Cleanup deprecation warnings: Switch to gn_libs.sqlite3

The gn_auth.auth.db.sqlite3 module is deprecated and should be
removed. This cleanup goes a ways towards that goal.

18 files changed, 38 insertions, 34 deletions

diff --git a/gn_auth/auth/authentication/oauth2/endpoints/revocation.py b/gn_auth/auth/authentication/oauth2/endpoints/revocation.py
index 0979694..e647214 100644
--- a/gn_auth/auth/authentication/oauth2/endpoints/revocation.py
+++ b/gn_auth/auth/authentication/oauth2/endpoints/revocation.py
@@ -1,9 +1,9 @@
 """Handle token revocation."""
 
 from flask import current_app
+from gn_libs import sqlite3 as db
 from authlib.oauth2.rfc7009 import RevocationEndpoint as _RevocationEndpoint
 
-from gn_auth.auth.db import sqlite3 as db
 from gn_auth.auth.authentication.oauth2.models.oauth2token import (
     save_token, OAuth2Token, revoke_token)
 
diff --git a/gn_auth/auth/authentication/oauth2/endpoints/utilities.py b/gn_auth/auth/authentication/oauth2/endpoints/utilities.py
index 490c141..82fd8e1 100644
--- a/gn_auth/auth/authentication/oauth2/endpoints/utilities.py
+++ b/gn_auth/auth/authentication/oauth2/endpoints/utilities.py
@@ -3,8 +3,8 @@ from typing import Optional
 
 from flask import current_app
 from pymonad.maybe import Nothing
+from gn_libs import sqlite3 as db
 
-from gn_auth.auth.db import sqlite3 as db
 from gn_auth.auth.authentication.oauth2.models.oauth2token import (
     OAuth2Token, token_by_access_token, token_by_refresh_token)
 
diff --git a/gn_auth/auth/authentication/oauth2/models/jwt_bearer_token.py b/gn_auth/auth/authentication/oauth2/models/jwt_bearer_token.py
index 71769e1..3a93265 100644
--- a/gn_auth/auth/authentication/oauth2/models/jwt_bearer_token.py
+++ b/gn_auth/auth/authentication/oauth2/models/jwt_bearer_token.py
@@ -3,9 +3,10 @@ import uuid
 import time
 from typing import Optional
 
+from flask import current_app as app
 from authlib.oauth2.rfc7523 import JWTBearerToken as _JWTBearerToken
+from gn_libs.sqlite3 import with_db_connection
 
-from gn_auth.auth.db.sqlite3 import with_db_connection
 from gn_auth.auth.authentication.users import user_by_id
 from gn_auth.auth.authentication.oauth2.models.oauth2client import (
     client as fetch_client)
@@ -19,8 +20,10 @@ class JWTBearerToken(_JWTBearerToken):
         #       OAuth2Client is a dataclass
         super().__init__(payload, header, options, params)
         self.user = with_db_connection(
+            app.config["SQL_URI"],
             lambda conn:user_by_id(conn, uuid.UUID(payload["sub"])))
         self.client = with_db_connection(
+            app.config["SQL_URI"],
             lambda conn: fetch_client(
                 conn, uuid.UUID(payload["oauth2_client_id"])
             )
diff --git a/gn_auth/auth/authentication/oauth2/models/oauth2client.py b/gn_auth/auth/authentication/oauth2/models/oauth2client.py
index b3ec91f..818399d 100644
--- a/gn_auth/auth/authentication/oauth2/models/oauth2client.py
+++ b/gn_auth/auth/authentication/oauth2/models/oauth2client.py
@@ -13,9 +13,9 @@ from requests.exceptions import JSONDecodeError
 from authlib.jose import KeySet, JsonWebKey
 from authlib.oauth2.rfc6749 import ClientMixin
 from pymonad.maybe import Just, Maybe, Nothing
+from gn_libs import sqlite3 as db
 from gn_libs.debug import make_peeker
 
