def initializeServicesAndCreateGenomes(self, file_name, file_type,
expected_response_type):
data_file = self.setTargetFile('SampleDataFiles', file_name)
file_processing_service = FileProcessingService(
data_file, file_type, self.number_of_genomes,
self.current_working_dir)
self.generated_folder = self.current_working_dir + file_processing_service.GENERATED_FOLDER_NAME
genomes_created = file_processing_service.createGenomes()
file_processing_service.data_file.close()
self.thirdPartyProgramCaller = ThirdPartyProgramCaller(
self.current_working_dir, file_type, genomes_created[0],
expected_response_type, self.number_of_genomes)
def processInputFileAndCreateGenomes(data_file, file_extension, path,
number_of_genomes):
file_parsing_service = FileProcessingService(data_file, file_extension,
number_of_genomes, path)
return file_parsing_service.createGenomes()
class FileProcessingServiceIT(unittest.TestCase):
log = logging.getLogger(__name__)
log.setLevel(logging.INFO)
def setUp(self):
self.current_working_dir = os.getcwd() # Should be this package.
def tearDown(self):
if self.file_processing_service:
self.file_processing_service.data_file.close()
if self.generated_folder != "/" and os.path.isdir(
self.generated_folder):
shutil.rmtree(self.generated_folder)
def setupFileProcessingService(self, data_file, file_type):
self.file_processing_service = FileProcessingService(
data_file, file_type, 10, self.current_working_dir)
self.generated_folder = self.current_working_dir + self.file_processing_service.GENERATED_FOLDER_NAME
def setupFileProcessingServiceForSim1(self, data_file, file_type):
self.sim1FileProcessingService = Sim1FileProcessingService(
data_file, file_type, 10, 5, self.current_working_dir)
def setTargetFile(self, path_name, file_name):
resource_path = '/'.join((path_name, file_name))
return open(resource_path)
def testOctaveGenomeFilesSuccessfullyCreated(self):
data_file = self.setTargetFile('SampleDataFiles',
'WNT_ERK_crosstalk.octave')
self.setupFileProcessingService(data_file, SupportedFileTypes.OCTAVE)
self.assertGenomeFilesCreatedSuccessfully(SupportedFileTypes.OCTAVE)
# TODO: test for MATLAB
def testRGenomeFilesSuccessfullyCreated(self):
# Note: This is R the program, not R an integer representing permutations.
data_file = self.setTargetFile('SampleDataFiles',
'booleanModelTest.r.t')
self.setupFileProcessingService(data_file, SupportedFileTypes.R)
self.assertGenomeFilesCreatedSuccessfully(SupportedFileTypes.R)
def assertGenomeFilesCreatedSuccessfully(self, file_type):
number_of_genomes = self.file_processing_service.number_of_genomes
self.log.info(
"Testing %s genomes are successfully created as %s files.",
number_of_genomes, file_type)
genomes_response = self.file_processing_service.createGenomes()
created_genome_files = genomes_response[0]
assert len(created_genome_files) == number_of_genomes
assert os.path.isdir(self.current_working_dir)
created_files = [file for file in os.listdir(self.generated_folder)]
assert len(created_files) == (2 * number_of_genomes) + 1
assert len([
file for file in created_files if re.findall(r'.*_key.*', file)
]) == number_of_genomes
def testSim1FileProcessingServiceForOctave(self):
data_file = self.setTargetFile('SampleDataFiles',
'WNT_ERK_crosstalk.octave')
self.setupFileProcessingService(data_file, SupportedFileTypes.MATLAB)
data_file_for_sim1 = self.setTargetFile(
'SampleDataFiles', 'run_simulation_readGenome.octave.u')
self.setupFileProcessingServiceForSim1(data_file_for_sim1,
SupportedFileTypes.OCTAVE)
number_of_genomes = self.sim1FileProcessingService.number_of_genomes
number_of_trials = self.sim1FileProcessingService.number_of_trials
self.log.info(
"Testing %s genomes are successfully created as Octave files.",
number_of_genomes)
self.file_processing_service.createGenomes()
self.assertSim1TrialFilesSuccessfullyCreated(number_of_genomes,
number_of_trials)
# TODO: Test for MATLAB
def testSim1FileProcessingServiceForR(self):
data_file = self.setTargetFile('SampleDataFiles',
'booleanModelTest.r.t')
self.setupFileProcessingService(data_file, SupportedFileTypes.R)
data_file_for_sim1 = self.setTargetFile(
'SampleDataFiles', 'booleanModelIntegerResponseSIM1.r.u')
self.setupFileProcessingServiceForSim1(data_file_for_sim1,
SupportedFileTypes.R)
number_of_genomes = self.sim1FileProcessingService.number_of_genomes
number_of_trials = self.sim1FileProcessingService.number_of_trials
self.log.info(
