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
def get_temporal_pattern(lst: KQMLList) -> tra.TemporalPattern:
pattern_type = lst.gets('type')
entities_lst = lst.get('entities')
entities = []
if entities_lst is None:
entities_lst = []
for e in entities_lst:
entity = get_molecular_entity(e)
entities.append(entity)
time_limit_lst = lst.get('time-limit')
if time_limit_lst is None:
time_limit = None
else:
time_limit = get_time_interval(time_limit_lst)
# TODO: handle more pattern-specific extra arguments
value_lst = lst.get('value')
if value_lst is not None:
value = get_molecular_quantity(value_lst)
else:
value = None
tp = tra.TemporalPattern(pattern_type, entities, time_limit, value=value)
return tp