def test_batch_drug_wildcard_query(self):
for trapi_version, queries in self.drug_batch_queries.items():
query = Query.load(trapi_version, None, query=queries[0])
interface = TrapiInterface(query=query)
interface.build_chp_queries()
interface.run_chp_queries()
response = interface.construct_trapi_response()
def test_simple_batch_query(self):
# These are simple queries
logger.info('Running batch simple query test.')
for trapi_version, queries in self.batch_queries.items():
query = Query.load(trapi_version, None, query=queries[0])
interface = TrapiInterface(query=query)
interface.build_chp_queries()
interface.run_chp_queries()
response = interface.construct_trapi_response()
def test_simple_single_query(self):
# This is a simple query
logger.info('Running single simple query test.')
for trapi_version, queries in self.queries.items():
query = Query.load(trapi_version, None, query=queries[1])
interface = TrapiInterface(query=query)
interface.build_chp_queries()
interface.run_chp_queries()
response = interface.construct_trapi_response()
def test_wildcard_batch_onehop_query(self):
for trapi_version, queries in self.wildcard_batch_queries.items():
for name, query_dict in queries.items():
#if name != 'gene_to_disease_proxy_context':
# continue
query = Query.load(trapi_version, None, query=query_dict)
interface = TrapiInterface(query=query)
interface.build_chp_queries()
interface.run_chp_queries()
response = interface.construct_trapi_response()
def test_inverse_wildcard_query(self):
for trapi_version, queries in self.gene_queries.items():
query = Query.load(trapi_version, None, query=queries[0])
for edge_id, edge in query.message.query_graph.edges.items():
predicate = edge.predicates[0]
inverse = edge.predicates[0].get_inverse()
edge.set_predicates(inverse)
interface = TrapiInterface(query=query)
interface.build_chp_queries()
interface.run_chp_queries()
response = interface.construct_trapi_response()
def test_inverse_query(self):
# This is a simple query
logger.info('Running default inverse query test.')
for trapi_version, queries in self.queries.items():
query = Query.load(trapi_version, None, query=queries[1])
for edge_id, edge in query.message.query_graph.edges.items():
predicate = edge.predicates[0]
inverse = edge.predicates[0].get_inverse()
edge.set_predicates(inverse)
interface = TrapiInterface(query=query)
interface.build_chp_queries()
interface.run_chp_queries()
response = interface.construct_trapi_response()
def process_request(self, request, trapi_version):
""" Helper function that extracts the query from the message.
"""
logger.info('Starting query.')
query = Query.load(self.trapi_version,
biolink_version=None,
query=request.data)
# Setup query in Base Processor
self.setup_query(query)
logger.info('Query loaded')
return query
def test_inverse_onehop_query(self):
for trapi_version, queries in self.standard_single_queries.items():
for name, query_dict in queries.items():
#if name != 'gene_to_disease_proxy_context':
# continue
query = Query.load(trapi_version, None, query=query_dict)
for edge_id, edge in query.message.query_graph.edges.items():
predicate = edge.predicates[0]
inverse = edge.predicates[0].get_inverse()
if inverse is not None:
edge.set_predicates(inverse)
interface = TrapiInterface(query=query)
interface.build_chp_queries()
interface.run_chp_queries()
response = interface.construct_trapi_response()
def test_ars_notnone_queries(self):
from trapi_model.query import Query
from trapi_model.exceptions import UnknownBiolinkEntity
ars_predicates_dir = os.path.join(self.ncats_test_dir,
'ars-requests/not-none')
# Run tests
for filename in os.listdir(ars_predicates_dir):
try:
if os.path.splitext(filename)[-1] == '.json':
filepath = os.path.join(ars_predicates_dir, filename)
query = Query.load('1.0', None, query_filepath=filepath)
query_dict = query.to_dict()
if query.is_batch_query():
batch = query.expand_batch_query()
except UnknownBiolinkEntity as ex:
logger.critical('Failed on file {} with {}'.format(
filename, ex.message))
def get_responses(self, queries=None, trapi_queries=None):
# Initialize interface
interface = TrapiInterface(
bkb_handler=self.bkb_handler,
dynamic_reasoner=self.dynamic_reasoner,
joint_reasoner=self.joint_reasoner,
)
# Load queries
if trapi_queries is None:
trapi_queries = [
Query.load(query["trapi_version"], None, query=query)
for query in queries
]
# Process trapi query
interface.setup_trapi_queries(trapi_queries)
# Build CHP queries
interface.build_chp_queries()
# Run CHP queries
interface.run_chp_queries()
# Get Responses
responses = interface.construct_trapi_responses()
return responses
def test_inverse_query(self):
standard_queries = copy.deepcopy(self.standard_queries)
descriptions = [
query.pop("test_description", None)
for query in self.standard_queries
]
# Make inverse queries
trapi_queries = [
Query.load(query["trapi_version"], None, query=query)
for query in standard_queries
]
for query in trapi_queries:
for edge_id, edge in query.message.query_graph.edges.items():
predicate = edge.predicates[0]
inverse = edge.predicates[0].get_inverse()
if inverse is not None:
edge.set_predicates(inverse)
# Switch subject and object
edge_subject = copy.deepcopy(edge.subject)
edge_object = copy.deepcopy(edge.object)
edge.subject = edge_object
edge.object = edge_subject
responses = self.get_responses(trapi_queries=trapi_queries)
