Merge branch 'develop' into bau/copyright-2024

.github/workflows/pytest.yml → .github/workflows/tests.yml

@@ -1,36 +1,42 @@
 # Workflow name
-name: PyTest and Black
+name: PyTest, Black and Pylint
 
 # Controls when the workflow will run
 on:
-  # Triggers the workflow on pull request (on main only) events
+  # Triggers the workflow on pull request (on main and develop only) events
   pull_request:
     branches:
       - main
+      - develop
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
-  # This workflow contains a single job called "test"
-  test:
+  # This workflow contains a single job called "tests"
+  tests:
     # The type of runner that the job will run on and timeout in minutes
-    name: Run Python Tests and Black formatter
+    name: Run Python Tests, Black formatter and Pylint
     runs-on: ubuntu-latest
     timeout-minutes: 10
 
+    # Include a strategy matrix in order to allow the job to run multiple times with different versions of Python
+    strategy:
+      matrix:
+        python-version: [3.8, 3.9]
+
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
       # Checks-out our repository under $GITHUB_WORKSPACE, so our job can access it
       - name: Check out repository code
         uses: actions/checkout@v3
 
-      # Set up Python version
-      - name: Set up Python 3.7
+    # Set up Python version from the matrix
+      - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
         with:
-          python-version: '3.7'
+          python-version: ${{ matrix.python-version }}
 
       # Runs a set of commands installing Python dependencies using the runners shell (Run a multi-line script)
       - name: Install Python dependencies
@@ -47,4 +53,9 @@ jobs:
       # Check code has been formatted
       - name: Run Black code formatter
         run: |
-          black . --check --verbose --diff --color
+          black . --check --verbose --diff --color
+
+      # Run Pylint
+      - name: Run Pylint
+        run: |
+          pylint $(git ls-files '*.py') --fail-under=9.5

.pylintrc

@@ -1,5 +1,7 @@
 [MASTER]
 init-hook="from pylint.config import find_pylintrc; import os, sys; sys.path.append(os.path.dirname(find_pylintrc()))"
 max-line-length=120
+ignore-paths=^graphql_service/tests/snapshots/.*$,
+             ^graphql_service/tests/fixtures/.*$
 
 disable=missing-class-docstring, missing-function-docstring, line-too-long

common/crossrefs.py

@@ -107,8 +107,8 @@ def _index_identifiers_org_data(self):
         Provide prefix-based indexes for the flat list of entities from
         the identifiers.org api
         """
-        for ns in self.identifiers_org_data["payload"]["namespaces"]:
-            self.id_org_indexed[ns["prefix"]] = ns
+        for namespace in self.identifiers_org_data["payload"]["namespaces"]:
+            self.id_org_indexed[namespace["prefix"]] = namespace
 
     def generate_url_from_id_org_data(self, xref_acc_id, id_org_ns_prefix):
         """
@@ -204,9 +204,9 @@ def find_url_using_ens_xref_db_name(self, xref_acc_id, xref_db_name):
             return xref_base + xref_acc_id
 
         # Now get the URL from identifiers.org using the id_org_ns_prefix and xref_id
-        URL = self.generate_url_from_id_org_data(xref_acc_id, id_org_ns_prefix)
+        url = self.generate_url_from_id_org_data(xref_acc_id, id_org_ns_prefix)
 
-        return URL
+        return url
 
     def annotate_crossref(self, xref):
         """

common/db.py

@@ -45,7 +45,9 @@ def get_collection_conn(self, uuid):
         # Fallback to the collection in the configuration file if no data collection is found for the given UUID
         if not data_collection:
             data_collection_name = self.config.get("mongo_default_collection")
-            print(f"Falling back to the default collection '{data_collection_name}' for '{uuid}' UUID")
+            print(
+                f"Falling back to the default collection '{data_collection_name}' for '{uuid}' UUID"
+            )
         else:
             data_collection_name = data_collection.get("collection")
             print(f"Using '{data_collection_name}' collection for '{uuid}' UUID")
@@ -85,20 +87,23 @@ class FakeMongoDbClient:
     """
     Sets up a mongomock collection for thoas code to test with
     """
+
     def __init__(self):
         mongo_client = mongomock.MongoClient()
         self.mongo_db = mongo_client.db
 
     def get_collection_conn(self, uuid):
-        lookup_service_collection = 'uuid_to_collection_mapping'
+        lookup_service_collection = "uuid_to_collection_mapping"
         query = {"uuid": uuid, "is_current": True}
         data_collection = self.mongo_db[lookup_service_collection].find_one(query)
 
