diff options
Diffstat (limited to 'gn3/auth')
| -rw-r--r-- | gn3/auth/authorisation/data/views.py | 8 | ||||
| -rw-r--r-- | gn3/auth/authorisation/groups/views.py | 4 |
2 files changed, 6 insertions, 6 deletions
diff --git a/gn3/auth/authorisation/data/views.py b/gn3/auth/authorisation/data/views.py index 1a4c031..e00df66 100644 --- a/gn3/auth/authorisation/data/views.py +++ b/gn3/auth/authorisation/data/views.py @@ -49,7 +49,7 @@ data = Blueprint("data", __name__) @data.route("species") def list_species() -> Response: """List all available species information.""" - with (gn3db.database_connection() as gn3conn, + with (gn3db.database_connection(app.config["SQL_URI"]) as gn3conn, gn3conn.cursor(DictCursor) as cursor): cursor.execute("SELECT * FROM Species") return jsonify(tuple(dict(row) for row in cursor.fetchall())) @@ -280,7 +280,7 @@ def migrate_users_data() -> Response: with (require_oauth.acquire("migrate-data") as the_token, db.connection(db_uri) as authconn, redis.Redis(decode_responses=True) as rconn, - gn3db.database_connection() as gn3conn): + gn3db.database_connection(app.config["SQL_URI"]) as gn3conn): if the_token.client.client_id in authorised_clients: by_user: dict[uuid.UUID, tuple[dict[str, str], ...]] = reduce( __org_by_user_id__, redis_resources(rconn), {}) @@ -315,7 +315,7 @@ def __search_mrna__(): query = __request_key__("query", "") limit = int(__request_key__("limit", 10000)) offset = int(__request_key__("offset", 0)) - with gn3db.database_connection() as gn3conn: + with gn3db.database_connection(app.config["SQL_URI"]) as gn3conn: __ungrouped__ = partial( ungrouped_mrna_data, gn3conn=gn3conn, search_query=query, selected=__request_key_list__("selected"), @@ -340,7 +340,7 @@ def __search_genotypes__(): query = __request_key__("query", "") limit = int(__request_key__("limit", 10000)) offset = int(__request_key__("offset", 0)) - with gn3db.database_connection() as gn3conn: + with gn3db.database_connection(app.config["SQL_URI"]) as gn3conn: __ungrouped__ = partial( ungrouped_genotype_data, gn3conn=gn3conn, search_query=query, selected=__request_key_list__("selected"), diff --git a/gn3/auth/authorisation/groups/views.py b/gn3/auth/authorisation/groups/views.py index d7a46c0..e933bcd 100644 --- a/gn3/auth/authorisation/groups/views.py +++ b/gn3/auth/authorisation/groups/views.py @@ -207,7 +207,7 @@ def ungrouped_data(dataset_type: str) -> Response: raise AuthorisationError(f"Invalid dataset type {dataset_type}") with require_oauth.acquire("profile group resource") as _the_token: - with gn3dbutils.database_connection() as gn3conn: + with gn3dbutils.database_connection(current_app.config["SQL_URI"]) as gn3conn: return jsonify(with_db_connection(partial( retrieve_ungrouped_data, gn3conn=gn3conn, dataset_type=dataset_type, @@ -226,7 +226,7 @@ def link_data() -> Response: raise InvalidData("Unexpected dataset type requested!") def __link__(conn: db.DbConnection): group = group_by_id(conn, group_id) - with gn3dbutils.database_connection() as gn3conn: + with gn3dbutils.database_connection(current_app.config["SQL_URI"]) as gn3conn: return link_data_to_group( conn, gn3conn, dataset_type, dataset_ids, group) |