diff options
Diffstat (limited to 'gn_auth/auth/authorisation/data')
| -rw-r--r-- | gn_auth/auth/authorisation/data/genotypes.py | 4 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/data/mrna.py | 4 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/data/phenotypes.py | 10 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/data/views.py | 6 |
4 files changed, 12 insertions, 12 deletions
diff --git a/gn_auth/auth/authorisation/data/genotypes.py b/gn_auth/auth/authorisation/data/genotypes.py index 41822a1..61963a6 100644 --- a/gn_auth/auth/authorisation/data/genotypes.py +++ b/gn_auth/auth/authorisation/data/genotypes.py @@ -5,7 +5,7 @@ from typing import Iterable from MySQLdb.cursors import DictCursor import gn_auth.auth.db as authdb -import gn_auth.db_utils as gn3db +import gn_auth.auth.db.mariadb as gn3db from gn_auth.auth.dictify import dictify from gn_auth.auth.authorisation.checks import authorised_p from gn_auth.auth.authorisation.groups.models import Group @@ -22,7 +22,7 @@ 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.Connection, + authconn: authdb.DbConnection, gn3conn: gn3db.DbConnection, 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 0b08571..79ea7c0 100644 --- a/gn_auth/auth/authorisation/data/mrna.py +++ b/gn_auth/auth/authorisation/data/mrna.py @@ -4,7 +4,7 @@ from typing import Iterable from MySQLdb.cursors import DictCursor import gn_auth.auth.db as authdb -import gn_auth.db_utils as gn3db +import gn_auth.auth.db.mariadb as gn3db from gn_auth.auth.dictify import dictify from gn_auth.auth.authorisation.checks import authorised_p from gn_auth.auth.authorisation.groups.models import Group @@ -21,7 +21,7 @@ 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.Connection, + authconn: authdb.DbConnection, gn3conn: gn3db.DbConnection, 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 2f4c564..d3cc33a 100644 --- a/gn_auth/auth/authorisation/data/phenotypes.py +++ b/gn_auth/auth/authorisation/data/phenotypes.py @@ -5,13 +5,13 @@ from typing import Any, Iterable from MySQLdb.cursors import DictCursor import gn_auth.auth.db as authdb -import gn_auth.db_utils as gn3db +import gn_auth.auth.db.mariadb as gn3db from gn_auth.auth.dictify import dictify from gn_auth.auth.authorisation.checks import authorised_p from gn_auth.auth.authorisation.groups.models import Group def linked_phenotype_data( - authconn: authdb.DbConnection, gn3conn: gn3db.Connection, + authconn: authdb.DbConnection, gn3conn: gn3db.DbConnection, species: str = "") -> Iterable[dict[str, Any]]: """Retrieve phenotype data linked to user groups.""" authkeys = ("SpeciesId", "InbredSetId", "PublishFreezeId", "PublishXRefId") @@ -52,7 +52,7 @@ def linked_phenotype_data( "group(s)."), oauth2_scope="profile group resource") def ungrouped_phenotype_data( - authconn: authdb.DbConnection, gn3conn: gn3db.Connection): + authconn: authdb.DbConnection, gn3conn: gn3db.DbConnection): """Retrieve phenotype data that is not linked to any user group.""" with gn3conn.cursor() as cursor: params = tuple( @@ -82,7 +82,7 @@ def ungrouped_phenotype_data( return tuple() -def __traits__(gn3conn: gn3db.Connection, params: tuple[dict, ...]) -> tuple[dict, ...]: +def __traits__(gn3conn: gn3db.DbConnection, params: tuple[dict, ...]) -> tuple[dict, ...]: """An internal utility function. Don't use outside of this module.""" if len(params) < 1: return tuple() @@ -115,7 +115,7 @@ def __traits__(gn3conn: gn3db.Connection, params: tuple[dict, ...]) -> tuple[dic "group(s)."), oauth2_scope="profile group resource") def link_phenotype_data( - authconn:authdb.DbConnection, gn3conn: gn3db.Connection, group: Group, + authconn:authdb.DbConnection, gn3conn: gn3db.DbConnection, 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 a25e9a2..9e55dd8 100644 --- a/gn_auth/auth/authorisation/data/views.py +++ b/gn_auth/auth/authorisation/data/views.py @@ -10,13 +10,13 @@ from MySQLdb.cursors import DictCursor from authlib.integrations.flask_oauth2.errors import _HTTPException from flask import request, jsonify, Response, Blueprint, current_app as app -import gn_auth.db_utils as gn3db +import gn_auth.auth.db.mariadb as gn3db from gn_auth import jobs from gn_auth.commands import run_async_cmd from gn_auth.db.traits import build_trait_name -from gn_auth.auth import db -from gn_auth.auth.db_utils import with_db_connection +from gn_auth.auth.db import sqlite3 as db +from gn_auth.auth.db.sqlite3 import with_db_connection from gn_auth.auth.authorisation.checks import require_json from gn_auth.auth.authorisation.errors import InvalidData, NotFoundError |