         # Fallback to the default collection if no collection found in the mappings
         # for the given UUID
         if not data_collection:
-            data_collection_name = 'collection1'
-            print(f"Falling back to the default collection '{data_collection_name}' for '{uuid}' UUID")
+            data_collection_name = "collection1"
+            print(
+                f"Falling back to the default collection '{data_collection_name}' for '{uuid}' UUID"
+            )
         else:
             data_collection_name = data_collection.get("collection")
             print(f"Using '{data_collection_name}' collection for '{uuid}' UUID")

common/extensions.py

@@ -16,6 +16,8 @@
 
 from ariadne.types import Extension, ContextValue
 
+from common import utils
+
 
 class QueryExecutionTimeExtension(Extension):
     def __init__(self):
@@ -29,4 +31,8 @@ def format(self, context):
             exec_time_in_secs = round(
                 (time.perf_counter_ns() - self.start_timestamp) / 1000000000, 2
             )
-            return {"execution_time_in_seconds": exec_time_in_secs}
+            return {
+                "execution_time_in_seconds": exec_time_in_secs,
+                "metadata_api_version": utils.get_ensembl_metadata_api_version(),
+            }
+        return None

common/utils.py

@@ -12,8 +12,9 @@
    limitations under the License.
 """
 
+
 def check_config_validity(config):
-    MANDATORY_FIELDS = [
+    mandatory_fields = [
         "mongo_host",
         "mongo_port",
         "mongo_user",
@@ -24,6 +25,23 @@ def check_config_validity(config):
         "grpc_host",
         "grpc_port",
     ]
-    for mandatory_field in MANDATORY_FIELDS:
+    for mandatory_field in mandatory_fields:
         if not config.get(mandatory_field):
-            raise KeyError(f"Missing information in configuration file - '{mandatory_field}'")
+            raise KeyError(
+                f"Missing information in configuration file - '{mandatory_field}'"
+            )
+
+
+def get_ensembl_metadata_api_version():
+    """
+    Get the Metadata API tag from requirement.txt file
+    """
+    version = "unknown"  # default version
+    with open("requirements.txt", "r", encoding="UTF-8") as file:
+        lines = file.readlines()
+        for line in lines:
+            if "ensembl-metadata-api" in line:
+                # Extract the tag part from the line
+                version = line.strip().split("@")[-1]
+                break
+    return version

graphql_service/resolver/gene_model.py

@@ -17,6 +17,7 @@
 
 from ariadne import QueryType, ObjectType
 from graphql import GraphQLResolveInfo
+from pymongo.collection import Collection
 
 from graphql_service.resolver.data_loaders import BatchLoaders
 
@@ -39,7 +40,6 @@
     MissingArgumentException,
 )
 
-from pymongo.collection import Collection
 
 # Define Query types for GraphQL
 # Don't forget to import these into ariadne_app.py if you add a new type
@@ -62,7 +62,7 @@
 def resolve_gene(
     _,
     info: GraphQLResolveInfo,
-    byId: Optional[Dict[str, str]] = None,
+    byId: Optional[Dict[str, str]] = None,  # pylint: disable=invalid-name
     by_id: Optional[Dict[str, str]] = None,
 ) -> Dict:
     "Load Gene via stable_id"
@@ -95,7 +95,6 @@ def resolve_gene(
     if not result:
         raise GeneNotFoundError(by_id=by_id)
 
