black

strider/caching.py

@@ -1,4 +1,5 @@
 """Caching/locking."""
+
 import asyncio
 from collections import OrderedDict, namedtuple
 from functools import wraps

strider/constraints.py

@@ -1,4 +1,5 @@
 """Constraint handling."""
+
 import operator
 import re
 from reasoner_pydantic import KnowledgeGraph, HashableSequence

strider/fetcher.py

@@ -1,4 +1,5 @@
 """Fetcher 2.0."""
+
 from collections import defaultdict
 from collections.abc import Iterable
 import copy

strider/graph.py

@@ -1,4 +1,5 @@
 """Graph - a dict with extra methods."""
+
 import json
 
 

strider/knowledge_provider.py

@@ -75,7 +75,7 @@ async def processor(response, last_hop: bool):
                 self.normalizer.curie_map,
                 self.logger,
                 self.information_content_threshold,
-                last_hop
+                last_hop,
             )
 
         return processor

strider/node_sets.py

@@ -1,4 +1,5 @@
 """Node sets."""
+
 from collections import defaultdict
 from datetime import datetime
 from reasoner_pydantic import Message

strider/normalizer.py

@@ -1,4 +1,5 @@
 """Node Normalizer Utilities."""
+
 from collections import namedtuple
 import logging
 

strider/openapi.py

@@ -1,4 +1,5 @@
 """TRAPI FastAPI wrapper."""
+
 from typing import Any, Dict, List, Optional
 
 from fastapi import FastAPI

strider/query_planner.py

@@ -1,4 +1,5 @@
 """Query planner."""
+
 from collections import defaultdict, namedtuple
 import copy
 from itertools import chain

strider/server.py

@@ -7,6 +7,7 @@
 oo     .d8P   888 .  888      888  888   888  888    .o  888
 8""88888P'    "888" d888b    o888o `Y8bod88P" `Y8bod8P' d888b
 """
+
 import copy
 import datetime
 import json

strider/throttle.py

@@ -1,4 +1,5 @@
 """Strider TRAPI Throttle."""
+
 import asyncio
 from asyncio.queues import QueueEmpty
 from asyncio.tasks import Task
@@ -278,11 +279,9 @@ async def process_batch(
                         response_values[request_id] = ReasonerResponse(
                             message=Message()
                         )
-                        response_values[
-                            request_id
-                        ].message.query_graph = request_value_mapping[
-                            request_id
-                        ].message.query_graph.copy()
+                        response_values[request_id].message.query_graph = (
+                            request_value_mapping[request_id].message.query_graph.copy()
+                        )
                         response_values[request_id].message.knowledge_graph = (
                             message.knowledge_graph
                             or KnowledgeGraph(nodes={}, edges={})

strider/throttle_utils.py

@@ -1,4 +1,5 @@
 """Throttle Utility Functions."""
+
 from collections import defaultdict
 from reasoner_pydantic import Message, QueryGraph, AuxiliaryGraphs
 from reasoner_pydantic.kgraph import KnowledgeGraph

strider/trapi.py

@@ -1,4 +1,5 @@
 """TRAPI utilities."""
+
 from itertools import product
 import json
 import logging
@@ -228,7 +229,7 @@ def filter_message(
     curie_map: dict,
     logger: logging.Logger = logging.getLogger(),
     information_content_threshold: int = settings.information_content_threshold,
-    last_hop: bool = False
+    last_hop: bool = False,
 ) -> None:
     """Filter all nodes based on information content."""
     pinned_nodes = get_curies(message.query_graph)
@@ -265,14 +266,9 @@ def filter_message(
                     or (
                         # Nodes that appear in the blocklist shouldn't be shown
                         curie is not None
-                        and any(
-                            n in curie.identifiers for n in blocklist
-                        )
-                    )
-                    or (
-                        curie is None
-                        and node_binding.id in blocklist
+                        and any(n in curie.identifiers for n in blocklist)
                     )
+                    or (curie is None and node_binding.id in blocklist)
                 ):
                     keep = False
                     if node_binding.id in message.knowledge_graph.nodes:
@@ -290,15 +286,15 @@ def filter_message(
                             support_graph_id
                         ]
                         for edge_id in message.auxiliary_graphs[support_graph_id].edges:
-                            kept_knowledge_graph.edges[
-                                edge_id
-                            ] = message.knowledge_graph.edges[edge_id]
+                            kept_knowledge_graph.edges[edge_id] = (
+                                message.knowledge_graph.edges[edge_id]
+                            )
                     # add edges from result
                     for edge_bindings in analysis.edge_bindings.values():
                         for edge_binding in edge_bindings:
-                            kept_knowledge_graph.edges[
-                                edge_binding.id
-                            ] = message.knowledge_graph.edges[edge_binding.id]
+                            kept_knowledge_graph.edges[edge_binding.id] = (
+                                message.knowledge_graph.edges[edge_binding.id]
+                            )
                             # add support graphs from edge
                             for attribute in (
                                 kept_knowledge_graph.edges[edge_binding.id].attributes
@@ -309,15 +305,15 @@ def filter_message(
                                     == "biolink:support_graphs"
                                 ):
                                     for aux_graph_id in attribute.value:
-                                        kept_aux_graphs[
-                                            aux_graph_id
-                                        ] = message.auxiliary_graphs[aux_graph_id]
+                                        kept_aux_graphs[aux_graph_id] = (
+                                            message.auxiliary_graphs[aux_graph_id]
+                                        )
                                         for edge_id in message.auxiliary_graphs[
                                             aux_graph_id
                                         ].edges:
-                                            kept_knowledge_graph.edges[
-                                                edge_id
-                                            ] = message.knowledge_graph.edges[edge_id]
+                                            kept_knowledge_graph.edges[edge_id] = (
+                                                message.knowledge_graph.edges[edge_id]
+                                            )
                 # keep any results that don't have promiscuous nodes
                 # only add result if all the knowledge and aux graph stuff worked out
                 kept_results.append(result)

