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"""Handle data endpoints."""
import json
from functools import reduce
from flask import request, Response, Blueprint, current_app as app
from authlib.integrations.flask_oauth2.errors import _HTTPException
from gn3 import db_utils as gn3db
from gn3.db.traits import build_trait_name
from gn3.auth import db
from gn3.auth.authentication.oauth2.resource_server import require_oauth
from gn3.auth.authorisation.resources.models import (
user_resources, public_resources, attach_resources_data)
data = Blueprint("data", __name__)
@data.route("/authorisation", methods=["GET"])
def authorisation() -> Response:
"""Retrive the authorisation level for datasets/traits for the user."""
db_uri = app.config["AUTH_DB"]
the_user = "ANONYMOUS"
with db.connection(db_uri) as auth_conn, gn3db.database_connection() as gn3conn:
try:
with require_oauth.acquire("profile group resource") as the_token:
resources = attach_resources_data(
auth_conn, user_resources(auth_conn, the_token.user))
except _HTTPException as exc:
err_msg = json.loads(exc.body)
if err_msg["error"] == "missing_authorization":
resources = attach_resources_data(
auth_conn, public_resources(auth_conn))
else:
raise exc from None
# Access endpoint with somethin like:
# curl -X GET http://127.0.0.1:8080/api/oauth2/data/authorisation \
# -H "Content-Type: application/json" \
# -d '{"traits": ["HC_M2_0606_P::1442370_at", "BXDGeno::01.001.695", "BXDPublish::10001"]}'
args = request.get_json()
traits_names = args["traits"]
def __translate__(val):
return {
"ProbeSet": "mRNA",
"Geno": "Genotype",
"Publish": "Phenotype"
}[val]
traits = (
{
**{key:trait[key] for key in ("trait_fullname", "trait_name")},
"dataset_name": trait["db"]["dataset_name"],
"dataset_type": __translate__(trait["db"]["dataset_type"])
} for trait in
(build_trait_name(trait_fullname)
for trait_fullname in traits_names))
# Retrieve the dataset/trait IDs from traits above
# Compare the traits/dataset names/ids from request with resources' data
# - Any trait not in resources' data is marked inaccessible
# - Any trait in resources' data:
# - IF public is marked readable
# - IF private and user has read privilege: mark readable
# - ELSE mark inaccessible
return "NOT COMPLETED! ..."
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