diff options
Diffstat (limited to 'gn_auth/auth/authorisation')
| -rw-r--r-- | gn_auth/auth/authorisation/data/views.py | 25 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/resources/groups/views.py | 23 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/resources/views.py | 20 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/roles/models.py | 2 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/users/views.py | 10 |
5 files changed, 43 insertions, 37 deletions
diff --git a/gn_auth/auth/authorisation/data/views.py b/gn_auth/auth/authorisation/data/views.py index 86dafe5..7ed69e3 100644 --- a/gn_auth/auth/authorisation/data/views.py +++ b/gn_auth/auth/authorisation/data/views.py @@ -14,6 +14,7 @@ from flask import request, jsonify, Response, Blueprint, current_app as app from gn_auth import jobs from gn_auth.commands import run_async_cmd +from gn_auth.auth.requests import request_json from gn_auth.auth.errors import InvalidData, NotFoundError from gn_auth.auth.authorisation.resources.groups.models import group_by_id @@ -184,18 +185,18 @@ def __search_mrna__(): return jsonify(with_db_connection(__ungrouped__)) def __request_key__(key: str, default: Any = ""): - if bool(request.json): - return request.json.get(#type: ignore[union-attr] - key, request.args.get(key, request.json.get(key, default))) - return request.args.get(key, request.json.get(key, default)) + if bool(request_json()): + return request_json().get(#type: ignore[union-attr] + key, request.args.get(key, request_json().get(key, default))) + return request.args.get(key, request_json().get(key, default)) def __request_key_list__(key: str, default: tuple[Any, ...] = tuple()): - if bool(request.json): - return (request.json.get(key,[])#type: ignore[union-attr] - or request.args.getlist(key) or request.json.getlist(key) + if bool(request_json()): + return (request_json().get(key,[])#type: ignore[union-attr] + or request.args.getlist(key) or request_json().get(key) or list(default)) return (request.args.getlist(key) - or request.json.getlist(key) or list(default)) + or request_json().get(key) or list(default)) def __search_genotypes__(): query = __request_key__("query", "") @@ -240,7 +241,7 @@ def __search_phenotypes__(): @require_oauth("profile group resource") def search_unlinked_data(): """Search for various unlinked data.""" - dataset_type = request.json["dataset_type"] + dataset_type = request_json()["dataset_type"] search_fns = { "mrna": __search_mrna__, "genotype": __search_genotypes__, @@ -281,7 +282,7 @@ def link_genotypes() -> Response: return link_genotype_data(conn, group_by_id(conn, group_id), datasets) return jsonify(with_db_connection( - partial(__link__, **__values__(request.json)))) + partial(__link__, **__values__(request_json())))) @data.route("/link/mrna", methods=["POST"]) def link_mrna() -> Response: @@ -306,7 +307,7 @@ def link_mrna() -> Response: return link_mrna_data(conn, group_by_id(conn, group_id), datasets) return jsonify(with_db_connection( - partial(__link__, **__values__(request.json)))) + partial(__link__, **__values__(request_json())))) @data.route("/link/phenotype", methods=["POST"]) def link_phenotype() -> Response: @@ -334,4 +335,4 @@ def link_phenotype() -> Response: conn, gn3conn, group_by_id(conn, group_id), traits) return jsonify(with_db_connection( - partial(__link__, **__values__(request.json)))) + partial(__link__, **__values__(request_json())))) diff --git a/gn_auth/auth/authorisation/resources/groups/views.py b/gn_auth/auth/authorisation/resources/groups/views.py index 47bf047..401be00 100644 --- a/gn_auth/auth/authorisation/resources/groups/views.py +++ b/gn_auth/auth/authorisation/resources/groups/views.py @@ -7,13 +7,14 @@ from functools import partial from dataclasses import asdict from MySQLdb.cursors import DictCursor -from flask import request, jsonify, Response, Blueprint, current_app +from flask import jsonify, Response, Blueprint, current_app + +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.checks import authorised_p from gn_auth.auth.authorisation.privileges import privileges_by_ids from gn_auth.auth.errors import InvalidData, NotFoundError, AuthorisationError @@ -26,7 +27,7 @@ from .models import ( join_requests, group_role_by_id, GroupCreationError, accept_reject_join_request, group_users as _group_users, create_group as _create_group, add_privilege_to_group_role, - delete_privilege_from_group_role, create_group_role as _create_group_role) + delete_privilege_from_group_role) groups = Blueprint("groups", __name__) @@ -45,7 +46,7 @@ def list_groups(): def create_group(): """Create a new group.""" with require_oauth.acquire("profile group") as the_token: - group_name=request.json.get("group_name", "").strip() + group_name=request_json().get("group_name", "").strip() if not bool(group_name): raise GroupCreationError("Could not create the group.") @@ -53,7 +54,7 @@ def create_group(): with db.connection(db_uri) as conn: user = the_token.user new_group = _create_group( - conn, group_name, user, request.json.get("group_description")) + conn, group_name, user, request_json().get("group_description")) return jsonify({ **asdict(new_group), "group_leader": asdict(user) }) @@ -102,7 +103,7 @@ def request_to_join(group_id: uuid.UUID) -> Response: } with require_oauth.acquire("profile group") as the_token: - form = request.json + form = request_json() results = with_db_connection(partial( __request__, user=the_token.user, group_id=group_id, message=form.get( "message", "I hereby request that you add me to your group."))) @@ -121,7 +122,7 @@ def list_join_requests() -> Response: def accept_join_requests() -> Response: """Accept a join request.""" with require_oauth.acquire("profile group") as the_token: - form = request.json + form = request_json() request_id = uuid.UUID(form.get("request_id")) return jsonify(with_db_connection(partial( accept_reject_join_request, request_id=request_id, @@ -132,7 +133,7 @@ def accept_join_requests() -> Response: def reject_join_requests() -> Response: """Reject a join request.""" with require_oauth.acquire("profile group") as the_token: - form = request.json + form = request_json() request_id = uuid.UUID(form.get("request_id")) return jsonify(with_db_connection(partial( accept_reject_join_request, request_id=request_id, @@ -263,9 +264,9 @@ def unlinked_data(resource_type: str) -> Response: def link_data() -> Response: """Link selected data to specified group.""" with require_oauth.acquire("profile group resource") as _the_token: - form = request.json + form = request_json() group_id = uuid.UUID(form["group_id"]) - dataset_ids = form.getlist("dataset_ids") + dataset_ids = form.get("dataset_ids") dataset_type = form.get("dataset_type") if dataset_type not in ("mrna", "genotype", "phenotype"): raise InvalidData("Unexpected dataset type requested!") @@ -305,7 +306,7 @@ def __add_remove_priv_to_from_role__(conn: db.DbConnection, raise AuthorisationError( "You need to be a member of a group to edit roles.") try: - privilege_id = request.json.get("privilege_id", "") + privilege_id = request_json().get("privilege_id", "") assert bool(privilege_id), "Privilege to add must be provided." privileges = privileges_by_ids(conn, (privilege_id,)) if len(privileges) == 0: diff --git a/gn_auth/auth/authorisation/resources/views.py b/gn_auth/auth/authorisation/resources/views.py index 0e07ffa..5c2b66e 100644 --- a/gn_auth/auth/authorisation/resources/views.py +++ b/gn_auth/auth/authorisation/resources/views.py @@ -14,6 +14,8 @@ from authlib.integrations.flask_oauth2.errors import _HTTPException from flask import (make_response, request, jsonify, Response, Blueprint, current_app as app) +from gn_auth.auth.requests import request_json + from gn_auth.auth.db import sqlite3 as db from gn_auth.auth.db.sqlite3 import with_db_connection @@ -61,7 +63,7 @@ def list_resource_categories() -> Response: def create_resource() -> Response: """Create a new resource""" with require_oauth.acquire("profile group resource") as the_token: - form = request.json + form = request_json() resource_name = form.get("resource_name") resource_category_id = UUID(form.get("resource_category")) db_uri = app.config["AUTH_DB"] @@ -134,7 +136,7 @@ def view_resource_data(resource_id: UUID) -> Response: def link_data(): """Link group data to a specific resource.""" try: - form = request.json + form = request_json() assert "resource_id" in form, "Resource ID not provided." assert "data_link_id" in form, "Data Link ID not provided." assert "dataset_type" in form, "Dataset type not specified" @@ -158,7 +160,7 @@ def link_data(): def unlink_data(): """Unlink data bound to a specific resource.""" try: - form = request.json + form = request_json() assert "resource_id" in form, "Resource ID not provided." assert "data_link_id" in form, "Data Link ID not provided." @@ -247,7 +249,7 @@ def assign_role_to_user(resource_id: UUID) -> Response: """Assign