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kl/at and other minor fixes
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@uhbrar
uhbrar committed Sep 6, 2024
1 parent 99671a3 commit ee4df8f
Showing 1 changed file with 59 additions and 40 deletions.
99 changes: 59 additions & 40 deletions src/shadowfax.py
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Original file line number Diff line number Diff line change
Expand Up @@ -30,34 +30,38 @@ async def generate_from_strider(message):
return lookup_response.get("message", {})


async def shadowfax(message, guid, logger):
qgraph = message["message"]["query_graph"]
pinned_node_ids = []
for node in qgraph["nodes"].values():
if node.get("ids", None) is not None:
pinned_node_ids.append(node["ids"][0])
else:
unpinned_node_category = node.get("categories", ["biolink:NamedThing"])[0]
if len(pinned_node_ids) != 2:
logger.info(f"{guid}: Pathfinder queries requrie two pinned nodes.")
return message, 500

async def get_normalized_curies(curies, guid, logger):
async with httpx.AsyncClient(timeout=900) as client:
try:
normalized_pinned_ids = await client.post(
normalizer_response = await client.post(
url=node_norm_url + "get_normalized_nodes",
json={
"curies": list(pinned_node_ids),
"curies": list(curies),
"conflate": True,
"description": False,
"drug_chemical_conflate": True
}
)
normalized_pinned_ids.raise_for_status()
normalized_pinned_ids = normalized_pinned_ids.json()
normalizer_response.raise_for_status()
return normalizer_response.json()
except:
logger.info(f"{guid}: Failed to get a response from node norm")
return message, 500


async def shadowfax(message, guid, logger):
qgraph = message["message"]["query_graph"]
pinned_node_ids = []
for node in qgraph["nodes"].values():
if node.get("ids", None) is not None:
pinned_node_ids.append(node["ids"][0])
else:
unpinned_node_category = node.get("categories", ["biolink:NamedThing"])[0]
if len(pinned_node_ids) != 2:
logger.info(f"{guid}: Pathfinder queries require two pinned nodes.")
return message, 500

normalized_pinned_ids = await get_normalized_curies(pinned_node_ids, guid, logger)

source_node = normalized_pinned_ids.get(pinned_node_ids[0], {"id": {"identifier": pinned_node_ids[0]}})["id"]["identifier"]
source_category = normalized_pinned_ids.get(pinned_node_ids[0], {"type": ["biolink:NamedThing"]})["type"][0]
source_equivalent_ids = [i["identifier"] for i in normalized_pinned_ids.get(pinned_node_ids[0], {"equivalent_identifiers": []})["equivalent_identifiers"]]
Expand All @@ -83,23 +87,8 @@ async def shadowfax(message, guid, logger):
logger.info(f"{guid}: No curies found.")
return message, 200

async with httpx.AsyncClient(timeout=900) as client:
try:
normmalizer_input = {
"curies": list(curies),
"conflate": True,
"description": False,
"drug_chemical_conflate": True
}
normalizer_response = await client.post(
url=node_norm_url + "get_normalized_nodes",
json=normmalizer_input
)
normalizer_response.raise_for_status()
normalizer_response = normalizer_response.json()
except:
logger.info(f"{guid}: Failed to get a response from node norm")
return message, 500
normalizer_response = await get_normalized_curies(list(curies), guid, logger)

curie_info = defaultdict(dict)
for curie, normalizer_info in normalizer_response.items():
if normalizer_info:
Expand Down Expand Up @@ -178,9 +167,9 @@ async def shadowfax(message, guid, logger):
for lookup_message in lookup_messages:
# Build graph from results to avoid subclass loops
# Results do not concatenate when they have different qnode ids
lookup_message_object = Message.parse_obj(lookup_message)
merged_lookup_message.update(lookup_message_object)
lookup_results.extend(lookup_message_object.dict().get("results", []))
lookup_message_obj = Message.parse_obj(lookup_message)
merged_lookup_message.update(lookup_message_obj)
lookup_results.extend(lookup_message_obj.dict().get("results") or [])
merged_lookup_message_dict = merged_lookup_message.dict()
lookup_knowledge_graph = merged_lookup_message_dict.get("knowledge_graph", {"nodes": {}, "edges": {}})
lookup_aux_graphs = merged_lookup_message_dict.get("auxiliary_graphs", {})
Expand Down Expand Up @@ -300,14 +289,24 @@ async def shadowfax(message, guid, logger):
"predicate": "biolink:related_to",
"sources": [
{
"resource_id": "infores:shadowfax",
"resource_id": "infores:aragorn",
"resource_role": "primary_knowledge_source",
}
],
"attributes": [
{
"attribute_type_id": "biolink:support_graphs",
"value": aux_edges_keys
},
{
"attribute_type_id": "biolink:agent_type",
"value": "computational_model",
"attribute_source": "infores:aragorn"
},
{
"attribute_type_id": "biolink:knowledge_level",
"value": "prediction",
"attribute_source": "infores:aragorn"
}
]
}
Expand All @@ -317,14 +316,24 @@ async def shadowfax(message, guid, logger):
"predicate": "biolink:related_to",
"sources": [
{
"resource_id": "infores:shadowfax",
"resource_id": "infores:aragorn",
"resource_role": "primary_knowledge_source",
}
],
"attributes": [
{
"attribute_type_id": "biolink:support_graphs",
"value": before_curie_edges_keys
},
{
"attribute_type_id": "biolink:agent_type",
"value": "computational_model",
"attribute_source": "infores:aragorn"
},
{
"attribute_type_id": "biolink:knowledge_level",
"value": "prediction",
"attribute_source": "infores:aragorn"
}
]
}
Expand All @@ -334,14 +343,24 @@ async def shadowfax(message, guid, logger):
"predicate": "biolink:related_to",
"sources": [
{
"resource_id": "infores:shadowfax",
"resource_id": "infores:aragorn",
"resource_role": "primary_knowledge_source",
}
],
"attributes": [
{
"attribute_type_id": "biolink:support_graphs",
"value": after_curie_edges_keys
},
{
"attribute_type_id": "biolink:agent_type",
"value": "computational_model",
"attribute_source": "infores:aragorn"
},
{
"attribute_type_id": "biolink:knowledge_level",
"value": "prediction",
"attribute_source": "infores:aragorn"
}
]
}
Expand Down

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