def get_time_interval(lst: KQMLList) -> tra.TimeInterval:
try:
lb = lst.gets('lower-bound')
ub = lst.gets('upper-bound')
unit = lst.gets('unit')
return tra.TimeInterval(lb, ub, unit)
except Exception as e:
raise tra.InvalidTimeIntervalError(e)
def get_molecular_quantity(lst: KQMLList) -> tra.MolecularQuantity:
try:
quant_type = lst.gets('type')
value = lst.gets('value')
if quant_type == 'concentration':
unit = lst.gets('unit')
else:
unit = None
return tra.MolecularQuantity(quant_type, value, unit)
except Exception as e:
raise tra.InvalidMolecularQuantityError(e)
def get_molecular_condition(lst: KQMLList) -> tra.MolecularCondition:
try:
condition_type = lst.gets('type')
quantity_ref_lst = lst.get('quantity')
quantity = get_molecular_quantity_ref(quantity_ref_lst)
if condition_type == 'exact':
value = get_molecular_quantity(lst.get('value'))
elif condition_type == 'multiple':
value = lst.gets('value')
else:
value = None
return tra.MolecularCondition(condition_type, quantity, value)
except Exception as e:
raise tra.InvalidMolecularConditionError(e)
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 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
