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Update paths to renci python image #452

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merged 11 commits into from
Jul 23, 2024
Merged

Update paths to renci python image #452

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c051ff9
Update paths to renci python image
maximusunc Jul 19, 2024
52bf61c
Take out the v
maximusunc Jul 19, 2024
4d823fa
Add KL/AT to new edges
maximusunc Jul 22, 2024
2716e9a
Fix unbatching
maximusunc Jul 22, 2024
8a85776
Remove empty lists in qgraph temporarily for automats
maximusunc Jul 22, 2024
5f02d4a
Remove response models because they were breaking fastapi
maximusunc Jul 22, 2024
4e10c0a
Run black
maximusunc Jul 22, 2024
272b8f4
Fix tests for removal of empty lists
maximusunc Jul 22, 2024
9b93c12
Add agent type
maximusunc Jul 23, 2024
9a69426
Replace knowledge type if present
maximusunc Jul 23, 2024
fad7a60
Run black
maximusunc Jul 23, 2024
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2 changes: 1 addition & 1 deletion Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
# Use RENCI python base image
FROM renciorg/renci-python-image:v3.12.4
FROM ghcr.io/translatorsri/renci-python-image:3.12.4

# Add image info
LABEL org.opencontainers.image.source https://github.com/ranking-agent/strider
Expand Down
2 changes: 1 addition & 1 deletion Dockerfile.test
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
FROM python:3.12
FROM ghcr.io/translatorsri/renci-python-image:3.12.4

# Add image info
LABEL org.opencontainers.image.source https://github.com/ranking-agent/strider
Expand Down
4 changes: 2 additions & 2 deletions strider/server.py
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Original file line number Diff line number Diff line change
Expand Up @@ -371,7 +371,7 @@ async def sync_query(
return JSONResponse(query_results)


@APP.post("/asyncquery", response_model=ReasonerResponse)
@APP.post("/asyncquery")
async def async_query(
background_tasks: BackgroundTasks,
query: AsyncQuery = Body(..., example=AEXAMPLE),
Expand Down Expand Up @@ -406,7 +406,7 @@ async def async_query(
return


@APP.post("/multiquery", response_model=dict[str, ReasonerResponse])
@APP.post("/multiquery")
async def multi_query(
background_tasks: BackgroundTasks,
multiquery: dict[str, AsyncQuery] = Body(..., example=MEXAMPLE),
Expand Down
59 changes: 42 additions & 17 deletions strider/throttle_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -87,23 +87,6 @@ def filter_by_curie_mapping(
]
)

# Construct result-specific knowledge graph
filtered_msg.knowledge_graph = KnowledgeGraph(
nodes={
binding.id: message.knowledge_graph.nodes[binding.id]
for result in filtered_msg.results
for _, bindings in result.node_bindings.items()
for binding in bindings
},
edges={
binding.id: message.knowledge_graph.edges[binding.id]
for result in filtered_msg.results
for analysis in result.analyses
for _, bindings in analysis.edge_bindings.items()
for binding in bindings
},
)

# Construct result-specific auxiliary graphs
filtered_aux_graphs = [
aux_graph_id
Expand All @@ -130,6 +113,48 @@ def filter_by_curie_mapping(
}
)

# get all edge ids from the result
kgraph_edge_ids = [
binding.id
for result in filtered_msg.results
for analysis in result.analyses or []
for _, bindings in analysis.edge_bindings.items()
for binding in bindings
]

# get all edge ids from auxiliary graphs
kgraph_edge_ids.extend(
[
edge_id
for aux_graph_id in filtered_aux_graphs
for edge_id in message.auxiliary_graphs[aux_graph_id].edges or []
]
)

kgraph_node_ids = set(
binding.id
for result in filtered_msg.results
for _, bindings in result.node_bindings.items()
for binding in bindings
)

for aux_graph_id in filtered_aux_graphs:
for edge_id in message.auxiliary_graphs[aux_graph_id].edges or []:
kgraph_node_ids.add(message.knowledge_graph.edges[edge_id].subject)
kgraph_node_ids.add(message.knowledge_graph.edges[edge_id].object)

