Fix pylint errors.

24 files changed, 38 insertions, 37 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,
diff --git a/scripts/search_phenotypes.py b/scripts/search_phenotypes.py
index 3bf26dd..2423e93 100644
--- a/scripts/search_phenotypes.py
+++ b/scripts/search_phenotypes.py
@@ -26,7 +26,7 @@ def do_search(
     """Do the search and return the results"""
     search_uri = urljoin(host, (f"search/?page={page}&per_page={per_page}"
                                 f"&type=phenotype&query={query}"))
-    response = requests.get(search_uri)
+    response = requests.get(search_uri, timeout=300)
     results = response.json()
     if len(results) > 0:
         return (item for item in results)
@@ -75,7 +75,7 @@ def expire_redis_results(redisconn: redis.Redis, redisname: str):
 @click.option(
     "--redis-uri", default="redis://:@localhost:6379/0",
     help="The URI to the redis server.")
-def search(# pylint: disable=[too-many-arguments, too-many-locals]
+def search(# pylint: disable=[too-many-arguments, too-many-positional-arguments, too-many-locals]
         species: str, query: str, job_id: uuid.UUID, host: str, per_page: int,
         selected: str, auth_db_uri: str, gn3_db_uri: str, redis_uri: str):
     """
diff --git a/tests/unit/auth/fixtures/role_fixtures.py b/tests/unit/auth/fixtures/role_fixtures.py
index 1858712..63a3fca 100644
--- a/tests/unit/auth/fixtures/role_fixtures.py
+++ b/tests/unit/auth/fixtures/role_fixtures.py
@@ -163,7 +163,7 @@ def fxtr_system_roles(fxtr_users):
 
 
 @pytest.fixture(scope="function")
-def fxtr_resource_user_roles(# pylint: disable=[too-many-arguments, too-many-locals]
+def fxtr_resource_user_roles(# pylint: disable=[too-many-arguments, too-many-locals, too-many-positional-arguments]
         fxtr_resources,
         fxtr_users_in_group,
         fxtr_resource_ownership,
diff --git a/tests/unit/auth/test_groups.py b/tests/unit/auth/test_groups.py
index 16df56e..346beb9 100644
--- a/tests/unit/auth/test_groups.py
+++ b/tests/unit/auth/test_groups.py
@@ -27,7 +27,7 @@ PRIVILEGES = (
 
 @pytest.mark.unit_test
 @pytest.mark.parametrize("user", tuple(conftest.TEST_USERS[0:3]))
-def test_create_group_fails(# pylint: disable=[too-many-arguments]
+def test_create_group_fails(# pylint: disable=[too-many-arguments too-many-positional-arguments]
         fxtr_app, auth_testdb_path, mocker, fxtr_resource_user_roles, fxtr_oauth2_clients, user):# pylint: disable=[unused-argument]
     """
     GIVEN: an authenticated user
@@ -71,7 +71,7 @@ def __cleanup_create_group__(conn, user, group):
     ((conftest.TEST_USERS[3], Group(
         UUID("d32611e3-07fc-4564-b56c-786c6db6de2b"), "a_test_group",
         {"group_description": "A test group"})),))
-def test_create_group_succeeds(# pylint: disable=[too-many-arguments, unused-argument]
+def test_create_group_succeeds(# pylint: disable=[too-many-arguments too-many-positional-arguments, unused-argument]
         fxtr_app,
         auth_testdb_path,
         mocker,
@@ -102,7 +102,7 @@ def test_create_group_succeeds(# pylint: disable=[too-many-arguments, unused-arg
 