-from gn_auth.auth.db import sqlite3 as db
 from gn_auth.auth.errors import NotFoundError
 from gn_auth.auth.authentication.users import (User,
                                                fetch_users,
diff --git a/gn_auth/auth/authentication/oauth2/models/oauth2token.py b/gn_auth/auth/authentication/oauth2/models/oauth2token.py
index 6ec5c3d..eb13f43 100644
--- a/gn_auth/auth/authentication/oauth2/models/oauth2token.py
+++ b/gn_auth/auth/authentication/oauth2/models/oauth2token.py
@@ -8,8 +8,8 @@ from typing import Optional
 from authlib.oauth2.rfc6749 import TokenMixin
 from pymonad.tools import monad_from_none_or_value
 from pymonad.maybe import Just, Maybe, Nothing
+from gn_libs import sqlite3 as db
 
-from gn_auth.auth.db import sqlite3 as db
 from gn_auth.auth.errors import NotFoundError
 from gn_auth.auth.authentication.users import User, user_by_id
 
diff --git a/gn_auth/auth/authentication/oauth2/resource_server.py b/gn_auth/auth/authentication/oauth2/resource_server.py
index edab02c..c09f6b6 100644
--- a/gn_auth/auth/authentication/oauth2/resource_server.py
+++ b/gn_auth/auth/authentication/oauth2/resource_server.py
@@ -9,8 +9,8 @@ from authlib.oauth2.rfc6750 import BearerTokenValidator as _BearerTokenValidator
 from authlib.oauth2.rfc7523 import (
     JWTBearerTokenValidator as _JWTBearerTokenValidator)
 from authlib.integrations.flask_oauth2 import ResourceProtector
+from gn_libs import sqlite3 as db
 
-from gn_auth.auth.db import sqlite3 as db
 from gn_auth.auth.jwks import list_jwks, jwks_directory
 from gn_auth.auth.authentication.oauth2.models.jwt_bearer_token import (
     JWTBearerToken)
diff --git a/gn_auth/auth/authentication/oauth2/views.py b/gn_auth/auth/authentication/oauth2/views.py
index 8cc123f..e26fc95 100644
--- a/gn_auth/auth/authentication/oauth2/views.py
+++ b/gn_auth/auth/authentication/oauth2/views.py
@@ -16,9 +16,9 @@ from flask import (
     Blueprint,
     render_template,
     current_app as app)
+from gn_libs import sqlite3 as db
+from gn_libs.sqlite3 import with_db_connection
 
-from gn_auth.auth.db import sqlite3 as db
-from gn_auth.auth.db.sqlite3 import with_db_connection
 from gn_auth.auth.jwks import jwks_directory, list_jwks
 from gn_auth.auth.errors import NotFoundError, ForbiddenAccess
 from gn_auth.auth.authentication.users import valid_login, user_by_email
@@ -68,6 +68,7 @@ def authorise():
                 redirect_uri=request.args["redirect_uri"],
                 source_uri=f"{_src.scheme}://{_src.netloc}/",
                 display_forgot_password=with_db_connection(
+                    app.config["SQL_URI"],
                     __forgot_password_table_exists__))
 
         form = request.form
@@ -102,7 +103,7 @@ def authorise():
                 flash(email_passwd_msg, "alert alert-danger")
                 return redirect_response # type: ignore[return-value]
 
-        return with_db_connection(__authorise__)
+        return with_db_connection(app.config["SQL_URI"], __authorise__)
     except InvalidClientError as ice:
         return render_template(
             "oauth2/oauth2_error.html", error=ice), ice.status_code
diff --git a/gn_auth/auth/authentication/users.py b/gn_auth/auth/authentication/users.py
index fded79f..5c6a430 100644
--- a/gn_auth/auth/authentication/users.py
+++ b/gn_auth/auth/authentication/users.py
@@ -7,8 +7,8 @@ from dataclasses import dataclass
 import sqlite3
 from argon2 import PasswordHasher
 from argon2.exceptions import VerifyMismatchError
+from gn_libs import sqlite3 as db
 
