def test_configpossiblechecker(self):
#Test is SBML string can be converted with this module
#Checker is at the start of sbmltoconfig function
Biomodels_ID = 'BIOMD0000000012' #Represillator Model
onlinemodelstr = onlinegen.get_online_biomodel(Biomodels_ID)
onlinegen.configpossiblechecker(onlinemodelstr)
import BMSS.models.setup_sim as sm
import BMSS.simulation as sim
if __name__ == '__main__':
'''
Use following function to create SBML from BIOModel online database
Outputs both the sbmlstring and the XML file
'''
Biomodels_ID = 'BIOMD0000000012'
#Input biomodels ID number
SBMLfilename = 'Repressilator_TestModel_SBML.xml' #Name the XML file
outputpath = str(Path.cwd()/SBMLfilename)
onlinemodelstr = onlinegen.get_online_biomodel(Biomodels_ID, outputfile=outputpath)
antimony_str = te.sbmlToAntimony(onlinemodelstr)
'''
Use the following function to create SBML from local folder.
XML file must be in same folder as this Tutorial
'''
inputpath = str(Path.cwd()/'Repressilator_TestModel_SBML_1.xml')
with open(inputpath, 'r', encoding='utf8', errors='ignore') as f:
localmodelstr = f.read()
'''
To create config ini file from SBML file in folder
def test_configpossiblechecker_fail(self):
#SBML string is too complex for module
Biomodels_ID = 'MODEL1606100000' #Model too complicated to convert
onlinemodelstr = onlinegen.get_online_biomodel(Biomodels_ID)
onlinegen.configpossiblechecker(onlinemodelstr)
"description": description_store,
"reference": reference_store,
"species_parameter_descriptions": species_parameter_descriptions
}
eqn_sample = [
'', ' dPX = +(k_tl*X) -(kd_prot*PX)', ' dPY = +(k_tl*Y) -(kd_prot*PY)',
' dPZ = +(k_tl*Z) -(kd_prot*PZ)',
' dX = +(a0_tr + a_tr*KM**n/(KM**n + PZ**n)) -(kd_mRNA*X)',
' dY = +(a0_tr + a_tr*KM**n/(KM**n + PX**n)) -(kd_mRNA*Y)',
' dZ = +(a0_tr + a_tr*KM**n/(KM**n + PY**n)) -(kd_mRNA*Z)'
]
Biomodels_ID = 'BIOMD0000000012' #Represillator Model
output_path = tempfile.gettempdir()
onlinemodelstr = onlinegen.get_online_biomodel(Biomodels_ID)
sampleconfig, settings_sample = onlinegen.sbmltoconfig(onlinemodelstr,
system_type, tspan,
Model_name, output_path)
class TestConfigGen:
def test_makesampleconfig(self):
testconfig = onlinegen.gen_config(settings_test, system_type, tspan)
assert testconfig == sampleconfig, 'Config Statements are not the same'
def test_compare_equations(self):
#Tests whether reactions pertaining to the same species are combined
global eqn_sample
antimony_str_test = '''