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1 import os
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2 import unittest
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3 import ConfigParser
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4 import commons.pyRepetUnit.hmmer.HmmpfamClusterComponent
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5 from pyRepet.sql.RepetJobMySQL import *
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6 from pyRepet.util.file.FileUtils import *
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7
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8 class TestHmmpfamClusterComponent(unittest.TestCase):
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9
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10 def setUp(self):
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11
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12 self.component = commons.pyRepetUnit.hmmer.HmmpfamClusterComponent.HmmpfamClusterComponent()
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13
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14 def testLoadConfig(self):
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15 config = open("tmpConfig.cfg", "w")
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16 config.write("[profil_search]\n")
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17 config.write("ProfilDatabank: /repet_pipe/commons/pyRepetUnit/hmmer/datas/myhmms\n")
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18 config.write("[hmmer_config]\n")
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19 config.write("result_dir: /repet_results\n")
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20 config.write("query_dir: /repet_datas/hmmer_in_parallel\n")
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21 config.write("tmp_dir: /repet_tmp\n")
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22 config.write("[sge_config]\n")
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23 config.write("queue: main.q\n")
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24 config.write("groupid: fake\n")
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25 config.close()
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26 config = ConfigParser.ConfigParser()
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27 config.readfp( open("tmpConfig.cfg") )
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28 self.component.loadConfig(config)
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29 self.assertEquals( "/repet_pipe/commons/pyRepetUnit/hmmer/datas/myhmms", self.component.getProfilDatabank() )
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30 self.assertEquals( "/repet_results", self.component.getResultDir() )
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31 self.assertEquals( "/repet_datas/hmmer_in_parallel", self.component.getQueryDir() )
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32 self.assertEquals( "/repet_tmp", self.component.getTmpDir() )
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33 self.assertEquals( "main.q", self.component.getSGEQueue() )
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34 self.assertEquals( "fake", self.component.getSGEGroupId() )
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35 os.system("rm tmpConfig.cfg")
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36
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37 def testClean (self):
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38 fileUtils = FileUtils()
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39 if (fileUtils.isRessourceExists("dummyTmpDir")):
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40 os.system("rm -r dummyTmpDir")
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41
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42 if (fileUtils.isRessourceExists("dummyResultDir")):
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43 os.system("rm -r dummyResultDir")
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44
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45 os.mkdir("dummyTmpDir")
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46 os.system("touch dummyTmpDir/srptJob1_fake_HmmpfamJob1_2009-3-11_12394.py")
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47 os.system("touch dummyTmpDir/srptJob2_fake_HmmpfamJob1_2009-3-11_12394.py")
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48 os.system("touch dummyTmpDir/srptJob3_fake_HmmpfamJob1_2009-3-11_12394.py")
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49 os.system("touch dummyTmpDir/srptJob4_fake_HmmpfamJob1_2009-3-11_12394.py")
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50
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51 os.mkdir("dummyResultDir")
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52 os.system("touch dummyResultDir/batch_1.fa.hmmpfamOut")
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53 os.system("touch dummyResultDir/batch_2.fa.hmmpfamOut")
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54 os.system("touch dummyResultDir/batch_3.fa.hmmpfamOut")
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55 os.system("touch dummyResultDir/batch_4.fa.hmmpfamOut")
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56
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57 self.component.setTmpDir("dummyTmpDir")
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58 self.component.setResultDir("dummyResultDir")
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59
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60 self.component.clean()
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61
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62 self.assertFalse(fileUtils.isRessourceExists("dummyTmpDir/srptJob1_fake_HmmpfamJob1_2009-3-11_12394.py"))
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63 self.assertFalse(fileUtils.isRessourceExists("dummyTmpDir/srptJob1_fake_HmmpfamJob2_2009-3-11_12394.py"))
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64 self.assertFalse(fileUtils.isRessourceExists("dummyTmpDir/srptJob1_fake_HmmpfamJob3_2009-3-11_12394.py"))
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65 self.assertFalse(fileUtils.isRessourceExists("dummyTmpDir/srptJob1_fake_HmmpfamJob4_2009-3-11_12394.py"))
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66 self.assertFalse(fileUtils.isRessourceExists("dummyResultDir/batch_1.fa.hmmpfamOut"))
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67 self.assertFalse(fileUtils.isRessourceExists("dummyResultDir/batch_2.fa.hmmpfamOut"))
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68 self.assertFalse(fileUtils.isRessourceExists("dummyResultDir/batch_3.fa.hmmpfamOut"))
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69 self.assertFalse(fileUtils.isRessourceExists("dummyResultDir/batch_4.fa.hmmpfamOut"))
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70
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71 os.system("rm -r dummyTmpDir")
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72 os.system("rm -r dummyResultDir")
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73
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74
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75 if __name__ == "__main__":
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76 unittest.main()
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