a role on the specified resource to a user.""" with require_oauth.acquire("profile group resource role") as the_token: try: - form = request.json + form = request_json() group_role_id = form.get("group_role_id", "") user_email = form.get("user_email", "") assert bool(group_role_id), "The role must be provided." @@ -272,7 +274,7 @@ def unassign_role_to_user(resource_id: UUID) -> Response: """Unassign a role on the specified resource from a user.""" with require_oauth.acquire("profile group resource role") as the_token: try: - form = request.json + form = request_json() group_role_id = form.get("group_role_id", "") user_id = form.get("user_id", "") assert bool(group_role_id), "The role must be provided." @@ -399,7 +401,7 @@ def resource_roles(resource_id: UUID) -> Response: def resources_authorisation(): """Get user authorisations for given resource(s):""" try: - data = request.json + data = request_json() assert (data and "resource-ids" in data) resource_ids = tuple(UUID(resid) for resid in data["resource-ids"]) pubres = tuple( @@ -546,7 +548,7 @@ def unassign_resource_role_privilege(resource_id: UUID, role_id: UUID): "You are not authorised to edit/update this role.") # Actually unassign the privilege from the role - privilege_id = request.json.get("privilege_id") + privilege_id = request_json().get("privilege_id") if not privilege_id: raise AuthorisationError( "You need to provide a privilege to unassign") @@ -583,7 +585,7 @@ def resource_role_users(resource_id: UUID, role_id: UUID): @require_oauth("profile group resource") def create_resource_role(resource_id: UUID): """Create a role to act upon a specific resource.""" - role_name = request.json.get("role_name", "").strip() + role_name = request_json().get("role_name", "").strip() if not bool(role_name): raise BadRequest("You must provide the name for the new role.") @@ -594,7 +596,7 @@ def create_resource_role(resource_id: UUID): if not bool(resource): raise BadRequest("No resource with that ID exists.") - privileges = privileges_by_ids(conn, request.json.get("privileges", [])) + privileges = privileges_by_ids(conn, request_json().get("privileges", [])) if len(privileges) == 0: raise BadRequest( "You must provide at least one privilege for the new role.") diff --git a/gn_auth/auth/authorisation/roles/models.py b/gn_auth/auth/authorisation/roles/models.py index 03f88d7..dc1dfdc 100644 --- a/gn_auth/auth/authorisation/roles/models.py +++ b/gn_auth/auth/authorisation/roles/models.py @@ -137,7 +137,7 @@ def user_resource_roles( conn: db.DbConnection, user: User, resource: Resource -) -> tuple[Role]: +) -> tuple[Role, ...]: """Retrieve all roles assigned to a user for a particular resource.""" with db.cursor(conn) as cursor: cursor.execute( diff --git a/gn_auth/auth/authorisation/users/views.py b/gn_auth/auth/authorisation/users/views.py index cc70d76..8135ed3 100644 --- a/gn_auth/auth/authorisation/users/views.py +++ b/gn_auth/auth/authorisation/users/views.py @@ -22,6 +22,8 @@ from flask import ( from gn_auth.smtp import send_message, build_email_message +from gn_auth.auth.requests import request_json + from gn_auth.auth.db import sqlite3 as db from gn_auth.auth.db.sqlite3 import with_db_connection @@ -166,7 +168,7 @@ def register_user() -> Response: __assert_not_logged_in__(conn) try: - form = request.json + form = request_json() email = validate_email(form.get("email", "").strip(), check_deliverability=True) password = validate_password( @@ -204,7 +206,7 @@ def delete_verification_code(cursor, code: str): @users.route("/verify", methods=["GET", "POST"]) def verify_user(): """Verify users are not bots.""" - form = request.json + form = request_json() loginuri = redirect(url_for( "oauth2.auth.authorise", response_type=(request.args.get("response_type") @@ -308,7 +310,7 @@ def list_all_users() -> Response: @users.route("/handle-unverified", methods=["POST"]) def handle_unverified(): """Handle case where user tries to login but is unverified""" - form = request.json + form = request_json() # TODO: Maybe have a GN2_URI setting here? # or pass the client_id here? return render_template( @@ -321,7 +323,7 @@ def handle_unverified(): @users.route("/send-verification", methods=["POST"]) def send_verification_code(): """Send verification code email.""" - form = request.json + form = request_json() with (db.connection(current_app.config["AUTH_DB"]) as conn, db.cursor(conn) as cursor): user = user_by_email(conn, form["user_email"]) |