-from gn_auth.auth.db import sqlite3 as db
 from gn_auth.auth.errors import NotFoundError
 
 
diff --git a/gn_auth/auth/authorisation/checks.py b/gn_auth/auth/authorisation/checks.py
index 66bb723..15d4b99 100644
--- a/gn_auth/auth/authorisation/checks.py
+++ b/gn_auth/auth/authorisation/checks.py
@@ -2,12 +2,12 @@
 from functools import wraps
 from typing import Callable
 
+from gn_libs import sqlite3 as db
 from flask import request, current_app as app
 
 from gn_auth.auth.errors import InvalidData, AuthorisationError
 
 from . import privileges as auth_privs
-from ..db import sqlite3 as db
 from ..authentication.oauth2.resource_server import require_oauth
 
 def __system_privileges_in_roles__(conn, user): # TODO: Remove this hack.
diff --git a/gn_auth/auth/authorisation/data/genotypes.py b/gn_auth/auth/authorisation/data/genotypes.py
index b6f0464..d5af3ae 100644
--- a/gn_auth/auth/authorisation/data/genotypes.py
+++ b/gn_auth/auth/authorisation/data/genotypes.py
@@ -6,10 +6,9 @@ from functools import reduce
 from dataclasses import asdict
 
 from gn_libs import mysqldb as gn3db
+from gn_libs import sqlite3 as authdb
 from MySQLdb.cursors import DictCursor
 
-from gn_auth.auth.db import sqlite3 as authdb
-
 from gn_auth.auth.authorisation.checks import authorised_p
 from gn_auth.auth.authorisation.resources.groups.models import Group
 
diff --git a/gn_auth/auth/authorisation/data/mrna.py b/gn_auth/auth/authorisation/data/mrna.py
index 7cced10..dd589e0 100644
--- a/gn_auth/auth/authorisation/data/mrna.py
+++ b/gn_auth/auth/authorisation/data/mrna.py
@@ -6,10 +6,9 @@ from functools import reduce
 from dataclasses import asdict
 
 from gn_libs import mysqldb as gn3db
+from gn_libs import sqlite3 as authdb
 from MySQLdb.cursors import DictCursor
 
-from gn_auth.auth.db import sqlite3 as authdb
-
 from gn_auth.auth.authorisation.checks import authorised_p
 from gn_auth.auth.authorisation.resources.groups.models import Group
 
diff --git a/gn_auth/auth/authorisation/data/views.py b/gn_auth/auth/authorisation/data/views.py
index 1184d63..0ffc08e 100644
--- a/gn_auth/auth/authorisation/data/views.py
+++ b/gn_auth/auth/authorisation/data/views.py
@@ -14,6 +14,7 @@ from flask import request, jsonify, Response, Blueprint, current_app as app
 
 from gn_libs import mysqldb as gn3db
 from gn_libs import sqlite3 as db
+from gn_libs.sqlite3 import with_db_connection
 
 from gn_auth import jobs
 from gn_auth.commands import run_async_cmd
@@ -22,8 +23,6 @@ from gn_auth.auth.requests import request_json
 from gn_auth.auth.errors import InvalidData, NotFoundError
 from gn_auth.auth.authorisation.resources.groups.models import group_by_id
 
-from gn_auth.auth.db.sqlite3 import with_db_connection # Replace this with gn_libs alternative
-
 from ..checks import require_json
 
 from ...authentication.users import User
@@ -207,7 +206,7 @@ def __search_mrna__():
             ungrouped_mrna_data, gn3conn=gn3conn, search_query=query,
             selected=__request_key_list__("selected"),
             limit=limit, offset=offset)
-        return jsonify(with_db_connection(__ungrouped__))
+        return jsonify(with_db_connection(app.config["SQL_URI"], __ungrouped__))
 
 def __request_key__(key: str, default: Any = ""):
     if bool(request_json()):
@@ -232,7 +231,7 @@ def __search_genotypes__():
             ungrouped_genotype_data, gn3conn=gn3conn, search_query=query,
             selected=__request_key_list__("selected"),
             limit=limit, offset=offset)
-        return jsonify(with_db_connection(__ungrouped__))
+        return jsonify(with_db_connection(app.config["SQL_URI"], __ungrouped__))
 
 def __search_phenotypes__():
     # launch the external process to search for phenotypes
@@ -307,6 +306,7 @@ def link_genotypes() -> Response:
         return link_genotype_data(conn, group_by_id(conn, group_id), datasets)
 
     return jsonify(with_db_connection(
+        app.config["SQL_URI"],
         partial(__link__, **__values__(request_json()))))
 
