Change imports to new unified db module.

21 files changed, 42 insertions, 42 deletions

diff --git a/gn_auth/auth/authorisation/checks.py b/gn_auth/auth/authorisation/checks.py
index 02c6810..46a51fe 100644
--- a/gn_auth/auth/authorisation/checks.py
+++ b/gn_auth/auth/authorisation/checks.py
@@ -4,7 +4,7 @@ from typing import Callable
 
 from flask import request, current_app as app
 
-from gn_auth.auth import db
+from gn_auth.auth.db import sqlite3 as db
 
 from . import privileges as auth_privs
 from .errors import InvalidData, AuthorisationError
diff --git a/gn_auth/auth/authorisation/data/genotypes.py b/gn_auth/auth/authorisation/data/genotypes.py
index 41822a1..61963a6 100644
--- a/gn_auth/auth/authorisation/data/genotypes.py
+++ b/gn_auth/auth/authorisation/data/genotypes.py
@@ -5,7 +5,7 @@ from typing import Iterable
 from MySQLdb.cursors import DictCursor
 
 import gn_auth.auth.db as authdb
-import gn_auth.db_utils as gn3db
+import gn_auth.auth.db.mariadb as gn3db
 from gn_auth.auth.dictify import dictify
 from gn_auth.auth.authorisation.checks import authorised_p
 from gn_auth.auth.authorisation.groups.models import Group
@@ -22,7 +22,7 @@ def linked_genotype_data(conn: authdb.DbConnection) -> Iterable[dict]:
                   "group(s)."),
               oauth2_scope="profile group resource")
 def ungrouped_genotype_data(# pylint: disable=[too-many-arguments]
-        authconn: authdb.DbConnection, gn3conn: gn3db.Connection,
+        authconn: authdb.DbConnection, gn3conn: gn3db.DbConnection,
         search_query: str, selected: tuple[dict, ...] = tuple(),
         limit: int = 10000, offset: int = 0) -> tuple[
             dict, ...]:
diff --git a/gn_auth/auth/authorisation/data/mrna.py b/gn_auth/auth/authorisation/data/mrna.py
index 0b08571..79ea7c0 100644
--- a/gn_auth/auth/authorisation/data/mrna.py
+++ b/gn_auth/auth/authorisation/data/mrna.py
@@ -4,7 +4,7 @@ from typing import Iterable
 from MySQLdb.cursors import DictCursor
 
 import gn_auth.auth.db as authdb
-import gn_auth.db_utils as gn3db
+import gn_auth.auth.db.mariadb as gn3db
 from gn_auth.auth.dictify import dictify
 from gn_auth.auth.authorisation.checks import authorised_p
 from gn_auth.auth.authorisation.groups.models import Group
@@ -21,7 +21,7 @@ def linked_mrna_data(conn: authdb.DbConnection) -> Iterable[dict]:
                   "group(s)."),
               oauth2_scope="profile group resource")
 def ungrouped_mrna_data(# pylint: disable=[too-many-arguments]
-        authconn: authdb.DbConnection, gn3conn: gn3db.Connection,
+        authconn: authdb.DbConnection, gn3conn: gn3db.DbConnection,
         search_query: str, selected: tuple[dict, ...] = tuple(),
         limit: int = 10000, offset: int = 0) -> tuple[
             dict, ...]:
diff --git a/gn_auth/auth/authorisation/data/phenotypes.py b/gn_auth/auth/authorisation/data/phenotypes.py
index 2f4c564..d3cc33a 100644
--- a/gn_auth/auth/authorisation/data/phenotypes.py
+++ b/gn_auth/auth/authorisation/data/phenotypes.py
@@ -5,13 +5,13 @@ from typing import Any, Iterable
 from MySQLdb.cursors import DictCursor
 
 import gn_auth.auth.db as authdb
-import gn_auth.db_utils as gn3db
+import gn_auth.auth.db.mariadb as gn3db
 from gn_auth.auth.dictify import dictify
 from gn_auth.auth.authorisation.checks import authorised_p
 from gn_auth.auth.authorisation.groups.models import Group
 
