def _answer_query_using_bte(self, input_qnode_key: str, output_qnode_key: str, qg: QueryGraph,
answer_kg: QGOrganizedKnowledgeGraph, valid_bte_inputs_dict: Dict[str, Set[str]],
log: ARAXResponse) -> Tuple[QGOrganizedKnowledgeGraph, Set[str]]:
accepted_curies = set()
qedge_key = next(qedge_key for qedge_key in qg.edges)
qedge = qg.edges[qedge_key]
input_qnode = qg.nodes[input_qnode_key]
output_qnode = qg.nodes[output_qnode_key]
# Send this single-edge query to BTE, input curie by input curie (adding findings to our answer KG as we go)
for curie in input_qnode.id:
# Consider all different combinations of qnode types (can be multiple if gene/protein)
for input_qnode_category, output_qnode_category in itertools.product(input_qnode.category, output_qnode.category):
if eu.get_curie_prefix(curie) in valid_bte_inputs_dict['curie_prefixes']:
accepted_curies.add(curie)
try:
loop = asyncio.new_event_loop()
seqd = SingleEdgeQueryDispatcher(input_cls=input_qnode_category,
output_cls=output_qnode_category,
pred=qedge.predicate,
input_id=eu.get_curie_prefix(curie),
values=eu.get_curie_local_id(curie),
loop=loop)
log.debug(f"Sending query to BTE: {curie}-{qedge.predicate if qedge.predicate else ''}->{output_qnode_category}")
seqd.query()
reasoner_std_response = seqd.to_reasoner_std()
except Exception:
trace_back = traceback.format_exc()
error_type, error, _ = sys.exc_info()
log.error(f"Encountered a problem while using BioThings Explorer. {trace_back}",
error_code=error_type.__name__)
return answer_kg, accepted_curies
else:
answer_kg = self._add_answers_to_kg(answer_kg, reasoner_std_response, input_qnode_key, output_qnode_key, qedge_key, log)
return answer_kg, accepted_curies
def _answer_query_using_bte(self, input_qnode, output_qnode, qedge, answer_kg, valid_bte_inputs_dict):
accepted_curies = set()
# Send this single-edge query to BTE, once per input curie (adding findings to our answer KG as we go)
for curie in input_qnode.curie:
if eu.get_curie_prefix(curie) in valid_bte_inputs_dict['curie_prefixes']:
accepted_curies.add(curie)
try:
loop = asyncio.new_event_loop()
seqd = SingleEdgeQueryDispatcher(input_cls=input_qnode.type,
output_cls=output_qnode.type,
pred=qedge.type,
input_id=eu.get_curie_prefix(curie),
values=eu.get_curie_local_id(curie),
loop=loop)
self.response.debug(f"Sending query to BTE: {curie}-{qedge.type if qedge.type else ''}->{output_qnode.type}")
seqd.query()
reasoner_std_response = seqd.to_reasoner_std()
except Exception:
trace_back = traceback.format_exc()
error_type, error, _ = sys.exc_info()
self.response.error(f"Encountered a problem while using BioThings Explorer. {trace_back}",
error_code=error_type.__name__)
return answer_kg, accepted_curies
else:
answer_kg = self._add_answers_to_kg(answer_kg, reasoner_std_response, input_qnode.id, output_qnode.id, qedge.id)
return answer_kg, accepted_curies
def setUpClass(cls):
seqd = SingleEdgeQueryDispatcher(
input_cls="ChemicalSubstance",
output_cls="Protein",
pred="",
input_id="CHEMBL.COMPOUND",
values="CHEMBL112",
)
seqd.query()
cls.response = seqd.to_reasoner_std()
from biothings_explorer.user_query_dispatcher import SingleEdgeQueryDispatcher
seqd = SingleEdgeQueryDispatcher(output_cls = "ChemicalSubstance",
input_cls = "Disease",
pred = "physically_interacts_with",
input_id = "NCBIGene",
values = "1017")
query = seqd.query(verbose = True)
output = seqd.to_reasoner_std() # Still need to read documentation for this method
print()
print(output.keys())
# output: dict_keys(['query_graph', 'knowledge_graph', 'results'])
queryGraph = output["query_graph"]
knowledgeGraphNodes = output["knowledge_graph"]["nodes"][:5]
knowledgeGraphEdges = output["knowledge_graph"]["edges"][:5]
# output["results"][:5]
print("\nQuery Graph:")
print(queryGraph)
print("\nKnowledge Graph Nodes:")
print(knowledgeGraphNodes)
print("\nKnowledge Graph Edges:")
print(knowledgeGraphEdges)