 @data.route("/link/mrna", methods=["POST"])
@@ -332,6 +332,7 @@ def link_mrna() -> Response:
         return link_mrna_data(conn, group_by_id(conn, group_id), datasets)
 
     return jsonify(with_db_connection(
+        app.config["SQL_URI"],
         partial(__link__, **__values__(request_json()))))
 
 @data.route("/link/phenotype", methods=["POST"])
@@ -374,4 +375,5 @@ def link_phenotype() -> Response:
                                        pheno_traits_from_db(gn3conn, traits))
 
         return jsonify(with_db_connection(
+            app.config["SQL_URI"],
             partial(__link__, **__values__(request_json()))))
diff --git a/gn_auth/auth/authorisation/privileges/models.py b/gn_auth/auth/authorisation/privileges/models.py
index 77be7c0..cd23a0c 100644
--- a/gn_auth/auth/authorisation/privileges/models.py
+++ b/gn_auth/auth/authorisation/privileges/models.py
@@ -3,8 +3,8 @@ from dataclasses import dataclass
 from typing import Iterable, Optional
 
 import sqlite3
+from gn_libs import sqlite3 as db
 
-from gn_auth.auth.db import sqlite3 as db
 from gn_auth.auth.authentication.users import User
 
 
diff --git a/gn_auth/auth/authorisation/resources/checks.py b/gn_auth/auth/authorisation/resources/checks.py
index 252df2f..6dfd388 100644
--- a/gn_auth/auth/authorisation/resources/checks.py
+++ b/gn_auth/auth/authorisation/resources/checks.py
@@ -11,7 +11,6 @@ from gn_libs.privileges import check
 from .base import Resource
 from .system.models import system_resource
 
-from ...db import sqlite3 as db
 from ...authentication.users import User
 
 from ..privileges.models import db_row_to_privilege
@@ -31,7 +30,7 @@ def __organise_privileges_by_resource_id__(rows):
     return reduce(__organise__, rows, {})
 
 
-def authorised_for(conn: db.DbConnection,
+def authorised_for(conn: authdb.DbConnection,
                    user: User,
                    privileges: tuple[str, ...],
                    resource_ids: Sequence[uuid.UUID]) -> dict[uuid.UUID, bool]:
@@ -42,7 +41,7 @@ def authorised_for(conn: db.DbConnection,
     warnings.warn(DeprecationWarning(
         f"The function `{__name__}.authorised_for` is deprecated. Please use "
         f"`{__name__}.authorised_for_spec`"))
-    with db.cursor(conn) as cursor:
+    with authdb.cursor(conn) as cursor:
         cursor.execute(
             ("SELECT ur.*, rp.privilege_id FROM "
              "user_roles AS ur "
@@ -66,7 +65,7 @@ def authorised_for(conn: db.DbConnection,
 
 
 def authorised_for2(
-        conn: db.DbConnection,
+        conn: authdb.DbConnection,
         user: User,
         resource: Resource,
         privileges: tuple[str, ...]
@@ -77,7 +76,7 @@ def authorised_for2(
     warnings.warn(DeprecationWarning(
         f"The function `{__name__}.authorised_for2` is deprecated. Please use "
         f"`{__name__}.authorised_for_spec`"))
-    with db.cursor(conn) as cursor:
+    with authdb.cursor(conn) as cursor:
         _query = (
             "SELECT resources.resource_id, user_roles.user_id, roles.role_id, "
             "privileges.* "
@@ -101,7 +100,7 @@ def authorised_for2(
 
