Use code in gn_libs for MySQL/MariaDB connection.

Update the application to use the gn_libs code for connecting to the
database, rather than using a local module.

4 files changed, 4 insertions, 6 deletions

diff --git a/scripts/assign_data_to_default_admin.py b/scripts/assign_data_to_default_admin.py
index d10b687..69fc50c 100644
--- a/scripts/assign_data_to_default_admin.py
+++ b/scripts/assign_data_to_default_admin.py
@@ -11,10 +11,9 @@ from pathlib import Path
 from uuid import UUID, uuid4
 
 import click
+from gn_libs import mysqldb as biodb
 from MySQLdb.cursors import DictCursor
 
-from gn_auth.auth.db import mariadb as biodb
-
 import gn_auth.auth.db.sqlite3 as authdb
 from gn_auth.auth.authentication.users import User
 from gn_auth.auth.authorisation.roles.models import (
diff --git a/scripts/batch_assign_data_to_default_admin.py b/scripts/batch_assign_data_to_default_admin.py
index 3df123d..a468019 100644
--- a/scripts/batch_assign_data_to_default_admin.py
+++ b/scripts/batch_assign_data_to_default_admin.py
@@ -7,10 +7,10 @@ import logging
 from pathlib import Path
 
 import click
+from gn_libs import mysqldb as biodb
 from pymonad.maybe import Just, Maybe, Nothing
 from pymonad.tools import monad_from_none_or_value
 
-from gn_auth.auth.db import mariadb as biodb
 from gn_auth.auth.db import sqlite3 as authdb
 from gn_auth.auth.authentication.users import User
 from gn_auth.auth.authorisation.resources.groups.models import (
diff --git a/scripts/link_inbredsets.py b/scripts/link_inbredsets.py
index 5db7ea8..c78a050 100644
--- a/scripts/link_inbredsets.py
+++ b/scripts/link_inbredsets.py
@@ -6,11 +6,10 @@ import uuid
 from pathlib import Path
 
 import click
+from gn_libs import mysqldb as biodb
 
 import gn_auth.auth.db.sqlite3 as authdb
 
-from gn_auth.auth.db import mariadb as biodb
-
 from scripts.assign_data_to_default_admin import (
     sys_admins, admin_group, select_sys_admin)
 
diff --git a/scripts/search_phenotypes.py b/scripts/search_phenotypes.py
index 20d91c9..3bf26dd 100644
--- a/scripts/search_phenotypes.py
+++ b/scripts/search_phenotypes.py
@@ -11,9 +11,9 @@ from datetime import datetime, timedelta
 import click
 import redis
 import requests
+from gn_libs import mysqldb as gn3db
 
 from gn_auth import jobs
-from gn_auth.auth.db import mariadb as gn3db
 from gn_auth.auth.db import sqlite3 as authdb
 from gn_auth.settings import SQL_URI, AUTH_DB
 from gn_auth.auth.authorisation.data.phenotypes import linked_phenotype_data