"Testing %s genomes are successfully created as R files.",
number_of_genomes)
self.file_processing_service.createGenomes()
self.assertSim1TrialFilesSuccessfullyCreated(number_of_genomes,
number_of_trials)
def assertSim1TrialFilesSuccessfullyCreated(self, number_of_genomes,
number_of_trials):
trial_files_created = self.sim1FileProcessingService.createTrialFiles()
assert len(trial_files_created) == number_of_trials * number_of_genomes
assert os.path.isdir(self.current_working_dir)
total_created_files = [
file for file in os.listdir(self.generated_folder)
]
# 2*K files created + R*K trial files + SIM1MatrixFile
assert len(total_created_files) == (
2 * number_of_genomes) + len(trial_files_created) + 1
assert len([
file for file in total_created_files
if re.findall(r'trial\d*_genome\d*.*', file)
]) == len(trial_files_created)
def testDollarSignSyntaxValuesCorrectlyExtractedForR(self):
data_file = self.setTargetFile('SampleDataFiles',
'booleanModelTest.r.t')
self.setupFileProcessingService(data_file, SupportedFileTypes.R)
fp_service = self.file_processing_service
line_default = 'variableOne <- $gauss(0,1),name=varOne$;'
target_sequence_default = self.extractTargetSequencesFromLine(
line_default)[0]
assert fp_service.extractCoefficientName(
target_sequence_default) == 'varOne'
assert fp_service.extractDistributionName(
target_sequence_default) == SupportedDistributions.GAUSS
assert fp_service.extractParameters(target_sequence_default) == [
'0', '1'
]
line_no_name = 'variableOne <- $gamma(0,1)$;'
target_sequence_no_name = self.extractTargetSequencesFromLine(
line_no_name)[0]
assert fp_service.extractCoefficientName(
target_sequence_no_name) == 'coefficient1'
assert fp_service.extractDistributionName(
target_sequence_no_name) == SupportedDistributions.GAMMA
assert fp_service.extractParameters(target_sequence_no_name) == [
'0', '1'
]
line_quick = 'variableOne <- $0,name=varOne$;'
target_sequence_quick = self.extractTargetSequencesFromLine(
line_quick)[0]
assert fp_service.extractCoefficientName(
target_sequence_quick) == 'varOne'
assert fp_service.extractDistributionName(
target_sequence_quick) == SupportedDistributions.GAUSS
assert fp_service.extractParameters(target_sequence_quick) == ['0']
line_quick_no_name = 'variableOne <- $0$'
target_sequence_quick_no_name = self.extractTargetSequencesFromLine(
line_quick_no_name)[0]
assert fp_service.extractCoefficientName(
target_sequence_no_name) == 'coefficient2'
assert fp_service.extractDistributionName(
target_sequence_quick_no_name) == SupportedDistributions.GAUSS
assert fp_service.extractParameters(target_sequence_quick_no_name) == [
'0'
]
line_only_distribution_given = "$uniform(.8,1.2)$"
target_sequence_only_distribution_given = self.extractTargetSequencesFromLine(
line_only_distribution_given)[0]
assert fp_service.extractCoefficientName(
target_sequence_only_distribution_given) == 'coefficient3'
assert fp_service.extractDistributionName(
target_sequence_only_distribution_given
) == SupportedDistributions.UNIFORM
assert fp_service.extractParameters(
target_sequence_only_distribution_given) == ['.8', '1.2']
bool_default = '$boolean(0.5), name= B_AKT2$,'
target_sequence_bool_default = self.extractTargetSequencesFromLine(
bool_default)[0]
assert fp_service.extractCoefficientName(
target_sequence_bool_default) == 'B_AKT2'
assert fp_service.extractDistributionName(
target_sequence_bool_default) == SupportedDistributions.BOOLEAN
assert fp_service.extractParameters(target_sequence_bool_default) == [
'0.5'
]
def testDollarSignSyntaxValuesCorrectlyExtractedForMATLAB(self):
data_file = self.setTargetFile('SampleDataFiles',
'WNT_ERK_crosstalk.octave')
self.setupFileProcessingService(data_file, SupportedFileTypes.MATLAB)
fp_service = self.file_processing_service
line_default = 'variableOne=$gauss(0,1),name=varOne$;'
target_sequence_default = self.extractTargetSequencesFromLine(
line_default)[0]
assert fp_service.extractCoefficientName(
target_sequence_default) == 'varOne'
assert fp_service.extractDistributionName(
target_sequence_default) == SupportedDistributions.GAUSS
assert fp_service.extractParameters(target_sequence_default) == [
'0', '1'
]
line_no_name = 'variableOne=$gamma(0,1)$;'
target_sequence_no_name = self.extractTargetSequencesFromLine(
line_no_name)[0]
assert fp_service.extractCoefficientName(
target_sequence_no_name) == 'coefficient1'
assert fp_service.extractDistributionName(
target_sequence_no_name) == SupportedDistributions.GAMMA