# Construct result-specific knowledge graph
filtered_msg.knowledge_graph = KnowledgeGraph(
nodes={
node_id: message.knowledge_graph.nodes[node_id]
for node_id in kgraph_node_ids
},
edges={
edge_id: message.knowledge_graph.edges[edge_id]
for edge_id in kgraph_edge_ids
},
)

return filtered_msg


Expand Down
29 changes: 28 additions & 1 deletion strider/trapi.py
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Original file line number Diff line number Diff line change
Expand Up @@ -452,7 +452,18 @@ def convert_subclasses_to_aux_graphs(
"subject": subclass,
"object": node.id,
"predicate": "biolink:subclass_of",
"attributes": [],
"attributes": [
{
"attribute_type_id": "biolink:knowledge_level",
"value": "not_provided",
"attribute_source": "infores:aragorn",
},
{
"attribute_type_id": "biolink:agent_type",
"value": "automated_agent",
"attribute_source": "infores:aragorn",
},
],
"sources": [
{
"resource_id": kp_id,
Expand All @@ -472,6 +483,7 @@ def convert_subclasses_to_aux_graphs(
message.knowledge_graph.edges[primary_edge_id].object = node.id

had_support_graphs = False
had_knowledge_level = False
for attribute in message.knowledge_graph.edges[
primary_edge_id
].attributes:
Expand All @@ -481,6 +493,10 @@ def convert_subclasses_to_aux_graphs(
):
had_support_graphs = True
attribute.value.append(aux_edge_id)
if attribute.attribute_type_id == "biolink:knowledge_level":
had_knowledge_level = True
attribute.value = "logical_entailment"
attribute.attribute_source = "infores:aragorn"
if not had_support_graphs:
message.knowledge_graph.edges[primary_edge_id].attributes.add(
Attribute.parse_obj(
Expand All @@ -492,6 +508,17 @@ def convert_subclasses_to_aux_graphs(
)
)

if not had_knowledge_level:
message.knowledge_graph.edges[primary_edge_id].attributes.add(
Attribute.parse_obj(
{
"attribute_type_id": "biolink:knowledge_level",
"value": "logical_entailment",
"attribute_source": "infores:aragorn",
}
)
)

