diff options
Diffstat (limited to 'gn_auth/auth/authorisation')
20 files changed, 91 insertions, 91 deletions
diff --git a/gn_auth/auth/authorisation/data/genotypes.py b/gn_auth/auth/authorisation/data/genotypes.py index 8f901a5..41822a1 100644 --- a/gn_auth/auth/authorisation/data/genotypes.py +++ b/gn_auth/auth/authorisation/data/genotypes.py @@ -4,11 +4,11 @@ from typing import Iterable from MySQLdb.cursors import DictCursor -import gn3.auth.db as authdb -import gn3.db_utils as gn3db -from gn3.auth.dictify import dictify -from gn3.auth.authorisation.checks import authorised_p -from gn3.auth.authorisation.groups.models import Group +import gn_auth.auth.db as authdb +import gn_auth.db_utils 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_genotype_data(conn: authdb.DbConnection) -> Iterable[dict]: """Retrive genotype data that is linked to user groups.""" diff --git a/gn_auth/auth/authorisation/data/mrna.py b/gn_auth/auth/authorisation/data/mrna.py index bdfc5c1..0b08571 100644 --- a/gn_auth/auth/authorisation/data/mrna.py +++ b/gn_auth/auth/authorisation/data/mrna.py @@ -3,11 +3,11 @@ import uuid from typing import Iterable from MySQLdb.cursors import DictCursor -import gn3.auth.db as authdb -import gn3.db_utils as gn3db -from gn3.auth.dictify import dictify -from gn3.auth.authorisation.checks import authorised_p -from gn3.auth.authorisation.groups.models import Group +import gn_auth.auth.db as authdb +import gn_auth.db_utils 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_mrna_data(conn: authdb.DbConnection) -> Iterable[dict]: """Retrieve mRNA Assay data that is linked to user groups.""" diff --git a/gn_auth/auth/authorisation/data/phenotypes.py b/gn_auth/auth/authorisation/data/phenotypes.py index ff98295..2f4c564 100644 --- a/gn_auth/auth/authorisation/data/phenotypes.py +++ b/gn_auth/auth/authorisation/data/phenotypes.py @@ -4,11 +4,11 @@ from typing import Any, Iterable from MySQLdb.cursors import DictCursor -import gn3.auth.db as authdb -import gn3.db_utils as gn3db -from gn3.auth.dictify import dictify -from gn3.auth.authorisation.checks import authorised_p -from gn3.auth.authorisation.groups.models import Group +import gn_auth.auth.db as authdb +import gn_auth.db_utils 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, diff --git a/gn_auth/auth/authorisation/data/views.py b/gn_auth/auth/authorisation/data/views.py index 8adf862..a25e9a2 100644 --- a/gn_auth/auth/authorisation/data/views.py +++ b/gn_auth/auth/authorisation/data/views.py @@ -10,31 +10,31 @@ 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 gn3.db_utils as gn3db -from gn3 import jobs -from gn3.commands import run_async_cmd -from gn3.db.traits import build_trait_name +import gn_auth.db_utils 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 gn3.auth import db -from gn3.auth.db_utils import with_db_connection +from gn_auth.auth import db +from gn_auth.auth.db_utils import with_db_connection -from gn3.auth.authorisation.checks import require_json -from gn3.auth.authorisation.errors import InvalidData, NotFoundError +from gn_auth.auth.authorisation.checks import require_json +from gn_auth.auth.authorisation.errors import InvalidData, NotFoundError -from gn3.auth.authorisation.groups.models import group_by_id +from gn_auth.auth.authorisation.groups.models import group_by_id -from gn3.auth.authorisation.users.models import user_resource_roles +from gn_auth.auth.authorisation.users.models import user_resource_roles -from gn3.auth.authorisation.resources.checks import authorised_for -from gn3.auth.authorisation.resources.models import ( +from gn_auth.auth.authorisation.resources.checks import authorised_for +from gn_auth.auth.authorisation.resources.models import ( user_resources, public_resources, attach_resources_data) -from gn3.auth.authentication.users import User -from gn3.auth.authentication.oauth2.resource_server import require_oauth +from gn_auth.auth.authentication.users import User +from gn_auth.auth.authentication.oauth2.resource_server import require_oauth -from gn3.auth.authorisation.data.phenotypes import link_phenotype_data -from