strider/utils.py

@@ -1,4 +1,5 @@
 """General utilities."""
+
 import copy
 import json
 from json.decoder import JSONDecodeError

tests/helpers/context.py

@@ -1,4 +1,5 @@
 """Test utilities."""
+
 import asyncio
 from contextlib import asynccontextmanager, AsyncExitStack
 from functools import partial, wraps

tests/helpers/logger.py

@@ -1,4 +1,5 @@
 """Logging setup."""
+
 import logging
 
 

tests/helpers/mock_responses.py

@@ -597,7 +597,7 @@
                     "categories": [
                         "biolink:SmallMolecule",
                     ],
-                }
+                },
             },
             "edges": {
                 "e0": {
@@ -676,7 +676,7 @@
                         },
                     }
                 ],
-            }
+            },
         ],
     },
 }

tests/helpers/normalizer.py

@@ -1,4 +1,5 @@
 """LOTR node normalizer."""
+
 import csv
 from typing import List
 

tests/helpers/redisMock.py

@@ -1,4 +1,5 @@
 """Mock Redis."""
+
 import fakeredis.aioredis as fakeredis
 import gzip
 import json

tests/test_constraints.py

@@ -1,4 +1,5 @@
 """Test constraints."""
+
 from reasoner_pydantic import Message, AttributeConstraint, Node
 from strider.constraints import satisfies_attribute_constraint, enforce_constraints
 

tests/test_kp_responses.py

@@ -1,4 +1,5 @@
 """Test weird kp responses."""
+
 import httpx
 import json
 import pytest

tests/test_lookup.py

@@ -1,4 +1,5 @@
 """Test Strider."""
+
 import json
 
 from fastapi.responses import Response

tests/test_node_sets.py

@@ -1,4 +1,5 @@
 """Test node set handling."""
+
 import logging
 
 from reasoner_pydantic import (

tests/test_postproc.py

@@ -6,7 +6,11 @@
 from tests.helpers.context import (
     with_norm_overlay,
 )
-from tests.helpers.mock_responses import kp_response, response_with_aux_graphs, blocked_response
+from tests.helpers.mock_responses import (
+    kp_response,
+    response_with_aux_graphs,
+    blocked_response,
+)
 
 from strider.config import settings
 
@@ -95,6 +99,7 @@ async def test_aux_graph_filtering():
     assert len(list(msg.message.auxiliary_graphs.keys())) == 0
     assert len(msg.message.results) == 1
 
+
 @pytest.mark.asyncio
 @pytest.mark.asyncio
 @with_norm_overlay(
@@ -128,6 +133,7 @@ async def test_blocklist():
     assert "MESH:D014867" not in msg.message.knowledge_graph.nodes
     assert len(msg.message.results) == 0
 
+
 @pytest.mark.asyncio
 @with_norm_overlay(
     settings.normalizer_url,

tests/test_server.py

@@ -1,4 +1,5 @@
 """Test Strider."""
+
 import asyncio
 import json
 import redis.asyncio

tests/test_throttle_cache.py

@@ -1,4 +1,5 @@
 """Test Strider TRAPI Throttle LRU Caching."""
+
 import json
 import pytest
 

tests/test_traversal.py

@@ -1,4 +1,5 @@
 """Test traversal."""
+
 import pytest
 
 from strider.traversal import NoAnswersError, get_traversals

tests/test_util.py

@@ -1,4 +1,5 @@
 """Test utilities."""
+
 from strider.utils import remove_null_values
 from strider.trapi import filter_ancestor_types