 def linked_phenotype_data(
-        authconn: authdb.DbConnection, gn3conn: gn3db.Connection,
+        authconn: authdb.DbConnection, gn3conn: gn3db.DbConnection,
         species: str = "") -> Iterable[dict[str, Any]]:
     """Retrieve phenotype data linked to user groups."""
     authkeys = ("SpeciesId", "InbredSetId", "PublishFreezeId", "PublishXRefId")
@@ -52,7 +52,7 @@ def linked_phenotype_data(
                   "group(s)."),
               oauth2_scope="profile group resource")
 def ungrouped_phenotype_data(
-        authconn: authdb.DbConnection, gn3conn: gn3db.Connection):
+        authconn: authdb.DbConnection, gn3conn: gn3db.DbConnection):
     """Retrieve phenotype data that is not linked to any user group."""
     with gn3conn.cursor() as cursor:
         params = tuple(
@@ -82,7 +82,7 @@ def ungrouped_phenotype_data(
 
     return tuple()
 
-def __traits__(gn3conn: gn3db.Connection, params: tuple[dict, ...]) -> tuple[dict, ...]:
+def __traits__(gn3conn: gn3db.DbConnection, params: tuple[dict, ...]) -> tuple[dict, ...]:
     """An internal utility function. Don't use outside of this module."""
     if len(params) < 1:
         return tuple()
@@ -115,7 +115,7 @@ def __traits__(gn3conn: gn3db.Connection, params: tuple[dict, ...]) -> tuple[dic
                   "group(s)."),
               oauth2_scope="profile group resource")
 def link_phenotype_data(
-        authconn:authdb.DbConnection, gn3conn: gn3db.Connection, group: Group,
+        authconn:authdb.DbConnection, gn3conn: gn3db.DbConnection, group: Group,
         traits: tuple[dict, ...]) -> dict:
     """Link phenotype traits to a user group."""
     with authdb.cursor(authconn) as cursor:
diff --git a/gn_auth/auth/authorisation/data/views.py b/gn_auth/auth/authorisation/data/views.py
index a25e9a2..9e55dd8 100644
--- a/gn_auth/auth/authorisation/data/views.py
+++ b/gn_auth/auth/authorisation/data/views.py
@@ -10,13 +10,13 @@ from MySQLdb.cursors import DictCursor
 from authlib.integrations.flask_oauth2.errors import _HTTPException
 from flask import request, jsonify, Response, Blueprint, current_app as app
 
-import gn_auth.db_utils as gn3db
+import gn_auth.auth.db.mariadb as gn3db
 from gn_auth import jobs
 from gn_auth.commands import run_async_cmd
 from gn_auth.db.traits import build_trait_name
 
-from gn_auth.auth import db
-from gn_auth.auth.db_utils 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.authorisation.checks import require_json
 from gn_auth.auth.authorisation.errors import InvalidData, NotFoundError
diff --git a/gn_auth/auth/authorisation/groups/data.py b/gn_auth/auth/authorisation/groups/data.py
index d05747b..2d9ddb5 100644
--- a/gn_auth/auth/authorisation/groups/data.py
+++ b/gn_auth/auth/authorisation/groups/data.py
@@ -1,14 +1,14 @@
 """Handles the resource objects' data."""
 from MySQLdb.cursors import DictCursor
 
-from gn_auth import db_utils as gn3db
-from gn_auth.auth import db as authdb
+from gn_auth.auth.db import mariadb as gn3db
+from gn_auth.auth.db import sqlite3 as authdb
 from gn_auth.auth.authorisation.groups import Group
 from gn_auth.auth.authorisation.checks import authorised_p
 from gn_auth.auth.authorisation.errors import NotFoundError
 
 def __fetch_mrna_data_by_ids__(
-        conn: gn3db.Connection, dataset_ids: tuple[str, ...]) -> tuple[
+        conn: gn3db.DbConnection, dataset_ids: tuple[str, ...]) -> tuple[
             dict, ...]:
     """Fetch mRNA Assay data by ID."""
     with conn.cursor(DictCursor) as cursor:
@@ -26,7 +26,7 @@ def __fetch_mrna_data_by_ids__(
         raise NotFoundError("Could not find mRNA Assay data with the given ID.")
 
