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"""The views/routes for the resources package"""
import uuid
from flask import request, jsonify, Response, Blueprint, current_app as app
from gn3.auth.db_utils import with_db_connection
from .models import (
resource_by_id, resource_categories, link_data_to_resource,
resource_category_by_id, create_resource as _create_resource)
from ..errors import InvalidData
from ... import db
from ...dictify import dictify
from ...authentication.oauth2.resource_server import require_oauth
resources = Blueprint("resources", __name__)
@resources.route("/categories", methods=["GET"])
@require_oauth("profile group resource")
def list_resource_categories() -> Response:
"""Retrieve all resource categories"""
db_uri = app.config["AUTH_DB"]
with db.connection(db_uri) as conn:
return jsonify(tuple(
dictify(category) for category in resource_categories(conn)))
@resources.route("/create", methods=["POST"])
@require_oauth("profile group resource")
def create_resource() -> Response:
"""Create a new resource"""
with require_oauth.acquire("profile group resource") as the_token:
form = request.form
resource_name = form.get("resource_name")
resource_category_id = uuid.UUID(form.get("resource_category"))
db_uri = app.config["AUTH_DB"]
with db.connection(db_uri) as conn:
resource = _create_resource(
conn, resource_name, resource_category_by_id(
conn, resource_category_id),
the_token.user)
return jsonify(dictify(resource))
@resources.route("/view/<uuid:resource_id>")
@require_oauth("profile group resource")
def view_resource(resource_id: uuid.UUID) -> Response:
"""View a particular resource's details."""
with require_oauth.acquire("profile group resource") as the_token:
db_uri = app.config["AUTH_DB"]
with db.connection(db_uri) as conn:
return jsonify(dictify(resource_by_id(
conn, the_token.user, resource_id)))
@resources.route("/data/link", methods=["POST"])
@require_oauth("profile group resource")
def link_data():
"""Link group data to a specific resource."""
try:
form = request.form
assert "resource_id" in form, "Resource ID not provided."
assert "dataset_id" in form, "Dataset ID not provided."
assert "dataset_type" in form, "Dataset type not specified"
assert form["dataset_type"].lower() in (
"mrna", "genotype", "phenotype"), "Invalid dataset type provided."
with require_oauth.acquire("profile group resource") as the_token:
def __link__(conn: db.DbConnection):
return link_data_to_resource(
conn, the_token.user, uuid.UUID(form["resource_id"]),
form["dataset_type"], form["dataset_id"])
return jsonify(with_db_connection(__link__))
except AssertionError as aserr:
raise InvalidData(aserr.args[0]) from aserr
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