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.

10 files changed, 26 insertions, 25 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
diff --git a/gn_auth/auth/authorisation/resources/groups/data.py b/gn_auth/auth/authorisation/resources/groups/data.py
index 702955d..ad0dfba 100644
--- a/gn_auth/auth/authorisation/resources/groups/data.py
+++ b/gn_auth/auth/authorisation/resources/groups/data.py
@@ -1,7 +1,7 @@
 """Handles the resource objects' data."""
+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.errors import NotFoundError
@@ -9,7 +9,7 @@ from gn_auth.auth.authorisation.checks import authorised_p
 from gn_auth.auth.authorisation.resources.groups import Group
 
 def __fetch_mrna_data_by_ids__(
-        conn: gn3db.DbConnection, dataset_ids: tuple[str, ...]) -> tuple[
+        conn: gn3db.Connection, dataset_ids: tuple[str, ...]) -> tuple[
             dict, ...]:
     """Fetch mRNA Assay data by ID."""
     with conn.cursor(DictCursor) as cursor:
@@ -27,7 +27,7 @@ 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.DbConnection, dataset_ids: tuple[str, ...]) -> tuple[
+        conn: gn3db.Connection, dataset_ids: tuple[str, ...]) -> tuple[
             dict, ...]:
     """Fetch genotype data by ID."""
     with conn.cursor(DictCursor) as cursor:
@@ -45,7 +45,7 @@ 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.DbConnection, dataset_ids: tuple[str, ...]) -> tuple[
+        conn: gn3db.Connection, dataset_ids: tuple[str, ...]) -> tuple[
             dict, ...]:
     """Fetch phenotype data by ID."""
     with conn.cursor(DictCursor) as cursor:
@@ -67,7 +67,7 @@ def __fetch_pheno_data_by_ids__(
             "Could not find Phenotype/Publish data with the given IDs.")
 
 def __fetch_data_by_id(
-        conn: gn3db.DbConnection, dataset_type: str,
+        conn: gn3db.Connection, dataset_type: str,
         dataset_ids: tuple[str, ...]) -> tuple[dict, ...]:
     """Fetch data from MySQL by IDs."""
     fetch_fns = {
@@ -83,7 +83,7 @@ def __fetch_data_by_id(
                   "group(s)."),
               oauth2_scope="profile group resource")
 def link_data_to_group(
-        authconn: authdb.DbConnection, gn3conn: gn3db.DbConnection,
+        authconn: authdb.DbConnection, gn3conn: gn3db.Connection,
         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/resources/groups/views.py b/gn_auth/auth/authorisation/resources/groups/views.py
index 920f504..368284f 100644
--- a/gn_auth/auth/authorisation/resources/groups/views.py
+++ b/gn_auth/auth/authorisation/resources/groups/views.py
@@ -9,10 +9,10 @@ from dataclasses import asdict
 from MySQLdb.cursors import DictCursor
 from flask import jsonify, Response, Blueprint, current_app
 
-from gn_auth.auth.requests import request_json
+from gn_libs import mysqldb as gn3db
 
+from gn_auth.auth.requests import request_json
 from gn_auth.auth.db import sqlite3 as db
-from gn_auth.auth.db import mariadb as gn3db
 from gn_auth.auth.db.sqlite3 import with_db_connection
 
 from gn_auth.auth.authorisation.privileges import privileges_by_ids
@@ -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.DbConnection,
+        authconn: db.DbConnection, gn3conn: gn3db.Connection,
         group: Group) -> tuple[dict, ...]:
     """
     Retrieve all phenotype data linked to a group but not linked to any
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