 def __fetch_geno_data_by_ids__(
-        conn: gn3db.Connection, dataset_ids: tuple[str, ...]) -> tuple[
+        conn: gn3db.DbConnection, dataset_ids: tuple[str, ...]) -> tuple[
             dict, ...]:
     """Fetch genotype data by ID."""
     with conn.cursor(DictCursor) as cursor:
@@ -44,7 +44,7 @@ def __fetch_geno_data_by_ids__(
         raise NotFoundError("Could not find Genotype data with the given ID.")
 
 def __fetch_pheno_data_by_ids__(
-        conn: gn3db.Connection, dataset_ids: tuple[str, ...]) -> tuple[
+        conn: gn3db.DbConnection, dataset_ids: tuple[str, ...]) -> tuple[
             dict, ...]:
     """Fetch phenotype data by ID."""
     with conn.cursor(DictCursor) as cursor:
@@ -66,7 +66,7 @@ def __fetch_pheno_data_by_ids__(
             "Could not find Phenotype/Publish data with the given IDs.")
 
 def __fetch_data_by_id(
-        conn: gn3db.Connection, dataset_type: str,
+        conn: gn3db.DbConnection, dataset_type: str,
         dataset_ids: tuple[str, ...]) -> tuple[dict, ...]:
     """Fetch data from MySQL by IDs."""
     fetch_fns = {
@@ -82,7 +82,7 @@ def __fetch_data_by_id(
                   "group(s)."),
               oauth2_scope="profile group resource")
 def link_data_to_group(
-        authconn: authdb.DbConnection, gn3conn: gn3db.Connection,
+        authconn: authdb.DbConnection, gn3conn: gn3db.DbConnection,
         dataset_type: str, dataset_ids: tuple[str, ...], group: Group) -> tuple[
             dict, ...]:
     """Link the given data to the specified group."""
diff --git a/gn_auth/auth/authorisation/groups/models.py b/gn_auth/auth/authorisation/groups/models.py
index 9008bef..0ffd3a7 100644
--- a/gn_auth/auth/authorisation/groups/models.py
+++ b/gn_auth/auth/authorisation/groups/models.py
@@ -7,7 +7,7 @@ from typing import Any, Sequence, Iterable, Optional, NamedTuple
 from flask import g
 from pymonad.maybe import Just, Maybe, Nothing
 
-from gn_auth.auth import db
+from gn_auth.auth.db import sqlite3 as db
 from gn_auth.auth.dictify import dictify
 from gn_auth.auth.authentication.users import User, user_by_id
 
diff --git a/gn_auth/auth/authorisation/groups/views.py b/gn_auth/auth/authorisation/groups/views.py
index d1724cc..a63e09d 100644
--- a/gn_auth/auth/authorisation/groups/views.py
+++ b/gn_auth/auth/authorisation/groups/views.py
@@ -7,11 +7,11 @@ from functools import partial
 from MySQLdb.cursors import DictCursor
 from flask import request, jsonify, Response, Blueprint, current_app
 
-from gn_auth.auth import db
-from gn_auth import db_utils as gn3db
+from gn_auth.auth.db import sqlite3 as db
+from gn_auth.auth.db import mariadb as gn3db
 
 from gn_auth.auth.dictify import dictify
-from gn_auth.auth.db_utils import with_db_connection
+from gn_auth.auth.db.sqlite3 import with_db_connection
 
 from .data import link_data_to_group
 from .models import (
@@ -169,7 +169,7 @@ def unlinked_genotype_data(
         return tuple(dict(row) for row in cursor.fetchall())
 
 def unlinked_phenotype_data(
-        authconn: db.DbConnection, gn3conn: gn3db.Connection,
+        authconn: db.DbConnection, gn3conn: gn3db.DbConnection,
         group: Group) -> tuple[dict, ...]:
     """
     Retrieve all phenotype data linked to a group but not linked to any
diff --git a/gn_auth/auth/authorisation/privileges.py b/gn_auth/auth/authorisation/privileges.py
index 1b0f06c..a348b92 100644
--- a/gn_auth/auth/authorisation/privileges.py
+++ b/gn_auth/auth/authorisation/privileges.py
@@ -1,7 +1,7 @@
 """Handle privileges"""
 from typing import Any, Iterable, NamedTuple
 
