def test_missing_monomer_condition():
stmts = [Activation(Agent('BRAF'), Agent('KRAS'))]
model = tra_module.assemble_model(stmts)
entity = Agent('HRAS')
quantity = tra.MolecularQuantityReference('total', entity)
condition = tra.MolecularCondition('multiple', quantity, 10)
tra.apply_condition(model, condition)
def get_molecular_quantity_ref(lst: KQMLList) -> tra.MolecularQuantityReference:
try:
quant_type = lst.gets('type')
entity_lst = lst.get('entity')
entity = get_molecular_entity(entity_lst)
return tra.MolecularQuantityReference(quant_type, entity)
except Exception as e:
raise tra.InvalidMolecularQuantityRefError(e)
def test_seq_hyp_test():
stmts = [Activation(Agent('BRAF'), Agent('KRAS'))]
model = tra_module.assemble_model(stmts)
entity = Agent('KRAS', activity=ActivityCondition('activity', True))
quantity = tra.MolecularQuantityReference('total', entity)
quant = tra.MolecularQuantity('qualitative', 'high')
pattern = tra.TemporalPattern('sometime_value', [entity],
None,
value=quant)
t = tra.TRA()
from bioagents.tra.model_checker import HypothesisTester
ht = HypothesisTester(alpha=0.1, beta=0.1, delta=0.05, prob=0.8)
res = t.check_property(model,
pattern,
conditions=None,
max_time=20000,
num_times=100,
hypothesis_tester=ht)
sat_rate, num_sim, kpat, pat_obj, fig_path = res
assert sat_rate == 1.0
assert num_sim == 18