gn3.auth.authorisation.data.mrna import link_mrna_data, ungrouped_mrna_data -from gn3.auth.authorisation.data.genotypes import ( +from gn_auth.auth.authorisation.data.phenotypes import link_phenotype_data +from gn_auth.auth.authorisation.data.mrna import link_mrna_data, ungrouped_mrna_data +from gn_auth.auth.authorisation.data.genotypes import ( link_genotype_data, ungrouped_genotype_data) data = Blueprint("data", __name__) diff --git a/gn_auth/auth/authorisation/groups/data.py b/gn_auth/auth/authorisation/groups/data.py index ee6f70e..d05747b 100644 --- a/gn_auth/auth/authorisation/groups/data.py +++ b/gn_auth/auth/authorisation/groups/data.py @@ -1,11 +1,11 @@ """Handles the resource objects' data.""" from MySQLdb.cursors import DictCursor -from gn3 import db_utils as gn3db -from gn3.auth import db as authdb -from gn3.auth.authorisation.groups import Group -from gn3.auth.authorisation.checks import authorised_p -from gn3.auth.authorisation.errors import NotFoundError +from gn_auth import db_utils as gn3db +from gn_auth.auth import db 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[ diff --git a/gn_auth/auth/authorisation/groups/models.py b/gn_auth/auth/authorisation/groups/models.py index 5a3ae50..9008bef 100644 --- a/gn_auth/auth/authorisation/groups/models.py +++ b/gn_auth/auth/authorisation/groups/models.py @@ -7,9 +7,9 @@ from typing import Any, Sequence, Iterable, Optional, NamedTuple from flask import g from pymonad.maybe import Just, Maybe, Nothing -from gn3.auth import db -from gn3.auth.dictify import dictify -from gn3.auth.authentication.users import User, user_by_id +from gn_auth.auth import db +from gn_auth.auth.dictify import dictify +from gn_auth.auth.authentication.users import User, user_by_id from ..checks import authorised_p from ..privileges import Privilege diff --git a/gn_auth/auth/authorisation/groups/views.py b/gn_auth/auth/authorisation/groups/views.py index 628df36..d1724cc 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 gn3.auth import db -from gn3 import db_utils as gn3db +from gn_auth.auth import db +from gn_auth import db_utils as gn3db -from gn3.auth.dictify import dictify -from gn3.auth.db_utils import with_db_connection +from gn_auth.auth.dictify import dictify +from gn_auth.auth.db_utils import with_db_connection from .data import link_data_to_group from .models import ( diff --git a/gn_auth/auth/authorisation/resources/checks.py b/gn_auth/auth/authorisation/resources/checks.py index fafde76..a341dbd 100644 --- a/gn_auth/auth/authorisation/resources/checks.py +++ b/gn_auth/auth/authorisation/resources/checks.py @@ -3,8 +3,8 @@ from uuid import UUID from functools import reduce from typing import Sequence -from gn3.auth import db -from gn3.auth.authentication.users import User +from gn_auth.auth import db +from gn_auth.auth.authentication.users import User def __organise_privileges_by_resource_id__(rows): def __organise__(privs, row): diff --git a/gn_auth/auth/authorisation/resources/models.py b/gn_auth/auth/authorisation/resources/models.py index b301a93..d96979f 100644 --- a/gn_auth/auth/authorisation/resources/models.py +++ b/gn_auth/auth/authorisation/resources/models.py @@ -5,10 +5,10 @@ from uuid import UUID, uuid4 from functools import reduce, partial from typing import Any, Dict, Sequence, Optional, NamedTuple -from gn3.auth import db -from gn3.auth.dictify import dictify -from gn3.auth.authentication.users import User -from gn3.auth.db_utils import with_db_connection +from gn_auth.auth import db +from gn_auth.auth.dictify import dictify +from gn_auth.auth.authentication.users import User +from gn_auth.auth.db_utils import with_db_connection from .checks import authorised_for diff --git a/gn_auth/auth/authorisation/resources/views.py b/gn_auth/auth/authorisation/resources/views.py index 3b2bbeb..9645303 100644 --- a/gn_auth/auth/authorisation/resources/views.py +++ b/gn_auth/auth/authorisation/resources/views.py @@ -6,7 +6,7 @@ from functools import reduce from flask import request, jsonify, Response, Blueprint, current_app as app -from gn3.auth.db_utils import with_db_connection +from gn_auth.auth.db_utils