-from gn_auth.auth import db
+from gn_auth.auth.db import sqlite3 as db
 from gn_auth.auth.authentication.users import User
 
 class Privilege(NamedTuple):
diff --git a/gn_auth/auth/authorisation/resources/checks.py b/gn_auth/auth/authorisation/resources/checks.py
index a341dbd..0c57b17 100644
--- a/gn_auth/auth/authorisation/resources/checks.py
+++ b/gn_auth/auth/authorisation/resources/checks.py
@@ -3,7 +3,7 @@ from uuid import UUID
 from functools import reduce
 from typing import Sequence
 
-from gn_auth.auth import db
+from gn_auth.auth.db import sqlite3 as db
 from gn_auth.auth.authentication.users import User
 
 def __organise_privileges_by_resource_id__(rows):
diff --git a/gn_auth/auth/authorisation/resources/models.py b/gn_auth/auth/authorisation/resources/models.py
index d96979f..8c035c9 100644
--- a/gn_auth/auth/authorisation/resources/models.py
+++ b/gn_auth/auth/authorisation/resources/models.py
@@ -5,10 +5,10 @@ from uuid import UUID, uuid4
 from functools import reduce, partial
 from typing import Any, Dict, Sequence, Optional, NamedTuple
 
-from gn_auth.auth import db
+from gn_auth.auth.db import sqlite3 as db
 from gn_auth.auth.dictify import dictify
 from gn_auth.auth.authentication.users import User
-from gn_auth.auth.db_utils import with_db_connection
+from gn_auth.auth.db.sqlite3 import with_db_connection
 
 from .checks import authorised_for
 
diff --git a/gn_auth/auth/authorisation/resources/views.py b/gn_auth/auth/authorisation/resources/views.py
index 9645303..157d5a3 100644
--- a/gn_auth/auth/authorisation/resources/views.py
+++ b/gn_auth/auth/authorisation/resources/views.py
@@ -6,7 +6,7 @@ from functools import reduce
 
 from flask import request, jsonify, Response, Blueprint, current_app as app
 
-from gn_auth.auth.db_utils import with_db_connection
+from gn_auth.auth.db.sqlite3 import with_db_connection
 
 from .checks import authorised_for
 from .models import (
diff --git a/gn_auth/auth/authorisation/roles/models.py b/gn_auth/auth/authorisation/roles/models.py
index 742a90e..0fecfc1 100644
--- a/gn_auth/auth/authorisation/roles/models.py
+++ b/gn_auth/auth/authorisation/roles/models.py
@@ -5,7 +5,7 @@ from typing import Any, Sequence, Iterable, NamedTuple
 
 from pymonad.either import Left, Right, Either
 
-from gn_auth.auth import db
+from gn_auth.auth.db import sqlite3 as db
 from gn_auth.auth.dictify import dictify
 from gn_auth.auth.authentication.users import User
 from gn_auth.auth.authorisation.errors import AuthorisationError
diff --git a/gn_auth/auth/authorisation/roles/views.py b/gn_auth/auth/authorisation/roles/views.py
index 6510365..4fc51f7 100644
--- a/gn_auth/auth/authorisation/roles/views.py
+++ b/gn_auth/auth/authorisation/roles/views.py
@@ -3,7 +3,7 @@ import uuid
 
 from flask import jsonify, Response, Blueprint, current_app
 
-from gn_auth.auth import db
+from gn_auth.auth.db import sqlite3 as db
 from gn_auth.auth.dictify import dictify
 
 from .models import user_role
diff --git a/gn_auth/auth/authorisation/users/admin/ui.py b/gn_auth/auth/authorisation/users/admin/ui.py
index 4351a68..9087412 100644
--- a/gn_auth/auth/authorisation/users/admin/ui.py
+++ b/gn_auth/auth/authorisation/users/admin/ui.py
@@ -3,7 +3,7 @@ from functools import wraps
 from flask import flash, url_for, redirect
 
 from gn_auth.auth.authentication.users import User
-from gn_auth.auth.db_utils import with_db_connection
+from gn_auth.auth.db.sqlite3 import with_db_connection
 from gn_auth.auth.authorisation.roles.models import user_roles
 
