def handle_data_entity(context, phenotype: PhenotypeModel, define_name, final):
print('data entity')
pe = PhenotypeEntity(define_name, 'define', final=final)
call = get_method_call(context.getChild(0))
# hasSepsis = PhenotypeEntity('hasSepsis', 'define',
# library='ClarityNLP',
# funct='ProviderAssertion',
# named_arguments={
# "termsets": ['Sepsis'],
# "documentsets": [
# 'ProviderNotes',
# "Radiology"
# ]
# })
pe["funct"] = call["funct"]
pe["library"] = call["library"]
named_args = call["named_arguments"]
args = call["arguments"]
if named_args:
pe["named_arguments"] = named_args
if args and len(args) > 0:
pe["arguments"] = args
if not phenotype.data_entities:
phenotype.data_entities = list()
phenotype.data_entities.append(pe)
def handle_tuple(context, phenotype: PhenotypeModel, define_name, final):
log('tuple')
obj = get_obj_context(context.getChild(0).getChild(1), to_string=True)
num_children = len(context.children)
op_raw_text = ''
tuple_name = '{}_Step1'.format(define_name)
if num_children == 2:
operation = parse_operation(context.getChild(1), tuple_name, final)
if operation:
if not phenotype.operations:
phenotype.operations = list()
phenotype.operations.append(operation)
op_raw_text = operation.get('raw_text')
else:
operation = None
raw_text = '''
Tuple {}
{}
'''
if not operation:
where = ''
else:
where = 'where {}'.format(op_raw_text)
tuple_str = json.dumps(obj, indent=4)
pe = PhenotypeEntity(tuple_name, 'define', final=final, tuple_=True, tuple_object=obj, tuple_predicate=operation,
raw_text=raw_text.format(tuple_str, where), tuple_raw_text='Tuple {}'.format(tuple_str))
if not phenotype.tuples:
phenotype.tuples = list()
phenotype.tuples.append(pe)