From 6d9c61dc0072b96b12153e64940b465306f25bfb Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 7 Aug 2023 07:58:09 +0300
Subject: Change imports to new unified db module.

---
 gn_auth/auth/authorisation/data/genotypes.py  |  4 ++--
 gn_auth/auth/authorisation/data/mrna.py       |  4 ++--
 gn_auth/auth/authorisation/data/phenotypes.py | 10 +++++-----
 gn_auth/auth/authorisation/data/views.py      |  6 +++---
 4 files changed, 12 insertions(+), 12 deletions(-)

(limited to 'gn_auth/auth/authorisation/data')

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
-- 
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