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)
def test_compare_equations_fail(self):
#Typo in Reaction 10 where it generates PX instead of X
antimony_str_fail = '''
// Reactions:
Reaction1: X => ; kd_mRNA*X;
Reaction2: Y => ; kd_mRNA*Y;
Reaction3: Z => ; kd_mRNA*Z;
Reaction4: => PX; k_tl*X;
Reaction5: => PY; k_tl*Y;
Reaction6: => PZ; k_tl*Z;
Reaction7: PX => ; kd_prot*PX;
Reaction8: PY => ; kd_prot*PY;
Reaction9: PZ => ; kd_prot*PZ;
Reaction10: => PX; a0_tr + a_tr*KM^n/(KM^n + PZ^n);
Reaction11: => Y; a0_tr + a_tr*KM^n/(KM^n + PX^n);
Reaction12: => Z; a0_tr + a_tr*KM^n/(KM^n + PY^n);
'''
reaction_test = onlinegen.gen_reactions(antimony_str_fail)
eqn_clean = ['']
before = len(reaction_test)
after = 0
while before != after:
before = len(reaction_test)
reaction_test = onlinegen.clean_reactions(reaction_test)
after = len(reaction_test)
for eqn in reaction_test:
eqn = onlinegen.eqnreplace(eqn)
eqn_clean.append(eqn)
assert eqn_clean == eqn_sample, 'Reactions not sorted properly'
return reaction_test, eqn_clean
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;
Reaction2: Y => ; kd_mRNA*Y;
Reaction3: Z => ; kd_mRNA*Z;
Reaction4: => PX; k_tl*X;
Reaction5: => PY; k_tl*Y;
Reaction6: => PZ; k_tl*Z;
Reaction7: PX => ; kd_prot*PX;
Reaction8: PY => ; kd_prot*PY;
Reaction9: PZ => ; kd_prot*PZ;
Reaction10: => X; a0_tr + a_tr*KM^n/(KM^n + PZ^n);
Reaction11: => Y; a0_tr + a_tr*KM^n/(KM^n + PX^n);
Reaction12: => Z; a0_tr + a_tr*KM^n/(KM^n + PY^n);
'''
reaction_test = onlinegen.gen_reactions(antimony_str_test)
print(reaction_test)
eqn_clean = ['']
before = len(reaction_test)
after = 0
while before != after:
before = len(reaction_test)
reaction_test = onlinegen.clean_reactions(reaction_test)
after = len(reaction_test)
for eqn in reaction_test:
eqn = onlinegen.eqnreplace(eqn)
eqn_clean.append(eqn)
assert eqn_clean == eqn_sample, 'Reactions not sorted properly'
def test_missingparameterunit_fail(self):
#missing unit parameter t_ave
parametersunits_dict_fail = {
'beta': 'per_sec',
'alpha0': 'per_sec',
'alpha': 'per_sec',
'eff': 'per_sec',
'n': 'per_sec',
'KM': 'per_sec',
'tau_mRNA': 'per_sec',
'tau_prot': 'per_sec',
'kd_mRNA': 'per_sec',
'kd_prot': 'per_sec',
'k_tl': 'per_sec',
'a_tr': 'per_sec',
'ps_a': 'per_sec',
'ps_0': 'per_sec',
'a0_tr': 'per_sec',
}
settings_test = {
"Species": species_dict,
"parameters": parameter_dict,
"units": parametersunits_dict_fail,
"equations": equations,
"description": description_store
}
testconfig = onlinegen.gen_config(settings_test, system_type, tspan)
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)
def test_tspanchecker_fail_3(self):
#Start time larger than end time
tspan = '[6000, 600, 61]'
onlinegen.tspanchecker(tspan)
def test_tspanchecker_fail_2(self):
#Missing ']' at end of tspan
tspan = '0, 600, 61]'
onlinegen.tspanchecker(tspan)
def test_tspanchecker_fail_1(self):
#Missing '[' at start of tspan
tspan = '0, 600, 61]'
onlinegen.tspanchecker(tspan)
def test_tspanchecker(self):
#Check if tspan has been declared correctly
#Checker is at the start of sbmltoconfig function
tspan = '[0, 600, 61]'
onlinegen.tspanchecker(tspan)
def test_makesampleconfig(self):
testconfig = onlinegen.gen_config(settings_test, system_type, tspan)
assert testconfig == sampleconfig, 'Config Statements are not the same'
"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 = '''