def dtest_config_error(self):
configFile = self.getErrorInputFile("pcssConfigMissingFile.txt")
configSpecFile = "testConfig/testConfigSpec.txt"
obj = configobj.ConfigObj(configFile, configspec=configSpecFile)
with self.assertRaises(pcssErrors.PcssGlobalException) as pge:
pcssTools.SvmApplicationFeatureRunner(obj)
self.handleTestException(pge)
def test_svm_application_features_ump(self):
self.pcssConfig['fasta_file'] = self.getLargeFastaFile()
self.pcssConfig['svm_model_file'] = os.path.join(
self.pcssConfig['user_pcss_directory'], "data", "benchmark",
"userCustomModelFile")
self.pcssConfig['svm_benchmark_file'] = os.path.join(
self.pcssConfig['user_pcss_directory'], "data", "benchmark",
"userCustomBenchmarkFile")
self.runner = pcssTools.SvmApplicationFeatureRunner(self.pcssConfig)
self.runner.internalConfig[
'model_table_file'] = self.getFullModelTableFile()
self.clearErrorFiles()
self.runner.execute()
self.assertFalse(os.path.exists(self.runner.pdh.getPcssErrorFile()))
self.assertFalse(os.path.exists(
self.runner.pdh.getInternalErrorFile()))
self.compareToExpectedOutput(
self.runner.pdh.getFullOutputFile(
self.runner.internalConfig["annotation_output_file"]),
"svmApplication", False, True)
import pcssTools import pcssCluster import configobj import sys import os configFileName = sys.argv[1] #tempPcssConfig = configobj.ConfigObj(configFileName) #configSpec = tempPcssConfig["user_config_spec_file"] pcssConfig = configobj.ConfigObj(configFileName) runner = pcssTools.SvmApplicationFeatureRunner(pcssConfig) runner.execute()
def dtest_svm_application_feature_internal_error(self):
self.runner = pcssTools.SvmApplicationFeatureRunner(self.pcssConfig)
self.throwInternalException()
self.checkErrorThrown("internalError")
def dtest_svm_application_feature_pcss_error(self):
self.runner = pcssTools.SvmApplicationFeatureRunner(self.pcssConfig)
self.throwPcssException()
self.checkErrorThrown("pcssError")