fix pylint

common/db.py

@@ -11,11 +11,10 @@
    See the License for the specific language governing permissions and
    limitations under the License.
 """
-import graphql.error.graphql_error
+import logging
 import pymongo
 import mongomock
 import grpc
-import logging
 from ensembl.production.metadata.grpc import ensembl_metadata_pb2_grpc
 
 logger = logging.getLogger(__name__)
@@ -44,7 +43,7 @@ def get_database_conn(self, grpc_model, uuid):
             # chosen_db value will fall back to the default value, which is 'mongo_default_db' that is in the config
             # TODO: check why "except graphql.error.graphql_error.GraphQLError as grpc_exp:" didn't catch the error
             logger.debug(
-                f"[get_database_conn] Couldn't connected to gRPC Host: {grpc_exp}"
+                "[get_database_conn] Couldn't connect to gRPC Host: %s", grpc_exp
             )
 
         if grpc_response:
@@ -53,7 +52,7 @@ def get_database_conn(self, grpc_model, uuid):
             release_version = str(grpc_response.release_version).replace(".", "_")
             chosen_db = "release_" + release_version
 
-        logger.debug(f"[get_database_conn] Connected to '{chosen_db}' MongoDB")
+        logger.debug("[get_database_conn] Connected to '%s' MongoDB", chosen_db)
         data_database_connection = self.mongo_client[chosen_db]
         return data_database_connection
 
@@ -78,7 +77,7 @@ def connect_mongo(config):
             client.server_info()
             print(f"Connected to MongoDB, Host: {host}")
         except Exception as exc:
-            raise "Connection to mongo Failed" from exc
+            raise Exception("Connection to MongoDB failed") from exc
 
         return client
 

graphql_service/resolver/data_loaders.py

@@ -127,6 +127,9 @@ async def query_mongo(self, query: Dict, doc_type) -> List[Dict]:
         """
         # the collection name is the doc_type
         logger.info(
-            f"Getting '{doc_type}' from DB: '{self.database_conn.name}', collection '{doc_type}'"
+            "Getting '%s' from DB: '%s', collection '%s'",
+            doc_type,
+            self.database_conn.name,
+            doc_type,
         )
         return list(self.database_conn[doc_type].find(query))

graphql_service/resolver/exceptions.py

@@ -1,3 +1,16 @@
+"""
+.. See the NOTICE file distributed with this work for additional information
+   regarding copyright ownership.
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+       http://www.apache.org/licenses/LICENSE-2.0
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.
+"""
 from typing import Optional, Dict
 
 from graphql import GraphQLError

graphql_service/resolver/gene_model.py

@@ -94,11 +94,11 @@ def resolve_gene(
     connection_db = get_db_conn(info)
     gene_collection = connection_db["gene"]
 
-    logger.info(f"[resolve_gene] Getting Gene from DB: '{connection_db.name}'")
+    logger.info("[resolve_gene] Getting Gene from DB: '%s'", connection_db.name)
     try:
         result = gene_collection.find_one(query)
     except Exception as e:
-        logging.error(f"Exception: {e}")
+        logging.error("Exception: %s", e)
         raise DatabaseNotFoundError(db_name=connection_db.name)
 
     if not result:
@@ -120,12 +120,12 @@ def resolve_genes(_, info: GraphQLResolveInfo, by_symbol: Dict[str, str]) -> Lis
     set_db_conn_for_uuid(info, by_symbol["genome_id"])
     connection_db = get_db_conn(info)
     gene_collection = connection_db["gene"]
-    logger.info(f"[resolve_genes] Getting Gene from DB: '{connection_db.name}'")
+    logger.info("[resolve_genes] Getting Gene from DB: '%s'", connection_db.name)
 
     try:
         result = gene_collection.find(query)
     except Exception as e:
-        logging.error(f"Exception: {e}")
+        logging.error("Exception: %s", e)
         raise DatabaseNotFoundError(db_name=connection_db.name)
 
     # unpack cursor into a list. We're guaranteed relatively small results
@@ -240,13 +240,13 @@ def resolve_transcript(
     connection_db = get_db_conn(info)
     transcript_collection = connection_db["transcript"]
     logger.info(
-        f"[resolve_transcript] Getting Transcript from DB: '{connection_db.name}'"
+        "[resolve_transcript] Getting Transcript from DB: '%s'", connection_db.name
     )
 
     try:
         transcript = transcript_collection.find_one(query)
     except Exception as e:
-        logging.error(f"Exception: {e}")
+        logging.error("Exception: %s", e)
         raise DatabaseNotFoundError(db_name=connection_db.name)
 
     if not transcript:
@@ -267,7 +267,7 @@ def resolve_api(
         version_details = get_version_details()
         return {"api": version_details}
     except Exception as exp:
-        logging.error(f"Error resolving API version: {exp}")
+        logging.error("Error resolving API version: %s", exp)
         raise
 
