Fix pylint errors.

14 files changed, 21 insertions, 20 deletions

diff --git a/gn_auth/auth/authentication/oauth2/grants/jwt_bearer_grant.py b/gn_auth/auth/authentication/oauth2/grants/jwt_bearer_grant.py
index c200ce6..c802091 100644
--- a/gn_auth/auth/authentication/oauth2/grants/jwt_bearer_grant.py
+++ b/gn_auth/auth/authentication/oauth2/grants/jwt_bearer_grant.py
@@ -25,7 +25,7 @@ class JWTBearerTokenGenerator(_JWTBearerTokenGenerator):
 
     DEFAULT_EXPIRES_IN = 300
 
-    def get_token_data(#pylint: disable=[too-many-arguments]
+    def get_token_data(#pylint: disable=[too-many-arguments, too-many-positional-arguments]
             self, grant_type, client, expires_in=None, user=None, scope=None
     ):
         """Post process data to prevent JSON serialization problems."""
@@ -53,7 +53,7 @@ class JWTBearerTokenGenerator(_JWTBearerTokenGenerator):
             "oauth2_client_id": str(client.client_id)
         }
 
-    def generate(# pylint: disable=[too-many-arguments]
+    def generate(# pylint: disable=[too-many-arguments, too-many-positional-arguments]
             self,
             grant_type: str,
             client: OAuth2Client,
@@ -84,7 +84,7 @@ class JWTBearerTokenGenerator(_JWTBearerTokenGenerator):
         return token
 
 
-    def __call__(# pylint: disable=[too-many-arguments]
+    def __call__(# pylint: disable=[too-many-arguments, too-many-positional-arguments]
             self, grant_type, client, user=None, scope=None, expires_in=None,
             include_refresh_token=True
     ):
diff --git a/gn_auth/auth/authentication/oauth2/grants/refresh_token_grant.py b/gn_auth/auth/authentication/oauth2/grants/refresh_token_grant.py
index fd6804d..f897d89 100644
--- a/gn_auth/auth/authentication/oauth2/grants/refresh_token_grant.py
+++ b/gn_auth/auth/authentication/oauth2/grants/refresh_token_grant.py
@@ -34,18 +34,18 @@ class RefreshTokenGrant(grants.RefreshTokenGrant):
                     else Nothing)
             ).maybe(None, lambda _tok: _tok)
 
-    def authenticate_user(self, credential):
+    def authenticate_user(self, refresh_token):
         """Check that user is valid for given token."""
         with connection(app.config["AUTH_DB"]) as conn:
             try:
-                return user_by_id(conn, credential.user.user_id)
+                return user_by_id(conn, refresh_token.user.user_id)
             except NotFoundError as _nfe:
                 return None
 
         return None
 
-    def revoke_old_credential(self, credential):
+    def revoke_old_credential(self, refresh_token):
         """Revoke any old refresh token after issuing new refresh token."""
         with connection(app.config["AUTH_DB"]) as conn:
-            if credential.parent_of is not None:
-                revoke_refresh_token(conn, credential)
+            if refresh_token.parent_of is not None:
+                revoke_refresh_token(conn, refresh_token)
diff --git a/gn_auth/auth/authentication/oauth2/models/oauth2client.py b/gn_auth/auth/authentication/oauth2/models/oauth2client.py
index c7e1c90..1639e2e 100644
--- a/gn_auth/auth/authentication/oauth2/models/oauth2client.py
+++ b/gn_auth/auth/authentication/oauth2/models/oauth2client.py
@@ -74,6 +74,7 @@ class OAuth2Client(ClientMixin):
             return KeySet([JsonWebKey.import_key(key)
                            for key in requests.get(
                                    jwksuri,
+                                   timeout=300,
                                    allow_redirects=True).json()["jwks"]])
         except requests.ConnectionError as _connerr:
             app.logger.debug(
diff --git a/gn_auth/auth/authentication/oauth2/server.py b/gn_auth/auth/authentication/oauth2/server.py
index c2a175d..8ac5106 100644
--- a/gn_auth/auth/authentication/oauth2/server.py
+++ b/gn_auth/auth/authentication/oauth2/server.py
@@ -73,7 +73,7 @@ def create_save_token_func(token_model: type) -> Callable:
 
