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authorFrederick Muriuki Muriithi2023-04-15 19:35:53 +0300
committerFrederick Muriuki Muriithi2023-04-15 19:35:53 +0300
commitdbf0f9f0d34c9969aa6ae76f556745a9eb122106 (patch)
treec0a992202155e354dfac8a829e5dea197ceeef25 /gn3/auth/authorisation
parent2b7ecb52fa5f568d7d48fc324bae8231343543bd (diff)
downloadgenenetwork3-dbf0f9f0d34c9969aa6ae76f556745a9eb122106.tar.gz
Decouple `gn3.db_utils` from `flask.current_app`.
Decouple the `gn3.db_utils` module from the global `flask.current_app` object, ensuring that the database uri value is passed in as a required argument to the `gn3.db_utils.database_connection` function.
Diffstat (limited to 'gn3/auth/authorisation')
-rw-r--r--gn3/auth/authorisation/data/views.py8
-rw-r--r--gn3/auth/authorisation/groups/views.py4
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)