Skip to content

Commit

Permalink
Merge remote-tracking branch 'origin/2328patch' #2328
Browse files Browse the repository at this point in the history
  • Loading branch information
@amykglen
amykglen committed Aug 23, 2024
2 parents 5c7870c + 0da1648 commit 175dd89
Show file tree
Hide file tree
Showing 3 changed files with 53 additions and 10 deletions.
28 changes: 24 additions & 4 deletions code/ARAX/ARAXQuery/ARAX_expander.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@
from openapi_server.models.q_node import QNode
from openapi_server.models.edge import Edge
from openapi_server.models.attribute_constraint import AttributeConstraint
from openapi_server.models.attribute import Attribute
from Expand.kg2_querier import KG2Querier
from Expand.trapi_querier import TRAPIQuerier

Expand Down Expand Up @@ -59,6 +60,9 @@ def __init__(self):
"aggregator_knowledge_source": {"==": "*"}}
self.supported_qedge_qualifier_constraints = {"biolink:qualified_predicate", "biolink:object_direction_qualifier",
"biolink:object_aspect_qualifier"}
self.higher_level_treats_predicates = {"biolink:treats_or_applied_or_studied_to_treat",
"biolink:applied_to_treat",
"biolink:studied_to_treat"}

def describe_me(self):
"""
Expand Down Expand Up @@ -504,6 +508,16 @@ def apply(self, response, input_parameters, mode: str = "ARAX"):
for kedge_key in kedges_to_remove:
if kedge_key in overarching_kg.edges_by_qg_id[qedge_key]:
del overarching_kg.edges_by_qg_id[qedge_key][kedge_key]
# Remove KG2 SemMedDB treats_or_applied-type edges if this is an inferred treats query
if alter_kg2_treats_edges:
edge_keys_to_remove = {edge_key for edge_key, edge in overarching_kg.edges_by_qg_id[qedge_key].items()
if edge.predicate in self.higher_level_treats_predicates and
any(source.resource_id == "infores:rtx-kg2" for source in edge.sources) and
any(source.resource_id == "infores:semmeddb" for source in edge.sources)}
log.debug(f"Removing {len(edge_keys_to_remove)} KG2 semmeddb treats_or_applied-type edges "
f"fulfilling {qedge_key}")
for edge_key in edge_keys_to_remove:
del overarching_kg.edges_by_qg_id[qedge_key][edge_key]

if mode != "RTXKG2":
# Apply any kryptonite ("not") qedges
Expand Down Expand Up @@ -579,11 +593,17 @@ def apply(self, response, input_parameters, mode: str = "ARAX"):
# Second half of patch for #2328; edit KG2 'treats_or_applied_or_studied_to_treat' edges to just 'treats'
if mode != "RTXKG2" and do_issue_2328_patch and inferred_qedge_keys:
num_edges_altered = 0
higher_level_treats_predicates = {"biolink:treats_or_applied_or_studied_to_treat",
"biolink:applied_to_treat"}
for edge in message.knowledge_graph.edges.values():
is_kg2_edge = any(source.resource_id == "infores:rtx-kg2" for source in edge.sources)
if is_kg2_edge and edge.predicate in higher_level_treats_predicates:
if is_kg2_edge and edge.predicate in self.higher_level_treats_predicates:
# Record the original KG2 predicate in an attribute
edge.attributes.append(Attribute(attribute_type_id="biolink:original_predicate",
value=edge.predicate,
value_type_id="biolink:predicate",
description="Predicate as it appears in RTX-KG2, prior to "
"alteration by ARAX.",
attribute_source="infores:arax"))
# Then change the predicate to treats
edge.predicate = "biolink:treats"
num_edges_altered += 1
if num_edges_altered:
Expand Down Expand Up @@ -1132,7 +1152,7 @@ def _apply_any_kryptonite_edges(organized_kg: QGOrganizedKnowledgeGraph, full_qu
organized_kg.edges_by_qg_id[qedge_key].pop(edge_key)

if not organized_kg.edges_by_qg_id[qedge_key]:
log.warning(f"All {qedge_key} edges have been deleted due to an Exclude=true (i.e., 'kryptonite') edge!")
log.warning(f"All {qedge_key} edges have been deleted!")