 def make_jwt_token_generator(app):
     """Make token generator function."""
-    def __generator__(# pylint: disable=[too-many-arguments]
+    def __generator__(# pylint: disable=[too-many-arguments, too-many-positional-arguments]
             grant_type,
             client,
             user=None,
diff --git a/gn_auth/auth/authorisation/data/genotypes.py b/gn_auth/auth/authorisation/data/genotypes.py
index 7cae91a..ddb0add 100644
--- a/gn_auth/auth/authorisation/data/genotypes.py
+++ b/gn_auth/auth/authorisation/data/genotypes.py
@@ -22,7 +22,7 @@ def linked_genotype_data(conn: authdb.DbConnection) -> Iterable[dict]:
                   "You do not have sufficient privileges to link data to (a) "
                   "group(s)."),
               oauth2_scope="profile group resource")
-def ungrouped_genotype_data(# pylint: disable=[too-many-arguments]
+def ungrouped_genotype_data(# pylint: disable=[too-many-arguments, too-many-positional-arguments]
         authconn: authdb.DbConnection, gn3conn: gn3db.Connection,
         search_query: str, selected: tuple[dict, ...] = tuple(),
         limit: int = 10000, offset: int = 0) -> tuple[
diff --git a/gn_auth/auth/authorisation/data/mrna.py b/gn_auth/auth/authorisation/data/mrna.py
index 82a0f82..0cc644e 100644
--- a/gn_auth/auth/authorisation/data/mrna.py
+++ b/gn_auth/auth/authorisation/data/mrna.py
@@ -22,7 +22,7 @@ def linked_mrna_data(conn: authdb.DbConnection) -> Iterable[dict]:
                   "You do not have sufficient privileges to link data to (a) "
                   "group(s)."),
               oauth2_scope="profile group resource")
-def ungrouped_mrna_data(# pylint: disable=[too-many-arguments]
+def ungrouped_mrna_data(# pylint: disable=[too-many-arguments, too-many-positional-arguments]
         authconn: authdb.DbConnection, gn3conn: gn3db.Connection,
         search_query: str, selected: tuple[dict, ...] = tuple(),
         limit: int = 10000, offset: int = 0) -> tuple[
diff --git a/gn_auth/auth/authorisation/resources/genotypes/models.py b/gn_auth/auth/authorisation/resources/genotypes/models.py
index e8dca9b..464537e 100644
--- a/gn_auth/auth/authorisation/resources/genotypes/models.py
+++ b/gn_auth/auth/authorisation/resources/genotypes/models.py
@@ -68,7 +68,7 @@ def attach_resources_data(
     return __attach_data__(cursor.fetchall(), resources)
 
 
-def insert_and_link_data_to_resource(# pylint: disable=[too-many-arguments]
+def insert_and_link_data_to_resource(# pylint: disable=[too-many-arguments, too-many-positional-arguments]
         cursor,
         resource_id: uuid.UUID,
         group_id: uuid.UUID,
diff --git a/gn_auth/auth/authorisation/resources/inbredset/models.py b/gn_auth/auth/authorisation/resources/inbredset/models.py
index de1c18a..64d41e3 100644
--- a/gn_auth/auth/authorisation/resources/inbredset/models.py
+++ b/gn_auth/auth/authorisation/resources/inbredset/models.py
@@ -62,7 +62,7 @@ def assign_inbredset_group_owner_role(
     return resource
 