 
@@ -312,7 +312,8 @@ async def resolve_transcripts_page_transcripts(
     connection_db = get_db_conn(info)
     transcript_collection = connection_db["transcript"]
     logger.info(
-        f"[resolve_transcripts_page_transcripts] Getting Transcript from DB: '{connection_db.name}'"
+        "[resolve_transcripts_page_transcripts] Getting Transcript from DB: '%s'",
+        connection_db.name,
     )
 
     results = (
@@ -336,7 +337,8 @@ async def resolve_transcripts_page_metadata(
     connection_db = get_db_conn(info)
     transcript_collection = connection_db["transcript"]
     logger.info(
-        f"[resolve_transcripts_page_metadata] Getting Transcript from DB: '{connection_db.name}'"
+        "[resolve_transcripts_page_metadata] Getting Transcript from DB: '%s'",
+        connection_db.name,
     )
 
     return {
@@ -366,7 +368,7 @@ async def resolve_transcript_gene(transcript: Dict, info: GraphQLResolveInfo) ->
     connection_db = get_db_conn(info)
     gene_collection = connection_db["gene"]
     logger.info(
-        f"[resolve_transcript_gene] Getting Gene from DB: '{connection_db.name}'"
+        "[resolve_transcript_gene] Getting Gene from DB: '%s'", connection_db.name
     )
 
     gene = gene_collection.find_one(query)
@@ -417,7 +419,8 @@ def resolve_overlap(
     set_db_conn_for_uuid(info, genome_id)
     connection_db = get_db_conn(info)
     logger.info(
-        f"[resolve_overlap] Getting Gene and Transcript Overlap from DB: '{connection_db.name}'"
+        "[resolve_overlap] Getting Gene and Transcript Overlap from DB: '%s'",
+        connection_db.name,
     )
 
     return {
@@ -511,7 +514,7 @@ def resolve_product_by_id(
     connection_db = get_db_conn(info)
     protein_collection = connection_db["protein"]
     logger.info(
-        f"[resolve_product_by_id] Getting Protein from DB: '{connection_db.name}'"
+        "[resolve_product_by_id] Getting Protein from DB: '%s'", connection_db.name
     )
     # NB: 'MatureRNA' will be added in the future, with collection per type approach
     # with have two options (TBD)
@@ -581,7 +584,8 @@ async def resolve_assembly_from_region(
     connection_db = get_db_conn(info)
     assembly_collection = connection_db["assembly"]
     logger.info(
-        f"[resolve_assembly_from_region] Getting Assembly from DB: '{connection_db.name}'"
+        "[resolve_assembly_from_region] Getting Assembly from DB: '%s'",
+        connection_db.name,
     )
     assembly = assembly_collection.find_one(query)
 
@@ -672,7 +676,7 @@ async def resolve_region(_, info: GraphQLResolveInfo, by_name: Dict[str, str]) -
     set_db_conn_for_uuid(info, by_name["genome_id"])
     connection_db = get_db_conn(info)
     region_collection = connection_db["region"]
-    logger.info(f"[resolve_region] Getting Region from DB: '{connection_db.name}'")
+    logger.info("[resolve_region] Getting Region from DB: '%s'", connection_db.name)
 
     result = region_collection.find_one(query)
     if not result:
@@ -777,7 +781,7 @@ def get_version_details() -> Dict[str, str]:
             "Version section or keys not found in INI file. Using default values."
         )
     except Exception as exp:
-        logging.error(f"Error reading INI file: {exp}. Using default values.")
+        logging.error("Error reading INI file: %s. Using default values.", exp)
 
     return {"major": "0", "minor": "1", "patch": "0-beta"}
 

graphql_service/resolver/tests/test_data_loaders.py

@@ -12,7 +12,6 @@
    limitations under the License.
 """
 
-import mongomock
 import pytest
 
 from common.db import FakeMongoDbClient

graphql_service/resolver/tests/test_resolvers.py

@@ -18,8 +18,6 @@
 
 import graphql_service.resolver.gene_model as model
 from common.crossrefs import XrefResolver
-from graphql_service.resolver.data_loaders import BatchLoaders
-from common.db import FakeMongoDbClient
 from graphql_service.tests.snapshot_utils import prepare_mongo_instance
 
 

graphql_service/server.py

@@ -25,14 +25,13 @@
 from starlette import applications, middleware
 from starlette.middleware.cors import CORSMiddleware
 
-from common import crossrefs, db, extensions, utils
+from common import crossrefs, db, extensions, utils, logger
 from grpc_service import grpc_model
 from graphql_service.ariadne_app import (
     prepare_executable_schema,
     prepare_context_provider,
 )
 from dotenv import load_dotenv
-from common.logger import CommandLogger
 
 
 load_dotenv("connections.conf")
@@ -50,7 +49,7 @@
     log.setLevel(logging.DEBUG)
     logging.basicConfig(level=logging.DEBUG)
 
-    monitoring.register(CommandLogger(log))
+    monitoring.register(logger.CommandLogger(log))
 
     # Apollo Tracing extension will display information about which resolvers are used and their duration
     # https://ariadnegraphql.org/docs/apollo-tracing