@staticmethod
def _prune_kg(qnode_key_to_prune: str, prune_threshold: int, kg: QGOrganizedKnowledgeGraph,
Expand Down
12 changes: 8 additions & 4 deletions code/ARAX/ARAXQuery/Expand/trapi_querier.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -56,6 +56,9 @@ async def answer_one_hop_query_async(self, query_graph: QueryGraph,
"""
This function answers a one-hop (single-edge) query using the specified KP.
:param query_graph: A TRAPI query graph.
:param alter_kg2_treats_edges: If true, will query KG2 for higher-level treats-type predicates instead of just
'treats'. Any higher-level returned edges will later be altered to have 'treats'
predicates in ARAX_expander.py.
:return: An (almost) TRAPI knowledge graph containing all of the nodes and edges returned as
results for the query. (Organized by QG IDs.)
"""
Expand Down Expand Up @@ -90,10 +93,11 @@ async def answer_one_hop_query_async(self, query_graph: QueryGraph,
# Patch to address lack of answers from KG2 for treats queries after treats refactor #2328
if alter_kg2_treats_edges and self.kp_infores_curie == "infores:rtx-kg2":
for qedge in qg_copy.edges.values(): # Note there's only ever one qedge per QG here
qedge.predicates = ["biolink:treats_or_applied_or_studied_to_treat" if predicate == "biolink:treats" else predicate
for predicate in qedge.predicates]
log.info(f"For querying infores:rtx-kg2, edited the QG for this single-hop query to use "
f"the biolink:treats_or_applied_or_studied_to_treat predicate (instead of biolink:treats)")
qedge.predicates = list(set(qedge.predicates).union({"biolink:treats_or_applied_or_studied_to_treat",
"biolink:applied_to_treat",
"biolink:studied_to_treat"}))
log.info(f"For querying infores:rtx-kg2, edited {qedge_key} to use higher treats-type predicates: "
f"{qedge.predicates}")

# Answer the query using the KP and load its answers into our object model
final_kg = await self._answer_query_using_kp_async(qg_copy)
Expand Down
23 changes: 21 additions & 2 deletions code/ARAX/test/test_ARAX_expand.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1531,7 +1531,15 @@ def test_treats_patch_issue_2328():
"object": "disease",
"subject": "chemical",
"predicates": ["biolink:treats"],
"knowledge_type": "inferred"
"knowledge_type": "inferred",
"attribute_constraints": [
{
"id": "knowledge_source",
"name": "knowledge source",
"value": ["infores:rtx-kg2"],
"operator": "=="
}
]
}
}
}
Expand All @@ -1541,9 +1549,11 @@ def test_treats_patch_issue_2328():
if any(source.resource_id == "infores:rtx-kg2" for source in edge.sources)]
print(f"Answer includes {len(kg2_edges_treats)} edges from KG2")
assert kg2_edges_treats
print(kg2_edges_treats)
for edge in kg2_edges_treats:
assert edge.predicate == "biolink:treats"
assert edge.attributes
assert not any(source.resource_id == "infores:semmeddb" for source in edge.sources)

# Verify that the predicate editing doesn't happen outside of inferred mode
query = {
Expand All @@ -1559,7 +1569,15 @@ def test_treats_patch_issue_2328():
"t_edge": {
"object": "disease",
"subject": "chemical",
"predicates": ["biolink:treats_or_applied_or_studied_to_treat", "biolink:applied_to_treat"]
"predicates": ["biolink:treats_or_applied_or_studied_to_treat", "biolink:applied_to_treat"],
"attribute_constraints": [
{
"id": "knowledge_source",
"name": "knowledge source",
"value": ["infores:rtx-kg2"],
"operator": "=="
}
]
}
}
}
Expand All @@ -1570,6 +1588,7 @@ def test_treats_patch_issue_2328():
print(f"Answer includes {len(kg2_edges_treats_or)} edges from KG2")
assert kg2_edges_treats_or
assert any(edge for edge in kg2_edges_treats_or if edge.predicate == "biolink:treats_or_applied_or_studied_to_treat")
assert any(edge for edge in kg2_edges_treats_or if edge.predicate == "biolink:applied_to_treat")


if __name__ == "__main__":
Expand Down

0 comments on commit 175dd89

Please sign in to comment.