Fix linting errors caused by bump to Python 3.10migrate-to-python3.10

9 files changed, 17 insertions, 21 deletions

diff --git a/gn3/api/search.py b/gn3/api/search.py
index aa844ee..ada845d 100644
--- a/gn3/api/search.py
+++ b/gn3/api/search.py
@@ -147,12 +147,14 @@ def parse_position(spec: str) -> tuple[Maybe[int], Maybe[int]]:
         point = apply_si_suffix(spec)
         return Just(max(0, point - width)), Just(point + width)
 
+def to_megabases(val):
+    """Convert `val` to megabases."""
+    return str(Decimal(val)/10**6)
 
 def parse_position_field(location_slot: int, query: bytes) -> xapian.Query:
     """Parse position and return a xapian query."""
     start, end = parse_position(query.decode("utf-8"))
     # TODO: Convert the xapian index to use bases instead of megabases.
-    to_megabases = lambda x: str(Decimal(x)/10**6)
     return (xapian.NumberRangeProcessor(location_slot)
             (start.maybe("", to_megabases), end.maybe("", to_megabases))) # type: ignore
 
@@ -176,7 +178,6 @@ def parse_location_field(species_query: xapian.Query,
 
     def make_query(interval: ChromosomalInterval) -> xapian.Query:
         # TODO: Convert the xapian index to use bases instead of megabases.
-        to_megabases = lambda x: str(Decimal(x)/10**6)
         return combine_queries(xapian.Query.OP_AND,
                                species_query,
                                xapian.Query(chromosome_prefix + interval.chromosome),
diff --git a/gn3/auth/authentication/oauth2/endpoints/introspection.py b/gn3/auth/authentication/oauth2/endpoints/introspection.py
index a567363..29ade6a 100644
--- a/gn3/auth/authentication/oauth2/endpoints/introspection.py
+++ b/gn3/auth/authentication/oauth2/endpoints/introspection.py
@@ -24,7 +24,7 @@ class IntrospectionEndpoint(_IntrospectionEndpoint):
         """Query the token."""
         return _query_token(self, token_string, token_type_hint)
 
-    def introspect_token(self, token: OAuth2Token) -> dict:# pylint: disable=[no-self-use]
+    def introspect_token(self, token: OAuth2Token) -> dict:
         """Return the introspection information."""
         url = urlparse(flask_request.url)
         return {
@@ -43,6 +43,6 @@ class IntrospectionEndpoint(_IntrospectionEndpoint):
             "jti": token.token_id
         }
 
-    def check_permission(self, token, client, request):# pylint: disable=[unused-argument, no-self-use]
+    def check_permission(self, token, client, request):# pylint: disable=[unused-argument]
         """Check that the client has permission to introspect token."""
         return client.client_type == "internal"
diff --git a/gn3/auth/authentication/oauth2/endpoints/utilities.py b/gn3/auth/authentication/oauth2/endpoints/utilities.py
index 299f151..b85940d 100644
--- a/gn3/auth/authentication/oauth2/endpoints/utilities.py
+++ b/gn3/auth/authentication/oauth2/endpoints/utilities.py
@@ -12,7 +12,9 @@ def query_token(# pylint: disable=[unused-argument]
         endpoint_object: Any, token_str: str, token_type_hint) -> Optional[
             OAuth2Token]:
     """Retrieve the token from the database."""
-    __identity__ = lambda val: val
+    def __identity__(val):
+        """Identity function."""
+        return val
     token = Nothing
     with db.connection(current_app.config["AUTH_DB"]) as conn:
         if token_type_hint == "access_token":
diff --git a/gn3/auth/authentication/oauth2/grants/authorisation_code_grant.py b/gn3/auth/authentication/oauth2/grants/authorisation_code_grant.py
index f80d02e..fb8d436 100644
--- a/gn3/auth/authentication/oauth2/grants/authorisation_code_grant.py
+++ b/gn3/auth/authentication/oauth2/grants/authorisation_code_grant.py
@@ -41,7 +41,7 @@ class AuthorisationCodeGrant(grants.AuthorizationCodeGrant):
         """Retrieve the code from the database."""
         return __query_authorization_code__(code, client)
 
