Mercurial > repos > yufei-luo > s_mart
diff commons/pyRepetUnit/hmmer/tests/TestHmmpfamClusterComponent.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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/commons/pyRepetUnit/hmmer/tests/TestHmmpfamClusterComponent.py Mon Apr 29 03:20:15 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()