diff options
Diffstat (limited to 'gn_auth/auth/authorisation/data/views.py')
| -rw-r--r-- | gn_auth/auth/authorisation/data/views.py | 34 |
1 files changed, 25 insertions, 9 deletions
diff --git a/gn_auth/auth/authorisation/data/views.py b/gn_auth/auth/authorisation/data/views.py index 7ed69e3..9123949 100644 --- a/gn_auth/auth/authorisation/data/views.py +++ b/gn_auth/auth/authorisation/data/views.py @@ -11,6 +11,9 @@ from MySQLdb.cursors import DictCursor from authlib.integrations.flask_oauth2.errors import _HTTPException from flask import request, jsonify, Response, Blueprint, current_app as app + +from gn_libs import mysqldb as gn3db + from gn_auth import jobs from gn_auth.commands import run_async_cmd @@ -19,7 +22,6 @@ from gn_auth.auth.errors import InvalidData, NotFoundError from gn_auth.auth.authorisation.resources.groups.models import group_by_id from ...db import sqlite3 as db -from ...db import mariadb as gn3db from ...db.sqlite3 import with_db_connection from ..checks import require_json @@ -33,8 +35,8 @@ from ..resources.models import ( from ...authentication.users import User from ...authentication.oauth2.resource_server import require_oauth -from ..data.phenotypes import link_phenotype_data from ..data.mrna import link_mrna_data, ungrouped_mrna_data +from ..data.phenotypes import link_phenotype_data, pheno_traits_from_db from ..data.genotypes import link_genotype_data, ungrouped_genotype_data data = Blueprint("data", __name__) @@ -187,7 +189,7 @@ def __search_mrna__(): 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))) + key, request.args.get(key, default)) return request.args.get(key, request_json().get(key, default)) def __request_key_list__(key: str, default: tuple[Any, ...] = tuple()): @@ -310,6 +312,7 @@ def link_mrna() -> Response: partial(__link__, **__values__(request_json())))) @data.route("/link/phenotype", methods=["POST"]) +@require_oauth("profile group resource") def link_phenotype() -> Response: """Link phenotype data to group.""" def __values__(form): @@ -325,14 +328,27 @@ def link_phenotype() -> Response: raise InvalidData("Expected at least one dataset to be provided.") return { "group_id": uuid.UUID(form["group_id"]), - "traits": form["selected"] + "traits": form["selected"], + "using_raw_ids": bool(form.get("using-raw-ids") == "on") } - with gn3db.database_connection(app.config["SQL_URI"]) as gn3conn: - def __link__(conn: db.DbConnection, group_id: uuid.UUID, - traits: tuple[dict, ...]) -> dict: - return link_phenotype_data( - conn, gn3conn, group_by_id(conn, group_id), traits) + with (require_oauth.acquire("profile group resource") as token, + gn3db.database_connection(app.config["SQL_URI"]) as gn3conn): + def __link__( + conn: db.DbConnection, + group_id: uuid.UUID, + traits: tuple[dict, ...], + using_raw_ids: bool = False + ) -> dict: + if using_raw_ids: + return link_phenotype_data(conn, + token.user, + group_by_id(conn, group_id), + traits) + return link_phenotype_data(conn, + token.user, + group_by_id(conn, group_id), + pheno_traits_from_db(gn3conn, traits)) return jsonify(with_db_connection( partial(__link__, **__values__(request_json())))) |