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Fix aragorn mvp2 #63

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Merged
maximusunc merged 3 commits into from
Jan 7, 2026
Merged

Fix aragorn mvp2 #63

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c857dfb
Fix MVP2 query expansion to use more explicit keys
maximusunc Jan 7, 2026
f474ef7
Run black
maximusunc Jan 7, 2026
6e157b3
Bump patch version
maximusunc Jan 7, 2026
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2 changes: 1 addition & 1 deletion shepherd_server/openapi-config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ contact:
x-id: https://github.com/maximusunc
x-role: responsible developer
description: '<img src="/static/favicon.png" width="200px"><br /><br />Shepherd: Translator Autonomous Relay Agent Platform'
version: 0.5.3
version: 0.5.4
servers:
- description: Default server
url: https://shepherd.renci.org
Expand Down
8 changes: 4 additions & 4 deletions workers/aragorn_lookup/rules_with_types_cleaned_finalized.json
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Expand Up @@ -3602,7 +3602,7 @@
}
}
],
"{\"predicate\": \"biolink:affects\", \"qualifier_constraints\": [{\"qualifier_set\": [{\"qualifier_type_id\": \"biolink:object_aspect_qualifier\", \"qualifier_value\": \"activity\"}, {\"qualifier_type_id\": \"biolink:object_direction_qualifier\", \"qualifier_value\": \"increased\"}]}]}": [
"{\"object_aspect_qualifier\": \"activity\", \"object_direction_qualifier\": \"increased\", \"predicate\": \"biolink:affects\"}": [
{
"Rule": "?a decreased_abundance_biolink:affects ?b ?a increased_activity_or_abundance_biolink:affects ?b => ?a increased_activity_biolink:affects ?b",
"Head Coverage": "0.000279586",
Expand Down Expand Up @@ -5508,7 +5508,7 @@
}
}
],
"{\"predicate\": \"biolink:affects\", \"qualifier_constraints\": [{\"qualifier_set\": [{\"qualifier_type_id\": \"biolink:object_aspect_qualifier\", \"qualifier_value\": \"activity\"}, {\"qualifier_type_id\": \"biolink:object_direction_qualifier\", \"qualifier_value\": \"decreased\"}]}]}": [
"{\"object_aspect_qualifier\": \"activity\", \"object_direction_qualifier\": \"decreased\", \"predicate\": \"biolink:affects\"}": [
{
"Rule": "?a decreased_activity_or_abundance_biolink:affects ?b ?a increased_molecular_interaction_biolink:affects ?b => ?a decreased_activity_biolink:affects ?b",
"Head Coverage": "0.000033348",
Expand Down Expand Up @@ -7192,7 +7192,7 @@
}
}
],
"{\"predicate\": \"biolink:affects\", \"qualifier_constraints\": [{\"qualifier_set\": [{\"qualifier_type_id\": \"biolink:object_aspect_qualifier\", \"qualifier_value\": \"activity_or_abundance\"}, {\"qualifier_type_id\": \"biolink:object_direction_qualifier\", \"qualifier_value\": \"increased\"}]}]}": [
"{\"object_aspect_qualifier\": \"activity_or_abundance\", \"object_direction_qualifier\": \"increased\", \"predicate\": \"biolink:affects\"}": [
{
"Rule": "?a biolink:contributes_to ?f ?f increased_activity_or_abundance_biolink:affects ?b => ?a increased_activity_or_abundance_biolink:affects ?b",
"Head Coverage": "0.000551544",
Expand Down Expand Up @@ -8984,7 +8984,7 @@
}
}
],
"{\"predicate\": \"biolink:affects\", \"qualifier_constraints\": [{\"qualifier_set\": [{\"qualifier_type_id\": \"biolink:object_aspect_qualifier\", \"qualifier_value\": \"activity_or_abundance\"}, {\"qualifier_type_id\": \"biolink:object_direction_qualifier\", \"qualifier_value\": \"decreased\"}]}]}": [
"{\"object_aspect_qualifier\": \"activity_or_abundance\", \"object_direction_qualifier\": \"decreased\", \"predicate\": \"biolink:affects\"}": [
{
"Rule": "?b biolink:biomarker_for ?f ?a decreased_activity_or_abundance_biolink:affects ?f => ?a decreased_activity_or_abundance_biolink:affects ?b",
"Head Coverage": "0.009918784",
Expand Down
43 changes: 37 additions & 6 deletions workers/aragorn_lookup/worker.py
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Original file line number Diff line number Diff line change
Expand Up @@ -136,7 +136,7 @@ async def aragorn_lookup(task, logger: logging.Logger):
json=message,
)
else:
expanded_messages = expand_aragorn_query(message)
expanded_messages = expand_aragorn_query(message, logger)
requests = []
# send all messages to lookup service
async with httpx.AsyncClient(timeout=20) as client:
Expand Down Expand Up @@ -212,6 +212,11 @@ def get_infer_parameters(input_message):
target: the query node id of the target node
source_input: True if the source node is the input node, False if the target node is the input node
"""
predicate = ""
qualifiers = {}
source = ""
target = ""
query_edge = ""
for edge_id, edge in input_message["message"]["query_graph"]["edges"].items():
source = edge["subject"]
target = edge["object"]
Expand All @@ -234,13 +239,39 @@ def get_infer_parameters(input_message):
return input_id, predicate, qualifiers, source, source_input, target, query_edge


def get_rule_key(predicate, qualifiers):
keydict = {"predicate": predicate}
keydict.update(qualifiers)
def get_rule_key(
predicate: str,
qualifiers: dict[str, list],
logger: logging.Logger,
) -> str:
"""Given some query parameters, construct a string key for expanded queries lookup."""
keydict: dict[str, str] = {"predicate": predicate}
if len(qualifiers.keys()) > 0:
# this is a bunch of logic to parse the dict of list of dicts of lists
# We're currently expecting it to be a specific format with specific keys
qualifier_constraints = qualifiers.get("qualifier_constraints", [])
if len(qualifier_constraints) < 1:
return json.dumps(keydict)
if len(qualifier_constraints) > 1:
logger.warning(
"Got more than one qualifier_constraints dict, just using the first one."
)
qualifier_set = qualifier_constraints[0].get("qualifier_set", [])
if len(qualifier_set) < 1:
return json.dumps(keydict)
for qualifier in qualifier_set:
if qualifier.get("qualifier_type_id") == "biolink:object_aspect_qualifier":
keydict["object_aspect_qualifier"] = qualifier.get("qualifier_value")
elif (
qualifier.get("qualifier_type_id")
== "biolink:object_direction_qualifier"
):
keydict["object_direction_qualifier"] = qualifier.get("qualifier_value")
return json.dumps(keydict, sort_keys=True)


def expand_aragorn_query(input_message):
def expand_aragorn_query(input_message, logger: logging.Logger):
"""Given a query, split it into many related similar queries."""
# Contract:
# 1. there is a single edge in the query graph
# 2. The edge is marked inferred.
Expand All @@ -249,7 +280,7 @@ def expand_aragorn_query(input_message):
input_id, predicate, qualifiers, source, source_input, target, qedge_id = (
get_infer_parameters(input_message)
)
key = get_rule_key(predicate, qualifiers)
key = get_rule_key(predicate, qualifiers, logger)
# We want to run the non-inferred version of the query as well
qg = copy.deepcopy(input_message["message"]["query_graph"])
for eid, edge in qg["edges"].items():
Expand Down
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