assert fp_service.extractParameters(target_sequence_no_name) == [
'0', '1'
]
line_quick = 'variableOne=$0,name=varOne$;'
target_sequence_quick = self.extractTargetSequencesFromLine(
line_quick)[0]
assert fp_service.extractCoefficientName(
target_sequence_quick) == 'varOne'
assert fp_service.extractDistributionName(
target_sequence_quick) == SupportedDistributions.GAUSS
assert fp_service.extractParameters(target_sequence_quick) == ['0']
line_quick_no_name = 'variableOne=$0$'
target_sequence_quick_no_name = self.extractTargetSequencesFromLine(
line_quick_no_name)[0]
assert fp_service.extractCoefficientName(
target_sequence_no_name) == 'coefficient2'
assert fp_service.extractDistributionName(
target_sequence_quick_no_name) == SupportedDistributions.GAUSS
assert fp_service.extractParameters(target_sequence_quick_no_name) == [
'0'
]
def testMultipleTargetSequenceReplacementsPerLine(self):
data_file = self.setTargetFile('SampleDataFiles',
'WNT_ERK_crosstalk.octave')
self.setupFileProcessingService(data_file, SupportedFileTypes.MATLAB)
fp_service = self.file_processing_service
line_default = 'bogus_array = [$gauss(.1,.01),name=bogus_variable_one$ $gauss(.1,.01),name=bogus_variable_two$];'
target_sequences = self.extractTargetSequencesFromLine(line_default)
assert len(target_sequences) == 2
for i in range(0, len(target_sequences)):
target_sequence = target_sequences[i]
assert fp_service.extractCoefficientName(target_sequence).index(
"bogus_variable") == 0
assert fp_service.extractDistributionName(
target_sequence) == "gauss"
assert fp_service.extractParameters(target_sequence) == [
'.1', '.01'
]
def testDistributionsBehaveProperly(self):
data_file_octave = self.setTargetFile('SampleDataFiles',
'WNT_ERK_crosstalk.octave')
self.setupFileProcessingService(data_file_octave,
SupportedFileTypes.OCTAVE)
fp_service_octave = self.file_processing_service
self.assertDistributions(fp_service_octave)
data_file_r = self.setTargetFile('SampleDataFiles',
'booleanModelTest.r.t')
self.setupFileProcessingService(data_file_r, SupportedFileTypes.R)
fp_service_r = self.file_processing_service
self.assertDistributions(fp_service_r)
def assertDistributions(self, fp_service):
discrete_line = 'var discrete = $discrete([-3,-2,-1,0,1,2,3]), name=discrete$;'
self.assertAppropriateCoefficientValueParsed(fp_service, discrete_line,
float)
gauss_line = 'var gauss = $gauss(.1,.01),name=gauss$;'
self.assertAppropriateCoefficientValueParsed(fp_service, gauss_line,
float)
uniform_line = 'var uniform = $uniform(0,1),name=uniform$;'
self.assertAppropriateCoefficientValueParsed(fp_service, uniform_line,
float)
gamma_line = 'var gamma = $gamma(1,2),name=gamma$;'
self.assertAppropriateCoefficientValueParsed(fp_service, gamma_line,
float)
lognormal_line = 'var lognormal = $lognormal(.1,.01),name=lognormal$;'
self.assertAppropriateCoefficientValueParsed(fp_service,
lognormal_line, float)
binomial_line = 'var binomial = $binomial(1000,.3),name=binomial$;'
self.assertAppropriateCoefficientValueParsed(fp_service, binomial_line,
int)
poisson_line = 'var poisson = $poisson(500),name=poisson$;'
self.assertAppropriateCoefficientValueParsed(fp_service, poisson_line,
int)
boolean_line = 'var boolean = $boolean(.5),name=boolean$;'
self.assertAppropriateCoefficientValueParsed(fp_service, boolean_line,
int)
def assertAppropriateCoefficientValueParsed(self, fp_service, line,
expected_type):
target_sequence = self.extractTargetSequencesFromLine(line)[0]
distribution = fp_service.extractDistributionName(target_sequence)
params = fp_service.extractParameters(target_sequence)
coefficient_val = fp_service.retrieveCoefficientValueFromDistribution(
distribution, params)
assert isinstance(coefficient_val, expected_type)
def extractTargetSequencesFromLine(self, line):
return self.file_processing_service.extractTargetSequences(line)
def setupFileProcessingService(self, data_file, file_type):
self.file_processing_service = FileProcessingService(
data_file, file_type, 10, self.current_working_dir)
self.generated_folder = self.current_working_dir + self.file_processing_service.GENERATED_FOLDER_NAME
def __init__(self, u_file_instance, file_type, number_of_genomes, number_of_trials, path=os.getcwd()):
self.number_of_trials = SafeCastUtil.safeCast(number_of_trials, int, self.DEFAULT_NUM_TRIALS)
# Note r_trials is analogous to permutations
FileProcessingService.__init__(self, u_file_instance, file_type, number_of_genomes, path)