import with_db_connection from .checks import authorised_for from .models import ( diff --git a/gn_auth/auth/authorisation/roles/models.py b/gn_auth/auth/authorisation/roles/models.py index 97e11af..742a90e 100644 --- a/gn_auth/auth/authorisation/roles/models.py +++ b/gn_auth/auth/authorisation/roles/models.py @@ -5,10 +5,10 @@ from typing import Any, Sequence, Iterable, NamedTuple from pymonad.either import Left, Right, Either -from gn3.auth import db -from gn3.auth.dictify import dictify -from gn3.auth.authentication.users import User -from gn3.auth.authorisation.errors import AuthorisationError +from gn_auth.auth import db +from gn_auth.auth.dictify import dictify +from gn_auth.auth.authentication.users import User +from gn_auth.auth.authorisation.errors import AuthorisationError from ..checks import authorised_p from ..privileges import Privilege diff --git a/gn_auth/auth/authorisation/roles/views.py b/gn_auth/auth/authorisation/roles/views.py index 3670aab..6510365 100644 --- a/gn_auth/auth/authorisation/roles/views.py +++ b/gn_auth/auth/authorisation/roles/views.py @@ -3,8 +3,8 @@ import uuid from flask import jsonify, Response, Blueprint, current_app -from gn3.auth import db -from gn3.auth.dictify import dictify +from gn_auth.auth import db +from gn_auth.auth.dictify import dictify from .models import user_role diff --git a/gn_auth/auth/authorisation/users/admin/ui.py b/gn_auth/auth/authorisation/users/admin/ui.py index 242c7a6..4351a68 100644 --- a/gn_auth/auth/authorisation/users/admin/ui.py +++ b/gn_auth/auth/authorisation/users/admin/ui.py @@ -2,11 +2,11 @@ from functools import wraps from flask import flash, url_for, redirect -from gn3.auth.authentication.users import User -from gn3.auth.db_utils import with_db_connection -from gn3.auth.authorisation.roles.models import user_roles +from gn_auth.auth.authentication.users import User +from gn_auth.auth.db_utils import with_db_connection +from gn_auth.auth.authorisation.roles.models import user_roles -from gn3.session import logged_in, session_user, clear_session_info +from gn_auth.session import logged_in, session_user, clear_session_info def is_admin(func): """Verify user is a system admin.""" diff --git a/gn_auth/auth/authorisation/users/admin/views.py b/gn_auth/auth/authorisation/users/admin/views.py index c9f1887..ab04f91 100644 --- a/gn_auth/auth/authorisation/users/admin/views.py +++ b/gn_auth/auth/authorisation/users/admin/views.py @@ -17,17 +17,17 @@ from flask import ( render_template) -from gn3 import session -from gn3.auth import db -from gn3.auth.db_utils import with_db_connection +from gn_auth import session +from gn_auth.auth import db +from gn_auth.auth.db_utils import with_db_connection -from gn3.auth.authentication.oauth2.models.oauth2client import ( +from gn_auth.auth.authentication.oauth2.models.oauth2client import ( save_client, OAuth2Client, oauth2_clients, client as oauth2_client, delete_client as _delete_client) -from gn3.auth.authentication.users import ( +from gn_auth.auth.authentication.users import ( User, user_by_id, valid_login, diff --git a/gn_auth/auth/authorisation/users/collections/models.py b/gn_auth/auth/authorisation/users/collections/models.py index 7577fa8..eb9b188 100644 --- a/gn_auth/auth/authorisation/users/collections/models.py +++ b/gn_auth/auth/authorisation/users/collections/models.py @@ -6,7 +6,7 @@ from datetime import datetime from redis import Redis from email_validator import validate_email, EmailNotValidError -from gn3.auth.authorisation.errors import InvalidData, NotFoundError +from gn_auth.auth.authorisation.errors import InvalidData, NotFoundError from ..models import User diff --git a/gn_auth/auth/authorisation/users/collections/views.py b/gn_auth/auth/authorisation/users/collections/views.py index 1fa25a3..3dcc10f 100644 --- a/gn_auth/auth/authorisation/users/collections/views.py +++ b/gn_auth/auth/authorisation/users/collections/views.py @@ -4,13 +4,13 @@ from uuid import UUID from redis import Redis from flask import jsonify, request, Response, Blueprint, current_app -from gn3.auth import db -from gn3.auth.db_utils import