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, 13 insertions, 10 deletions

diff --git a/gn_auth/auth/authorisation/data/genotypes.py b/gn_auth/auth/authorisation/data/genotypes.py
index bdab8fa..7cae91a 100644
--- a/gn_auth/auth/authorisation/data/genotypes.py
+++ b/gn_auth/auth/authorisation/data/genotypes.py
@@ -3,9 +3,9 @@ import uuid
 from dataclasses import asdict
 from typing import Iterable
 
+from gn_libs import mysqldb as gn3db
 from MySQLdb.cursors import DictCursor
 
-from gn_auth.auth.db import mariadb as gn3db
 from gn_auth.auth.db import sqlite3 as authdb
 
 from gn_auth.auth.authorisation.checks import authorised_p
@@ -23,7 +23,7 @@ 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.DbConnection,
+        authconn: authdb.DbConnection, gn3conn: gn3db.Connection,
         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 60470a7..82a0f82 100644
--- a/gn_auth/auth/authorisation/data/mrna.py
+++ b/gn_auth/auth/authorisation/data/mrna.py
@@ -2,10 +2,11 @@
 import uuid
 from dataclasses import asdict
 from typing import Iterable
+
+from gn_libs import mysqldb as gn3db
 from MySQLdb.cursors import DictCursor
 
 from gn_auth.auth.db import sqlite3 as authdb
-from gn_auth.auth.db import mariadb as gn3db
 
 from gn_auth.auth.authorisation.checks import authorised_p
 from gn_auth.auth.authorisation.resources.groups.models import Group
@@ -22,7 +23,7 @@ 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.DbConnection,
+        authconn: authdb.DbConnection, gn3conn: gn3db.Connection,
         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 0a76237..08a0524 100644
--- a/gn_auth/auth/authorisation/data/phenotypes.py
+++ b/gn_auth/auth/authorisation/data/phenotypes.py
@@ -3,16 +3,16 @@ import uuid
 from dataclasses import asdict
 from typing import Any, Iterable
 
+from gn_libs import mysqldb as gn3db
 from MySQLdb.cursors import DictCursor
 
 from gn_auth.auth.db import sqlite3 as authdb
-from gn_auth.auth.db import mariadb as gn3db
 
 from gn_auth.auth.authorisation.checks import authorised_p
 from gn_auth.auth.authorisation.resources.groups.models import Group
 
 def linked_phenotype_data(
-        authconn: authdb.DbConnection, gn3conn: gn3db.DbConnection,
+        authconn: authdb.DbConnection, gn3conn: gn3db.Connection,
         species: str = "") -> Iterable[dict[str, Any]]:
     """Retrieve phenotype data linked to user groups."""
     authkeys = ("SpeciesId", "InbredSetId", "PublishFreezeId", "PublishXRefId")
@@ -53,7 +53,7 @@ def linked_phenotype_data(
                   "group(s)."),
               oauth2_scope="profile group resource")
 def ungrouped_phenotype_data(
-        authconn: authdb.DbConnection, gn3conn: gn3db.DbConnection):
+        authconn: authdb.DbConnection, gn3conn: gn3db.Connection):
     """Retrieve phenotype data that is not linked to any user group."""
     with gn3conn.cursor() as cursor:
         params = tuple(
@@ -83,7 +83,7 @@ def ungrouped_phenotype_data(
 
     return tuple()
 
-def __traits__(gn3conn: gn3db.DbConnection, params: tuple[dict, ...]) -> tuple[dict, ...]:
+def __traits__(gn3conn: gn3db.Connection, params: tuple[dict, ...]) -> tuple[dict, ...]:
     """An internal utility function. Don't use outside of this module."""
     if len(params) < 1:
         return tuple()
@@ -116,7 +116,7 @@ def __traits__(gn3conn: gn3db.DbConnection, params: tuple[dict, ...]) -> tuple[d
                   "group(s)."),
               oauth2_scope="profile group resource")
 def link_phenotype_data(
-        authconn:authdb.DbConnection, gn3conn: gn3db.DbConnection, group: Group,
+        authconn:authdb.DbConnection, gn3conn: gn3db.Connection, 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 7ed69e3..38eaad6 100644
--- a/gn_auth/auth/authorisation/data/views.py
+++ b/gn_auth/auth/authorisation/data/views.py
@@ -11,6 +11,9 @@ from MySQLdb.cursors import DictCursor
 from authlib.integrations.flask_oauth2.errors import _HTTPException
 from flask import request, jsonify, Response, Blueprint, current_app as app
 
+
+from gn_libs import mysqldb as gn3db
+
 from gn_auth import jobs
 from gn_auth.commands import run_async_cmd
 
@@ -19,7 +22,6 @@ from gn_auth.auth.errors import InvalidData, NotFoundError
 from gn_auth.auth.authorisation.resources.groups.models import group_by_id
 
 from ...db import sqlite3 as db
-from ...db import mariadb as gn3db
 from ...db.sqlite3 import with_db_connection
 
 from ..checks import require_json