 
-def link_data_to_resource(# pylint: disable=[too-many-arguments]
+def link_data_to_resource(# pylint: disable=[too-many-arguments, too-many-positional-arguments]
         cursor: sqlite3.Cursor,
         resource_id: UUID,
         species_id: int,
diff --git a/gn_auth/auth/authorisation/resources/models.py b/gn_auth/auth/authorisation/resources/models.py
index c1748f1..d136fec 100644
--- a/gn_auth/auth/authorisation/resources/models.py
+++ b/gn_auth/auth/authorisation/resources/models.py
@@ -39,7 +39,7 @@ from .phenotypes.models import (
 @authorised_p(("group:resource:create-resource",),
               error_description="Insufficient privileges to create a resource",
               oauth2_scope="profile resource")
-def create_resource(# pylint: disable=[too-many-arguments]
+def create_resource(# pylint: disable=[too-many-arguments, too-many-positional-arguments]
         cursor: sqlite3.Cursor,
         resource_name: str,
         resource_category: ResourceCategory,
diff --git a/gn_auth/auth/authorisation/resources/views.py b/gn_auth/auth/authorisation/resources/views.py
index 1c4104a..29ab3ed 100644
--- a/gn_auth/auth/authorisation/resources/views.py
+++ b/gn_auth/auth/authorisation/resources/views.py
@@ -137,7 +137,7 @@ def view_resource_data(resource_id: UUID) -> Response:
     with require_oauth.acquire("profile group resource") as the_token:
         db_uri = app.config["AUTH_DB"]
         count_per_page = __safe_get_requests_count__("count_per_page")
-        offset = (__safe_get_requests_page__("page") - 1)
+        offset = __safe_get_requests_page__("page") - 1
         with db.connection(db_uri) as conn:
             resource = resource_by_id(conn, the_token.user, resource_id)
             return jsonify(resource_data(
diff --git a/gn_auth/auth/authorisation/roles/models.py b/gn_auth/auth/authorisation/roles/models.py
index 2729b3b..6faeaca 100644
--- a/gn_auth/auth/authorisation/roles/models.py
+++ b/gn_auth/auth/authorisation/roles/models.py
@@ -271,7 +271,7 @@ def role_by_id(conn: db.DbConnection, role_id: UUID) -> Optional[Role]:
 
     _roles = db_rows_to_roles(results)
     if len(_roles) > 1:
-        raise Exception("Data corruption: Expected a single role.")
+        raise Exception("Data corruption: Expected a single role.")# pylint: disable=[broad-exception-raised]
 
     return _roles[0]
 
diff --git a/gn_auth/auth/authorisation/users/masquerade/models.py b/gn_auth/auth/authorisation/users/masquerade/models.py
index a155899..5c11f34 100644
--- a/gn_auth/auth/authorisation/users/masquerade/models.py
+++ b/gn_auth/auth/authorisation/users/masquerade/models.py
@@ -20,7 +20,7 @@ from ....db import sqlite3 as db
 from ....authentication.users import User
 from ....authentication.oauth2.models.oauth2token import OAuth2Token
 
-__FIVE_HOURS__ = (60 * 60 * 5)
+__FIVE_HOURS__ = 60 * 60 * 5
 
 def can_masquerade(func):
     """Security decorator."""
diff --git a/gn_auth/auth/authorisation/users/views.py b/gn_auth/auth/authorisation/users/views.py
index 7adcd06..2140928 100644
--- a/gn_auth/auth/authorisation/users/views.py
+++ b/gn_auth/auth/authorisation/users/views.py
@@ -196,7 +196,7 @@ def register_user() -> Response:
             current_app.logger.error(traceback.format_exc())
             raise(UserRegistrationError(f"Email Error: {str(enve)}")) from enve
 
-    raise Exception(
+    raise Exception(# pylint: disable=[broad-exception-raised]
         "unknown_error", "The system experienced an unexpected error.")
 
 def delete_verification_code(cursor, code: str):
diff --git a/gn_auth/smtp.py b/gn_auth/smtp.py
index 2f0e7f4..0040f35 100644
--- a/gn_auth/smtp.py
+++ b/gn_auth/smtp.py
@@ -16,7 +16,7 @@ def __read_mime__(filepath) -> dict:
     return {}
 
 
-def build_email_message(# pylint: disable=[too-many-arguments]
+def build_email_message(# pylint: disable=[too-many-arguments, too-many-positional-arguments]
         from_address: str,
         to_addresses: tuple[Address, ...],
         subject: str,
@@ -40,7 +40,7 @@ def build_email_message(# pylint: disable=[too-many-arguments]
     return msg
 
 
-def send_message(# pylint: disable=[too-many-arguments]
+def send_message(# pylint: disable=[too-many-arguments, too-many-positional-arguments]
         smtp_user: str,
         smtp_passwd: str,
         message: EmailMessage,