 
 def authorised_for_spec(
-        conn: db.DbConnection,
+        conn: authdb.DbConnection,
         user_id: uuid.UUID,
         resource_id: uuid.UUID,
         auth_spec: str
@@ -110,7 +109,7 @@ def authorised_for_spec(
     Check that a user, identified with `user_id`, has a set of privileges that
     satisfy the `auth_spec` for the resource identified with `resource_id`.
     """
-    with db.cursor(conn) as cursor:
+    with authdb.cursor(conn) as cursor:
         _query = (
             "SELECT resources.resource_id, user_roles.user_id, roles.role_id, "
             "privileges.* "
diff --git a/gn_auth/auth/authorisation/resources/groups/models.py b/gn_auth/auth/authorisation/resources/groups/models.py
index 60d4634..79bead4 100644
--- a/gn_auth/auth/authorisation/resources/groups/models.py
+++ b/gn_auth/auth/authorisation/resources/groups/models.py
@@ -11,8 +11,8 @@ from flask import g
 from pymonad.maybe import Just, Maybe, Nothing
 from pymonad.either import Left, Right, Either
 from pymonad.tools import monad_from_none_or_value
+from gn_libs import sqlite3 as db
 
-from gn_auth.auth.db import sqlite3 as db
 from gn_auth.auth.authentication.users import User, user_by_id
 
 from gn_auth.auth.authorisation.checks import authorised_p
diff --git a/gn_auth/auth/authorisation/roles/models.py b/gn_auth/auth/authorisation/roles/models.py
index 89403f8..89556a6 100644
--- a/gn_auth/auth/authorisation/roles/models.py
+++ b/gn_auth/auth/authorisation/roles/models.py
@@ -4,12 +4,12 @@ from functools import reduce
 from dataclasses import dataclass
 from typing import Sequence, Iterable, Optional
 
+from gn_libs import sqlite3 as db
 from pymonad.either import Left, Right, Either
 
 from gn_auth.auth.errors import NotFoundError, AuthorisationError
 from gn_auth.auth.authorisation.resources.base import Resource
 
-from ...db import sqlite3 as db
 from ...authentication.users import User
 
 from ..checks import authorised_p
diff --git a/gn_auth/auth/authorisation/users/views.py b/gn_auth/auth/authorisation/users/views.py
index 5cdb482..e454a80 100644
--- a/gn_auth/auth/authorisation/users/views.py
+++ b/gn_auth/auth/authorisation/users/views.py
@@ -23,6 +23,8 @@ from flask import (
     make_response,
     render_template)
 
+from gn_libs import sqlite3 as db
+from gn_libs.sqlite3 import with_db_connection
 from gn_libs.privileges.system import can_create_or_delete_user
 from gn_libs.privileges.resources import can_assign_role
 
@@ -30,8 +32,6 @@ from gn_auth.smtp import send_message, build_email_message
 
 from gn_auth.auth.requests import request_json
 
-from gn_auth.auth.db import sqlite3 as db
-from gn_auth.auth.db.sqlite3 import with_db_connection
 
 from gn_auth.auth.authorisation.resources.system.models import (
     system_resource,
@@ -366,8 +366,9 @@ def user_join_request_exists():
             "exists": False
         }
     with require_oauth.acquire("profile group") as the_token:
-        return jsonify(with_db_connection(partial(
-            __request_exists__, user=the_token.user)))
+        return jsonify(with_db_connection(
+            current_app.config["SQL_URI"],
+            partial(__request_exists__, user=the_token.user)))
 
 @users.route("/list", methods=["GET"])
 @require_oauth("profile user")
diff --git a/gn_auth/hooks.py b/gn_auth/hooks.py
index bd7380b..f15107f 100644
--- a/gn_auth/hooks.py
+++ b/gn_auth/hooks.py
@@ -5,7 +5,7 @@ from typing import List
 from flask import request_finished
 from flask import request, current_app
 
-from gn_auth.auth.db import sqlite3 as db
+from gn_libs import sqlite3 as db
 
 def register_hooks(app):
     """Initialise hooks system on the application."""