# create aux graph
message.auxiliary_graphs[aux_edge_id] = AuxiliaryGraph.parse_obj(
{
Expand Down
4 changes: 3 additions & 1 deletion strider/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -257,7 +257,9 @@ def remove_null_values(obj):
return {
key: remove_null_values(value)
for key, value in obj.items()
if value is not None
# TODO: also handle empty lists
# need to take this out when automats get fixed
if value is not None and value != []
}
elif isinstance(obj, list):
return [remove_null_values(el) for el in obj]
Expand Down
72 changes: 36 additions & 36 deletions tests/test_lookup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -58,23 +58,23 @@ async def test_mixed_canonical(monkeypatch, mocker):
"ids": ["CHEBI:6801"],
"categories": ["biolink:ChemicalSubstance"],
"set_interpretation": "BATCH",
"member_ids": [],
"constraints": [],
# "member_ids": [],
# "constraints": [],
},
"n1": {
"categories": ["biolink:Disease"],
"set_interpretation": "BATCH",
"member_ids": [],
"constraints": [],
# "member_ids": [],
# "constraints": [],
},
},
"edges": {
"n0n1": {
"subject": "n0",
"object": "n1",
"predicates": ["biolink:treats", "biolink:phenotype_of"],
"attribute_constraints": [],
"qualifier_constraints": [],
# "attribute_constraints": [],
# "qualifier_constraints": [],
},
},
},
Expand Down Expand Up @@ -121,23 +121,23 @@ async def test_symmetric_noncanonical(monkeypatch, mocker):
"ids": ["CHEBI:6801"],
"categories": ["biolink:ChemicalSubstance"],
"set_interpretation": "BATCH",
"member_ids": [],
"constraints": [],
# "member_ids": [],
# "constraints": [],
},
"n1": {
"categories": ["biolink:Disease"],
"set_interpretation": "BATCH",
"member_ids": [],
"constraints": [],
# "member_ids": [],
# "constraints": [],
},
},
"edges": {
"n0n1": {
"subject": "n0",
"object": "n1",
"predicates": ["biolink:genetically_interacts_with"],
"attribute_constraints": [],
"qualifier_constraints": [],
# "attribute_constraints": [],
# "qualifier_constraints": [],
},
},
},
Expand Down Expand Up @@ -236,23 +236,23 @@ async def test_protein_gene_conflation(monkeypatch, mocker):
"ids": ["MONDO:0008114"],
"categories": ["biolink:Disease"],
"set_interpretation": "BATCH",
"member_ids": [],
"constraints": [],
# "member_ids": [],
# "constraints": [],
},
"n1": {
"categories": ["biolink:Protein", "biolink:Gene"],
"set_interpretation": "BATCH",
"member_ids": [],
"constraints": [],
# "member_ids": [],
# "constraints": [],
},
},
"edges": {
"n0n1": {
"subject": "n0",
"object": "n1",
"predicates": ["biolink:related_to"],
"attribute_constraints": [],
"qualifier_constraints": [],
# "attribute_constraints": [],
# "qualifier_constraints": [],
},
},
},
Expand Down Expand Up @@ -296,24 +296,24 @@ async def test_gene_protein_conflation(monkeypatch, mocker):
"n0": {
"categories": ["biolink:Gene", "biolink:Protein"],
"set_interpretation": "BATCH",
"member_ids": [],
"constraints": [],
# "member_ids": [],
# "constraints": [],
},
"n1": {
"ids": ["MONDO:0008114"],
"categories": ["biolink:Disease"],
"set_interpretation": "BATCH",
"member_ids": [],
"constraints": [],
# "member_ids": [],
# "constraints": [],
},
},
"edges": {
"n0n1": {
"subject": "n0",
"object": "n1",
"predicates": ["biolink:related_to"],
"attribute_constraints": [],
"qualifier_constraints": [],
# "attribute_constraints": [],
# "qualifier_constraints": [],
},
},
},
Expand Down Expand Up @@ -361,23 +361,23 @@ async def test_node_set(monkeypatch, mocker):
"ids": ["CHEBI:6801"],
"categories": ["biolink:ChemicalSubstance"],
"set_interpretation": "BATCH",
"member_ids": [],
"constraints": [],
# "member_ids": [],
# "constraints": [],
},
"n1": {
"categories": ["biolink:Disease"],
"set_interpretation": "ALL",
"member_ids": [],
"constraints": [],
# "member_ids": [],
# "constraints": [],
},
},
"edges": {
"n0n1": {
"subject": "n0",
"object": "n1",
"predicates": ["biolink:treats"],
"attribute_constraints": [],
"qualifier_constraints": [],
# "attribute_constraints": [],
# "qualifier_constraints": [],
},
},
},
Expand Down Expand Up @@ -425,23 +425,23 @@ async def test_bypass_cache_is_sent_along_to_kps(monkeypatch, mocker):
"ids": ["CHEBI:6801"],
"categories": ["biolink:ChemicalSubstance"],
"set_interpretation": "BATCH",
"member_ids": [],
"constraints": [],
# "member_ids": [],
# "constraints": [],
},
"n1": {
"categories": ["biolink:Disease"],
"set_interpretation": "BATCH",
"member_ids": [],
"constraints": [],
# "member_ids": [],
# "constraints": [],
},
},
"edges": {
"n0n1": {
"subject": "n0",
"object": "n1",
"predicates": ["biolink:treats"],
"attribute_constraints": [],
"qualifier_constraints": [],
# "attribute_constraints": [],
# "qualifier_constraints": [],
},
},
},
Expand Down
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