 @pytest.mark.unit_test
 @pytest.mark.parametrize("user", conftest.TEST_USERS[1:])
-def test_create_group_raises_exception_with_non_privileged_user(# pylint: disable=[too-many-arguments]
+def test_create_group_raises_exception_with_non_privileged_user(# pylint: disable=[too-many-arguments too-many-positional-arguments]
         fxtr_app, auth_testdb_path, mocker, fxtr_users, fxtr_oauth2_clients, user):# pylint: disable=[unused-argument]
     """
     GIVEN: an authenticated user, without appropriate privileges
diff --git a/tests/unit/auth/test_migrations_add_data_to_table.py b/tests/unit/auth/test_migrations_add_data_to_table.py
index d9e2ca4..0945a20 100644
--- a/tests/unit/auth/test_migrations_add_data_to_table.py
+++ b/tests/unit/auth/test_migrations_add_data_to_table.py
@@ -40,7 +40,7 @@ test_params = (
 
 @pytest.mark.unit_test
 @pytest.mark.parametrize("migration_file,query,query_params,data", test_params)
-def test_apply_insert(# pylint: disable=[too-many-arguments]
+def test_apply_insert(# pylint: disable=[too-many-arguments, too-many-positional-arguments]
         auth_migrations_dir, backend, auth_testdb_path, migration_file, query,
         query_params, data):
     """
@@ -65,7 +65,7 @@ def test_apply_insert(# pylint: disable=[too-many-arguments]
 
