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authorFrederick Muriuki Muriithi2023-08-07 07:58:09 +0300
committerFrederick Muriuki Muriithi2023-08-07 09:26:12 +0300
commit6d9c61dc0072b96b12153e64940b465306f25bfb (patch)
treea4957c7967e56b4527c1e926744a65a3326935ce /gn_auth/auth/authorisation/groups
parent6ab6d46ab4b1611ed72bdbce85cf9324ce69b305 (diff)
downloadgn-auth-6d9c61dc0072b96b12153e64940b465306f25bfb.tar.gz
Change imports to new unified db module.
Diffstat (limited to 'gn_auth/auth/authorisation/groups')
-rw-r--r--gn_auth/auth/authorisation/groups/data.py14
-rw-r--r--gn_auth/auth/authorisation/groups/models.py2
-rw-r--r--gn_auth/auth/authorisation/groups/views.py8
3 files changed, 12 insertions, 12 deletions
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