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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/pyRepetUnit/hmmer/tests/TestHmmpfamClusterComponent.py	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,76 @@
+import os
+import unittest
+import ConfigParser
+import commons.pyRepetUnit.hmmer.HmmpfamClusterComponent
+from pyRepet.sql.RepetJobMySQL import *
+from pyRepet.util.file.FileUtils import *
+
+class TestHmmpfamClusterComponent(unittest.TestCase):
+
+     def setUp(self):
+         
+        self.component = commons.pyRepetUnit.hmmer.HmmpfamClusterComponent.HmmpfamClusterComponent()
+        
+     def testLoadConfig(self):
+        config = open("tmpConfig.cfg", "w")
+        config.write("[profil_search]\n")
+        config.write("ProfilDatabank: /repet_pipe/commons/pyRepetUnit/hmmer/datas/myhmms\n")
+        config.write("[hmmer_config]\n")
+        config.write("result_dir: /repet_results\n")
+        config.write("query_dir: /repet_datas/hmmer_in_parallel\n")
+        config.write("tmp_dir: /repet_tmp\n")
+        config.write("[sge_config]\n")
+        config.write("queue: main.q\n")
+        config.write("groupid: fake\n") 
+        config.close()
+        config = ConfigParser.ConfigParser()
+        config.readfp( open("tmpConfig.cfg") )
+        self.component.loadConfig(config)
+        self.assertEquals( "/repet_pipe/commons/pyRepetUnit/hmmer/datas/myhmms", self.component.getProfilDatabank() )
+        self.assertEquals( "/repet_results", self.component.getResultDir() )
+        self.assertEquals( "/repet_datas/hmmer_in_parallel", self.component.getQueryDir() )
+        self.assertEquals( "/repet_tmp", self.component.getTmpDir() )
+        self.assertEquals( "main.q", self.component.getSGEQueue() )
+        self.assertEquals( "fake", self.component.getSGEGroupId() )
+        os.system("rm tmpConfig.cfg") 
+        
+     def testClean (self):
+        fileUtils = FileUtils() 
+        if (fileUtils.isRessourceExists("dummyTmpDir")):
+             os.system("rm -r dummyTmpDir")
+         
+        if (fileUtils.isRessourceExists("dummyResultDir")):
+             os.system("rm -r dummyResultDir") 
+         
+        os.mkdir("dummyTmpDir")
+        os.system("touch dummyTmpDir/srptJob1_fake_HmmpfamJob1_2009-3-11_12394.py")
+        os.system("touch dummyTmpDir/srptJob2_fake_HmmpfamJob1_2009-3-11_12394.py")
+        os.system("touch dummyTmpDir/srptJob3_fake_HmmpfamJob1_2009-3-11_12394.py")
+        os.system("touch dummyTmpDir/srptJob4_fake_HmmpfamJob1_2009-3-11_12394.py")
+        
+        os.mkdir("dummyResultDir")
+        os.system("touch dummyResultDir/batch_1.fa.hmmpfamOut")
+        os.system("touch dummyResultDir/batch_2.fa.hmmpfamOut")
+        os.system("touch dummyResultDir/batch_3.fa.hmmpfamOut")
+        os.system("touch dummyResultDir/batch_4.fa.hmmpfamOut")
+
+        self.component.setTmpDir("dummyTmpDir")
+        self.component.setResultDir("dummyResultDir")
+        
+        self.component.clean()
+        
+        self.assertFalse(fileUtils.isRessourceExists("dummyTmpDir/srptJob1_fake_HmmpfamJob1_2009-3-11_12394.py"))
+        self.assertFalse(fileUtils.isRessourceExists("dummyTmpDir/srptJob1_fake_HmmpfamJob2_2009-3-11_12394.py"))
+        self.assertFalse(fileUtils.isRessourceExists("dummyTmpDir/srptJob1_fake_HmmpfamJob3_2009-3-11_12394.py"))
+        self.assertFalse(fileUtils.isRessourceExists("dummyTmpDir/srptJob1_fake_HmmpfamJob4_2009-3-11_12394.py"))
+        self.assertFalse(fileUtils.isRessourceExists("dummyResultDir/batch_1.fa.hmmpfamOut"))
+        self.assertFalse(fileUtils.isRessourceExists("dummyResultDir/batch_2.fa.hmmpfamOut"))
+        self.assertFalse(fileUtils.isRessourceExists("dummyResultDir/batch_3.fa.hmmpfamOut"))
+        self.assertFalse(fileUtils.isRessourceExists("dummyResultDir/batch_4.fa.hmmpfamOut"))
+        
+        os.system("rm -r dummyTmpDir")
+        os.system("rm -r dummyResultDir")
+       
+
+if __name__ == "__main__":
+	unittest.main()