 @pytest.mark.unit_test
 @pytest.mark.parametrize("migration_file,query,query_params,data", test_params)
-def test_rollback_insert(# pylint: disable=[too-many-arguments]
+def test_rollback_insert(# pylint: disable=[too-many-arguments, too-many-positional-arguments]
         auth_migrations_dir, backend, auth_testdb_path, migration_file, query,
         query_params, data):
     """
diff --git a/tests/unit/auth/test_migrations_add_remove_columns.py b/tests/unit/auth/test_migrations_add_remove_columns.py
index af85652..15dc3a2 100644
--- a/tests/unit/auth/test_migrations_add_remove_columns.py
+++ b/tests/unit/auth/test_migrations_add_remove_columns.py
@@ -51,7 +51,7 @@ def rolled_back_successfully(adding: bool, result_str: str, column: str) -> bool
 @pytest.mark.unit_test
 @pytest.mark.parametrize(
     "migration_file,the_table,the_column,adding", TEST_PARAMS)
-def test_apply_add_remove_column(# pylint: disable=[too-many-arguments]
+def test_apply_add_remove_column(# pylint: disable=[too-many-arguments too-many-positional-arguments]
         auth_migrations_dir, auth_testdb_path, backend, migration_file,
         the_table, the_column, adding):
     """
@@ -84,7 +84,7 @@ def test_apply_add_remove_column(# pylint: disable=[too-many-arguments]
 @pytest.mark.unit_test
 @pytest.mark.parametrize(
     "migration_file,the_table,the_column,adding", TEST_PARAMS)
-def test_rollback_add_remove_column(# pylint: disable=[too-many-arguments]
+def test_rollback_add_remove_column(# pylint: disable=[too-many-arguments too-many-positional-arguments]
         auth_migrations_dir, auth_testdb_path, backend, migration_file,
         the_table, the_column, adding):
     """
diff --git a/tests/unit/auth/test_migrations_indexes.py b/tests/unit/auth/test_migrations_indexes.py
index 1c543c4..2d0997f 100644
--- a/tests/unit/auth/test_migrations_indexes.py
+++ b/tests/unit/auth/test_migrations_indexes.py
@@ -30,7 +30,7 @@ migrations_tables_and_indexes = (
 @pytest.mark.unit_test
 @pytest.mark.parametrize(
     "migration_file,the_table,the_index", migrations_tables_and_indexes)
-def test_index_created(# pylint: disable=[too-many-arguments]
+def test_index_created(# pylint: disable=[too-many-arguments too-many-positional-arguments]
         auth_testdb_path, auth_migrations_dir, backend, migration_file,
         the_table, the_index):
     """
@@ -61,7 +61,7 @@ def test_index_created(# pylint: disable=[too-many-arguments]
 @pytest.mark.unit_test
 @pytest.mark.parametrize(
     "migration_file,the_table,the_index", migrations_tables_and_indexes)
-def test_index_dropped(# pylint: disable=[too-many-arguments]
+def test_index_dropped(# pylint: disable=[too-many-arguments too-many-positional-arguments]
         auth_testdb_path, auth_migrations_dir, backend, migration_file,
         the_table, the_index):
     """
diff --git a/tests/unit/auth/test_migrations_insert_data_into_empty_table.py b/tests/unit/auth/test_migrations_insert_data_into_empty_table.py
index 0cf9a1f..c699e81 100644
--- a/tests/unit/auth/test_migrations_insert_data_into_empty_table.py
+++ b/tests/unit/auth/test_migrations_insert_data_into_empty_table.py
@@ -16,7 +16,7 @@ test_params = (
 @pytest.mark.unit_test
 @pytest.mark.parametrize(
     "migration_file,table,row_count", test_params)
-def test_apply_insert(# pylint: disable=[too-many-arguments]
+def test_apply_insert(# pylint: disable=[too-many-arguments, too-many-positional-arguments]
         auth_testdb_path, auth_migrations_dir, backend, migration_file,
         table, row_count):
     """
@@ -45,7 +45,7 @@ def test_apply_insert(# pylint: disable=[too-many-arguments]
 @pytest.mark.unit_test
 @pytest.mark.parametrize(
     "migration_file,table,row_count", test_params)
-def test_rollback_insert(# pylint: disable=[too-many-arguments]
+def test_rollback_insert(# pylint: disable=[too-many-arguments, too-many-positional-arguments]
         auth_testdb_path, auth_migrations_dir, backend, migration_file,
         table, row_count):
     """
diff --git a/tests/unit/auth/test_resources.py b/tests/unit/auth/test_resources.py
index 7f0b43d..292f7dc 100644
--- a/tests/unit/auth/test_resources.py
+++ b/tests/unit/auth/test_resources.py
@@ -30,7 +30,7 @@ create_resource_failure = {
         (Resource(
             uuid.UUID("d32611e3-07fc-4564-b56c-786c6db6de2b"),
             "test_resource", resource_category, False),))))
-def test_create_resource(# pylint: disable=[too-many-arguments, unused-argument]
+def test_create_resource(# pylint: disable=[too-many-arguments, too-many-positional-arguments, unused-argument]
         mocker,
         fxtr_users_in_group,
         fxtr_resource_user_roles,
diff --git a/tests/unit/auth/test_resources_roles.py b/tests/unit/auth/test_resources_roles.py
index 39a198f..e43f25c 100644
--- a/tests/unit/auth/test_resources_roles.py
+++ b/tests/unit/auth/test_resources_roles.py
@@ -63,7 +63,7 @@ def test_create_group_role(mocker, fxtr_users_in_group, fxtr_oauth2_clients, use
     "user,expected", tuple(zip(conftest.TEST_USERS[0:1], (
         Role(UUID("d32611e3-07fc-4564-b56c-786c6db6de2b"), "a_test_role",
              True, PRIVILEGES),))))
-def test_create_role(# pylint: disable=[too-many-arguments, unused-argument]
+def test_create_role(# pylint: disable=[too-many-arguments, too-many-positional-arguments, unused-argument]
         fxtr_app,
         auth_testdb_path,
         mocker,
diff --git a/tests/unit/auth/test_roles.py b/tests/unit/auth/test_roles.py
index 251defb..c364549 100644
--- a/tests/unit/auth/test_roles.py
+++ b/tests/unit/auth/test_roles.py
@@ -26,7 +26,7 @@ PRIVILEGES = (
 @pytest.mark.parametrize(
     "user,expected", tuple(zip(conftest.TEST_USERS[1:], (
         create_role_failure, create_role_failure, create_role_failure))))
-def test_create_role_raises_exception_for_unauthorised_users(# pylint: disable=[too-many-arguments, unused-argument]
+def test_create_role_raises_exception_for_unauthorised_users(# pylint: disable=[too-many-arguments, unused-argument, too-many-positional-arguments]
         fxtr_app,
         auth_testdb_path,
         mocker,