-
     return result
 
 
@@ -180,14 +179,13 @@ def insert_gene_name_urls(gene_metadata: Dict, info: GraphQLResolveInfo) -> Dict
 def resolve_transcript(
     _,
     info: GraphQLResolveInfo,
-    bySymbol: Optional[Dict[str, str]] = None,
+    bySymbol: Optional[Dict[str, str]] = None,  # pylint: disable=invalid-name
     by_symbol: Optional[Dict[str, str]] = None,
-    byId: Optional[Dict[str, str]] = None,
+    byId: Optional[Dict[str, str]] = None,  # pylint: disable=invalid-name
     by_id: Optional[Dict[str, str]] = None,
 ) -> Dict:
     "Load Transcripts by symbol or stable_id"
 
-
     if by_symbol is None:
         by_symbol = bySymbol
     if by_id is None:
@@ -234,7 +232,8 @@ def resolve_transcript(
 
 @QUERY_TYPE.field("version")
 def resolve_api(
-    _: None, info: GraphQLResolveInfo  # the second argument must be named `info` to avoid a NameError
+    _: None,
+    info: GraphQLResolveInfo,  # the second argument must be named `info` to avoid a NameError
 ) -> Dict[str, Dict[str, str]]:
     """
     Resolve the API version.
@@ -243,8 +242,8 @@ def resolve_api(
     try:
         version_details = get_version_details()
         return {"api": version_details}
-    except Exception as e:
-        logging.error(f"Error resolving API version: {e}")
+    except Exception as exp:
+        logging.error(f"Error resolving API version: {exp}")
         raise
 
 
@@ -348,8 +347,8 @@ async def resolve_transcript_gene(transcript: Dict, info: GraphQLResolveInfo) ->
 def resolve_overlap(
     _,
     info: GraphQLResolveInfo,
-    genomeId: Optional[str] = None,
-    regionName: Optional[str] = None,
+    genomeId: Optional[str] = None,  # pylint: disable=invalid-name
+    regionName: Optional[str] = None,  # pylint: disable=invalid-name
     start: Optional[int] = None,
     end: Optional[int] = None,
     by_slice: Optional[Dict[str, Any]] = None,
@@ -702,21 +701,23 @@ def get_version_details() -> Dict[str, str]:
     config = configparser.ConfigParser()
 
     try:
-        if not config.read('version_config.ini'):
+        if not config.read("version_config.ini"):
             raise FileNotFoundError("INI file not found.")
 
-        version_data = config['version']
+        version_data = config["version"]
         return {
-            "major": version_data['major'],
-            "minor": version_data['minor'],
-            "patch": version_data['patch']
+            "major": version_data["major"],
+            "minor": version_data["minor"],
+            "patch": version_data["patch"],
         }
     except FileNotFoundError:
         logging.error("Version config file not found. Using default values.")
     except KeyError:
-        logging.error("Version section or keys not found in INI file. Using default values.")
-    except Exception as e:
-        logging.error(f"Error reading INI file: {e}. Using default values.")
+        logging.error(
+            "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.")
 
     return {"major": "0", "minor": "1", "patch": "0-beta"}
 
@@ -750,8 +751,7 @@ def set_col_conn_for_uuid(info, uuid):
 
     col_conn = info.context["mongo_db_client"].get_collection_conn(uuid)
 
-    conn = {'col_conn': col_conn,
-            'data_loader': BatchLoaders(col_conn)}
+    conn = {"col_conn": col_conn, "data_loader": BatchLoaders(col_conn)}
 
     parent_key = get_path_parent_key(info)
     info.context.setdefault(parent_key, conn)
@@ -763,12 +763,12 @@ def set_col_conn_for_uuid(info, uuid):
 
 def get_col_conn(info):
     parent_key = get_path_parent_key(info)
-    return info.context[parent_key]['col_conn']
+    return info.context[parent_key]["col_conn"]
 
 
 def get_data_loader(info):
     parent_key = get_path_parent_key(info)
-    return info.context[parent_key]['data_loader']
+    return info.context[parent_key]["data_loader"]
 
 
 def get_path_parent_key(info):