-    def delete_authorization_code(self, authorization_code):# pylint: disable=[no-self-use]
+    def delete_authorization_code(self, authorization_code):
         """Delete the authorisation code."""
         with db.connection(app.config["AUTH_DB"]) as conn:
             with db.cursor(conn) as cursor:
diff --git a/gn3/auth/authentication/oauth2/models/oauth2token.py b/gn3/auth/authentication/oauth2/models/oauth2token.py
index 72e20cc..981e730 100644
--- a/gn3/auth/authentication/oauth2/models/oauth2token.py
+++ b/gn3/auth/authentication/oauth2/models/oauth2token.py
@@ -51,7 +51,9 @@ class OAuth2Token(NamedTuple):
         return self.revoked
 
 def __token_from_resultset__(conn: db.DbConnection, rset) -> Maybe:
-    __identity__ = lambda val: val
+    def __identity__(val):
+        """Identity function."""
+        return val
     try:
         the_user = user_by_id(conn, uuid.UUID(rset["user_id"]))
     except NotFoundError as _nfe:
diff --git a/gn3/auth/db.py b/gn3/auth/db.py
index 2ba6619..97f3982 100644
--- a/gn3/auth/db.py
+++ b/gn3/auth/db.py
@@ -10,40 +10,32 @@ class DbConnection(Protocol):
     """Type annotation for a generic database connection object."""
     def cursor(self) -> Any:
         """A cursor object"""
-        ...
 
     def commit(self) -> Any:
         """Commit the transaction."""
-        ...
 
     def rollback(self) -> Any:
         """Rollback the transaction."""
-        ...
 
 class DbCursor(Protocol):
     """Type annotation for a generic database cursor object."""
     def execute(self, *args, **kwargs) -> Any:
         """Execute a single query"""
-        ...
 
     def executemany(self, *args, **kwargs) -> Any:
         """
         Execute parameterized SQL statement sql against all parameter sequences
         or mappings found in the sequence parameters.
         """
-        ...
 
     def fetchone(self, *args, **kwargs):
         """Fetch single result if present, or `None`."""
-        ...
 
     def fetchmany(self, *args, **kwargs):
         """Fetch many results if present or `None`."""
-        ...
 
     def fetchall(self, *args, **kwargs):
         """Fetch all results if present or `None`."""
-        ...
 
 @contextlib.contextmanager
 def connection(db_path: str, row_factory: Callable = sqlite3.Row) -> Iterator[DbConnection]:
diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py
index 9f02ad2..192ad7f 100644
--- a/gn3/computations/partial_correlations.py
+++ b/gn3/computations/partial_correlations.py
@@ -421,9 +421,8 @@ def literature_correlation_by_list(
     `web.webqtl.correlation.CorrelationPage.getLiteratureCorrelationByList`
     function in GeneNetwork1.
     """
-    if any((lambda t: (
-            bool(t.get("tissue_corr")) and
-            bool(t.get("tissue_p_value"))))(trait)
+    if any((bool(trait.get("tissue_corr")) and
+            bool(trait.get("tissue_p_value")))
            for trait in trait_list):
         temporary_table_name = f"LITERATURE{random_string(8)}"
         query1 = (
@@ -491,7 +490,7 @@ def tissue_correlation_by_list(
             "tissue_p_value": result["p-val"]
         }
 
-    if any((lambda t: bool(t.get("l_corr")))(trait) for trait in trait_list):
+    if any(bool((trait)) for trait in trait_list):
         prim_trait_symbol_value_dict = fetch_gene_symbol_tissue_value_dict_for_trait(
             (primary_trait_symbol,), tissue_probeset_freeze_id, conn)
         if primary_trait_symbol.lower() in prim_trait_symbol_value_dict:
diff --git a/gn3/db/case_attributes.py b/gn3/db/case_attributes.py
index 1d82f00..0794c0b 100644
--- a/gn3/db/case_attributes.py
+++ b/gn3/db/case_attributes.py
@@ -90,7 +90,8 @@ def approve_case_attribute(conn: Any, case_attr_audit_id: int) -> int:
                 elif diff_data.get("Deletion"):
                     data = diff_data.get("Deletion")
                     cursor.execute(
-                        "DELETE FROM CaseAttribute " "WHERE Id = %s",
+                        "DELETE FROM CaseAttribute "
+                        "WHERE Id = %s",
                         (data.get("id"),),
                     )
                 # Modification
diff --git a/gn3/db_utils.py b/gn3/db_utils.py
index 7d6a445..8bf7be7 100644
--- a/gn3/db_utils.py
+++ b/gn3/db_utils.py
@@ -21,7 +21,6 @@ class Connection(Protocol):
     """Type Annotation for MySQLdb's connection object"""
     def cursor(self, *args) -> Any:
         """A cursor in which queries may be performed"""
-        ...
 
 
 @contextlib.contextmanager