with_db_connection -from gn3.auth.authorisation.checks import require_json -from gn3.auth.authorisation.errors import NotFoundError +from gn_auth.auth import db +from gn_auth.auth.db_utils import with_db_connection +from gn_auth.auth.authorisation.checks import require_json +from gn_auth.auth.authorisation.errors import NotFoundError -from gn3.auth.authentication.users import User, user_by_id -from gn3.auth.authentication.oauth2.resource_server import require_oauth +from gn_auth.auth.authentication.users import User, user_by_id +from gn_auth.auth.authentication.oauth2.resource_server import require_oauth from .models import ( add_traits, diff --git a/gn_auth/auth/authorisation/users/masquerade/models.py b/gn_auth/auth/authorisation/users/masquerade/models.py index 9f24b6b..c45d761 100644 --- a/gn_auth/auth/authorisation/users/masquerade/models.py +++ b/gn_auth/auth/authorisation/users/masquerade/models.py @@ -5,13 +5,13 @@ from datetime import datetime from flask import current_app as app -from gn3.auth import db +from gn_auth.auth import db -from gn3.auth.authorisation.errors import ForbiddenAccess -from gn3.auth.authorisation.roles.models import user_roles +from gn_auth.auth.authorisation.errors import ForbiddenAccess +from gn_auth.auth.authorisation.roles.models import user_roles -from gn3.auth.authentication.users import User -from gn3.auth.authentication.oauth2.models.oauth2token import ( +from gn_auth.auth.authentication.users import User +from gn_auth.auth.authentication.oauth2.models.oauth2token import ( OAuth2Token, save_token) __FIVE_HOURS__ = (60 * 60 * 5) diff --git a/gn_auth/auth/authorisation/users/masquerade/views.py b/gn_auth/auth/authorisation/users/masquerade/views.py index 43286a1..9e42945 100644 --- a/gn_auth/auth/authorisation/users/masquerade/views.py +++ b/gn_auth/auth/authorisation/users/masquerade/views.py @@ -4,12 +4,12 @@ from functools import partial from flask import request, jsonify, Response, Blueprint -from gn3.auth.db_utils import with_db_connection -from gn3.auth.authorisation.errors import InvalidData -from gn3.auth.authorisation.checks import require_json +from gn_auth.auth.db_utils import with_db_connection +from gn_auth.auth.authorisation.errors import InvalidData +from gn_auth.auth.authorisation.checks import require_json -from gn3.auth.authentication.users import user_by_id -from gn3.auth.authentication.oauth2.resource_server import require_oauth +from gn_auth.auth.authentication.users import user_by_id +from gn_auth.auth.authentication.oauth2.resource_server import require_oauth from .models import masquerade_as diff --git a/gn_auth/auth/authorisation/users/models.py b/gn_auth/auth/authorisation/users/models.py index 89c1d22..71fa390 100644 --- a/gn_auth/auth/authorisation/users/models.py +++ b/gn_auth/auth/authorisation/users/models.py @@ -2,12 +2,12 @@ import uuid from functools import reduce -from gn3.auth import db -from gn3.auth.authorisation.roles.models import Role -from gn3.auth.authorisation.checks import authorised_p -from gn3.auth.authorisation.privileges import Privilege +from gn_auth.auth import db +from gn_auth.auth.authorisation.roles.models import Role +from gn_auth.auth.authorisation.checks import authorised_p +from gn_auth.auth.authorisation.privileges import Privilege -from gn3.auth.authentication.users import User +from gn_auth.auth.authentication.users import User @authorised_p( ("system:user:list",), diff --git a/gn_auth/auth/authorisation/users/views.py b/gn_auth/auth/authorisation/users/views.py index 826e222..7783dca 100644 --- a/gn_auth/auth/authorisation/users/views.py +++ b/gn_auth/auth/authorisation/users/views.py @@ -7,9 +7,9 @@ import sqlite3 from email_validator import validate_email, EmailNotValidError from flask import request, jsonify, Response, Blueprint, current_app -from gn3.auth import db -from gn3.auth.dictify import dictify -from gn3.auth.db_utils import with_db_connection +from gn_auth.auth import db +from gn_auth.auth.dictify import dictify +from gn_auth.auth.db_utils import with_db_connection from .models import list_users from .masquerade.views import masq |