 from gn_auth.session import logged_in, session_user, clear_session_info
diff --git a/gn_auth/auth/authorisation/users/admin/views.py b/gn_auth/auth/authorisation/users/admin/views.py
index ab04f91..4a37bc5 100644
--- a/gn_auth/auth/authorisation/users/admin/views.py
+++ b/gn_auth/auth/authorisation/users/admin/views.py
@@ -18,8 +18,8 @@ from flask import (
 
 
 from gn_auth import session
-from gn_auth.auth import db
-from gn_auth.auth.db_utils 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.authentication.oauth2.models.oauth2client import (
     save_client,
diff --git a/gn_auth/auth/authorisation/users/collections/views.py b/gn_auth/auth/authorisation/users/collections/views.py
index 3dcc10f..9900205 100644
--- a/gn_auth/auth/authorisation/users/collections/views.py
+++ b/gn_auth/auth/authorisation/users/collections/views.py
@@ -4,8 +4,8 @@ from uuid import UUID
 from redis import Redis
 from flask import jsonify, request, Response, Blueprint, current_app
 
-from gn_auth.auth import db
-from gn_auth.auth.db_utils 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.authorisation.checks import require_json
 from gn_auth.auth.authorisation.errors import NotFoundError
 
diff --git a/gn_auth/auth/authorisation/users/masquerade/models.py b/gn_auth/auth/authorisation/users/masquerade/models.py
index c45d761..9779764 100644
--- a/gn_auth/auth/authorisation/users/masquerade/models.py
+++ b/gn_auth/auth/authorisation/users/masquerade/models.py
@@ -5,7 +5,7 @@ from datetime import datetime
 
 from flask import current_app as app
 
-from gn_auth.auth import db
+from gn_auth.auth.db import sqlite3 as db
 
 from gn_auth.auth.authorisation.errors import ForbiddenAccess
 from gn_auth.auth.authorisation.roles.models import user_roles
diff --git a/gn_auth/auth/authorisation/users/masquerade/views.py b/gn_auth/auth/authorisation/users/masquerade/views.py
index 9e42945..7bd8ddb 100644
--- a/gn_auth/auth/authorisation/users/masquerade/views.py
+++ b/gn_auth/auth/authorisation/users/masquerade/views.py
@@ -4,7 +4,7 @@ from functools import partial
 
 from flask import request, jsonify, Response, Blueprint
 
-from gn_auth.auth.db_utils import with_db_connection
+from gn_auth.auth.db.sqlite3 import with_db_connection
 from gn_auth.auth.authorisation.errors import InvalidData
 from gn_auth.auth.authorisation.checks import require_json
 
diff --git a/gn_auth/auth/authorisation/users/models.py b/gn_auth/auth/authorisation/users/models.py
index 71fa390..61489cf 100644
--- a/gn_auth/auth/authorisation/users/models.py
+++ b/gn_auth/auth/authorisation/users/models.py
@@ -2,7 +2,7 @@
 import uuid
 from functools import reduce
 
-from gn_auth.auth import db
+from gn_auth.auth.db import sqlite3 as db
 from gn_auth.auth.authorisation.roles.models import Role
 from gn_auth.auth.authorisation.checks import authorised_p
 from gn_auth.auth.authorisation.privileges import Privilege
diff --git a/gn_auth/auth/authorisation/users/views.py b/gn_auth/auth/authorisation/users/views.py
index 7783dca..0646e3a 100644
--- a/gn_auth/auth/authorisation/users/views.py
+++ b/gn_auth/auth/authorisation/users/views.py
@@ -7,9 +7,9 @@ import sqlite3
 from email_validator import validate_email, EmailNotValidError
 from flask import request, jsonify, Response, Blueprint, current_app
 
-from gn_auth.auth import db
+from gn_auth.auth.db import sqlite3 as db
 from gn_auth.auth.dictify import dictify
-from gn_auth.auth.db_utils import with_db_connection
+from gn_auth.auth.db.sqlite3 import with_db_connection
 
 from .models import list_users
 from .masquerade.views import masq