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authorFrederick Muriuki Muriithi2023-03-14 13:07:23 +0300
committerFrederick Muriuki Muriithi2023-03-14 13:08:05 +0300
commit616560ada0104f148d9cb54405122a3e6a3d6ea1 (patch)
tree91cf1b740dbc4cd61a96f457fd34c050ec7311d1 /gn3
parent6197e350b2696ab77f76f3b29dfaef253961c241 (diff)
downloadgenenetwork3-616560ada0104f148d9cb54405122a3e6a3d6ea1.tar.gz
auth: Fix some linting and typing issues.
Diffstat (limited to 'gn3')
-rw-r--r--gn3/auth/authorisation/data/views.py37
1 files changed, 25 insertions, 12 deletions
diff --git a/gn3/auth/authorisation/data/views.py b/gn3/auth/authorisation/data/views.py
index 50d1659..03c32b3 100644
--- a/gn3/auth/authorisation/data/views.py
+++ b/gn3/auth/authorisation/data/views.py
@@ -39,7 +39,7 @@ from gn3.auth.authorisation.errors import ForbiddenAccess, AuthorisationError
from gn3.auth.authentication.oauth2.resource_server import require_oauth
from gn3.auth.authentication.users import User, user_by_id, set_user_password
from gn3.auth.authentication.oauth2.models.oauth2token import (
- OAuth2Token, save_token)
+ OAuth2Token, save_token, revoke_token)
from gn3.auth.authentication.oauth2.models.oauth2client import (
client_by_id_and_secret)
@@ -163,7 +163,7 @@ def __parametrise__(group: Group, datasets: Sequence[dict],
def user_redis_resources(rconn: redis.Redis, user_id: uuid.UUID) -> tuple[
tuple[dict], tuple[dict], tuple[dict]]:
"""Acquire any resources from redis."""
- return reduce(# type: ignore[var-annotated]
+ return reduce(# type: ignore[return-value]
__redis_datasets_by_type__,
(dataset for dataset in
(dataset for _key,dataset in {
@@ -213,7 +213,7 @@ def generate_sysadmin_token() -> OAuth2Token:
def migrate_data(
authconn: db.DbConnection, gn3conn: gn3db.Connection,
redis_resources: tuple[tuple[dict], tuple[dict], tuple[dict]],
- user: User, group: Group) -> tuple[dict[str, str], ...]:
+ group: Group) -> tuple[dict[str, str], ...]:
"""Migrate data attached to the user to the user's group."""
redis_mrna, redis_geno, redis_pheno = redis_resources
## BEGIN: Escalate privileges temporarily to enable fetching of data
@@ -227,6 +227,8 @@ def migrate_data(
retrieve_ungrouped_data(authconn, gn3conn, "genotype"), redis_geno)
pheno_datasets = __unmigrated_data__(
retrieve_ungrouped_data(authconn, gn3conn, "phenotype"), redis_pheno)
+
+ save_token(authconn, revoke_token(new_token))
## =====================================
## END: Escalate privileges temporarily to enable fetching of data
@@ -263,7 +265,7 @@ def migrate_user() -> Response:
set_user_password(cursor, user, password)
return user
try:
- db_uri = app.config.get("AUTH_DB").strip()
+ db_uri = app.config.get("AUTH_DB", "").strip()
with (db.connection(db_uri) as authconn,
redis.Redis(decode_responses=True) as rconn):
client_id = uuid.UUID(request.form.get("client_id"))
@@ -306,22 +308,25 @@ def migrate_user_data(user_id: uuid.UUID) -> Response:
This is a temporary endpoint and should be removed after all the data has
been migrated.
"""
- db_uri = app.config.get("AUTH_DB").strip()
+ db_uri = app.config.get("AUTH_DB", "").strip()
if bool(db_uri) and os.path.exists(db_uri):
authorised_clients = app.config.get(
"OAUTH2_CLIENTS_WITH_DATA_MIGRATION_PRIVILEGE", [])
with require_oauth.acquire("migrate-data") as the_token:
if the_token.client.client_id in authorised_clients:
user = the_token.user
+ if not user_id == user.user_id:
+ raise AuthorisationError(
+ "You cannot trigger migration of another user's data.")
with (db.connection(db_uri) as authconn,
redis.Redis(decode_responses=True) as rconn,
gn3db.database_connection() as gn3conn):
redis_resources = user_redis_resources(rconn, user.user_id)
- user_resource_data = tuple()
+ user_resource_data: tuple = tuple()
if any(bool(item) for item in redis_resources):
group = migrate_user_group(authconn, user)
user_resource_data = migrate_data(
- authconn, gn3conn, redis_resources, user, group)
+ authconn, gn3conn, redis_resources, group)
## TODO: Maybe delete user from redis...
return jsonify({
"description": (
@@ -333,8 +338,16 @@ def migrate_user_data(user_id: uuid.UUID) -> Response:
raise ForbiddenAccess("You cannot access this endpoint.")
- return jsonify({
- "error": "Unavailable",
- "error_description": (
- "The data migration service is currently unavailable.")
- }), 503
+ return app.response_class(
+ response=json.dumps({
+ "error": "Unavailable",
+ "error_description": (
+ "The data migration service is currently unavailable.")
+ }),
+ status=500, mimetype="application/json")
+
+ # return jsonify({
+ # "error": "Unavailable",
+ # "error_description": (
+ # "The data migration service is currently unavailable.")
+ # }), 503