s_mart: smart_toolShed/commons/core/checker/test/Test

annotate smart_toolShed/commons/core/checker/test/Test_OldConfigChecker.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

author	yufei-luo
date	Thu, 17 Jan 2013 10:52:14 -0500
parents
children

rev	line source
0 e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	1 # Copyright INRA (Institut National de la Recherche Agronomique)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	2 # http://www.inra.fr
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	3 # http://urgi.versailles.inra.fr
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	4 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	5 # This software is governed by the CeCILL license under French law and
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	6 # abiding by the rules of distribution of free software. You can use,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	7 # modify and/ or redistribute the software under the terms of the CeCILL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	8 # license as circulated by CEA, CNRS and INRIA at the following URL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	9 # "http://www.cecill.info".
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	10 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	11 # As a counterpart to the access to the source code and rights to copy,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	12 # modify and redistribute granted by the license, users are provided only
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	13 # with a limited warranty and the software's author, the holder of the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	14 # economic rights, and the successive licensors have only limited
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	15 # liability.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	16 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	17 # In this respect, the user's attention is drawn to the risks associated
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	18 # with loading, using, modifying and/or developing or reproducing the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	19 # software by the user in light of its specific status of free software,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	20 # that may mean that it is complicated to manipulate, and that also
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	21 # therefore means that it is reserved for developers and experienced
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	22 # professionals having in-depth computer knowledge. Users are therefore
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	23 # encouraged to load and test the software's suitability as regards their
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	24 # requirements in conditions enabling the security of their systems and/or
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	25 # data to be ensured and, more generally, to use and operate it in the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	26 # same conditions as regards security.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	27 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	28 # The fact that you are presently reading this means that you have had
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	29 # knowledge of the CeCILL license and that you accept its terms.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	30
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	31
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	32 import unittest
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	33 import os
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	34 from commons.core.checker.OldConfigChecker import ConfigChecker
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	35 from commons.core.checker.ConfigException import ConfigException
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	36
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	37 class Test_ConfigChecker( unittest.TestCase ):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	38
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	39 def setUp(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	40 pass
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	41
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	42 def tearDown(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	43 pass
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	44
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	45
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	46 def testFileNotFound(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	47 exceptionExpected = None
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	48 configChecker = ConfigChecker("",{})
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	49 try :
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	50 configChecker.check("noExistsFile.cfg")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	51 except ConfigException, ce:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	52 exceptionExpected = ce
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	53
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	54 self.assertTrue(exceptionExpected != None)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	55 msg = exceptionExpected.messages[0]
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	56 self.assertTrue(msg.startswith("CONFIG FILE not found - "))
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	57
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	58
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	59 def testNoSectionInConfigFile (self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	60 exceptionExpected = None
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	61 dummyFile = open("dummyFile.cfg", "w")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	62 configChecker = ConfigChecker("dummySection",{})
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	63 try :
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	64 configChecker.check("dummyFile.cfg")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	65 except ConfigException, ce:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	66 exceptionExpected = ce
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	67
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	68 self.assertTrue(exceptionExpected != None)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	69 msg = exceptionExpected.messages[0]
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	70 self.assertTrue(msg.startswith("[dummySection]" + " section not found - "))
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	71
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	72 os.remove("dummyFile.cfg")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	73
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	74
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	75 def testNoOptionInConfigFile (self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	76 exceptionExpected = None
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	77 MockConfigFile("dummyConfig.cfg",{})
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	78 configChecker = ConfigChecker("blaster_config",{"dummy":""})
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	79 try :
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	80 configChecker.check("dummyConfig.cfg")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	81 except ConfigException, ce:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	82 exceptionExpected = ce
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	83
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	84 self.assertTrue(exceptionExpected != None)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	85 msg = exceptionExpected.messages[0]
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	86 self.assertTrue(msg.startswith("[blaster_config] - No option 'dummy' in section: 'blaster_config'"))
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	87 os.remove("dummyConfig.cfg")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	88
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	89
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	90 class MockConfigFile:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	91
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	92 def __init__ (self, fileName, optionsDict):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	93 self._fileName = fileName
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	94 config = open(fileName, "w");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	95 config.write("[blaster_config]\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	96 for key in optionsDict.keys():
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	97 config.write(key + ":" + optionsDict[key] + "\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	98 config.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	99
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	100
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	101 test_suite = unittest.TestSuite()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	102 test_suite.addTest( unittest.makeSuite( Test_ConfigChecker ) )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	103 if __name__ == "__main__":
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	104 unittest.TextTestRunner(verbosity=2).run( test_suite )

Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/commons/core/checker/test/Test_OldConfigChecker.py @ 0:e0f8dcca02ed