'''
To create config ini file from SBML file in folder
Reading the data inside the xml file to a variable
data
'''
config_output_path = Path.cwd()
Model_name = "Repressilator_TestModel"
antimony_str = te.sbmlToAntimony(onlinemodelstr)
system_type = 'Test_Model, Repressilator'
tspan = '[0, 600, 601]'
#Name the Tspan to be simulated [x, y ,z] x = start time, y = end time, z = number of points inbetween
inicomplete, settings_database = onlinegen.sbmltoconfig(onlinemodelstr, system_type, tspan, Model_name, config_output_path)
#Returns the config file statement and the nested dictionary of the settings
#Change onlinemodelstr to localmodelstr to convert local xml file
'''
To plot based on Tutorial 2 Simulation
Refer to Tutorial 2 for in detail explaination
of each line
'''
#Add model to database; refer to Tutorial 1 Part 2
filename = 'Repressilator_TestModel_coremodel.ini' #Enter config to be added to database
sim_system_type = mh.config_to_database(filename)
"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 = '''
// Reactions:
Reaction1: X => ; kd_mRNA*X;