInParallel.py	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,63 @@
+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()