diff options
Diffstat (limited to 'gn_auth/auth/authorisation/groups')
| -rw-r--r-- | gn_auth/auth/authorisation/groups/data.py | 14 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/groups/models.py | 2 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/groups/views.py | 8 |
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 |