Fix mypy errors

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"])