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"""The views/routes for the resources package"""
import uuid
from functools import partial
from flask import request, jsonify, Response, Blueprint, current_app as app
from gn3 import db_utils as gn3dbutils
from gn3.auth.db_utils import with_db_connection
from .data import link_data_to_group, retrieve_ungrouped_data
from .models import (
resource_by_id, resource_categories, resource_category_by_id,
create_resource as _create_resource)
from ..errors import InvalidData, AuthorisationError
from ..groups.models import user_group, DUMMY_GROUP, group_by_id
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("/<string:resource_type>/unlinked-data")
@require_oauth("profile group resource")
def unlinked_data(resource_type: str) -> Response:
"""View data linked to the group but not linked to any resource."""
if resource_type not in ("all", "mrna", "genotype", "phenotype"):
raise AuthorisationError(f"Invalid resource type {resource_type}")
with require_oauth.acquire("profile group resource") as the_token:
db_uri = app.config["AUTH_DB"]
with db.connection(db_uri) as conn, db.cursor(conn) as cursor:
ugroup = user_group(cursor, the_token.user).maybe(# type: ignore[misc]
DUMMY_GROUP, lambda grp: grp)
if ugroup == DUMMY_GROUP:
return jsonify(tuple())
type_filter = {
"all": "",
"mrna": 'WHERE dataset_type="mRNA"',
"genotype": 'WHERE dataset_type="Genotype"',
"phenotype": 'WHERE dataset_type="Phenotype"'
}[resource_type]
except_filter = (
"SELECT group_id, dataset_type, "
"dataset_id AS dataset_or_trait_id FROM mrna_resources "
"UNION "
"SELECT group_id, dataset_type, "
"trait_id AS dataset_or_trait_id FROM genotype_resources "
"UNION "
"SELECT group_id, dataset_type, "
"trait_id AS dataset_or_trait_id FROM phenotype_resources")
ids_query = ("SELECT group_id, dataset_type, dataset_or_trait_id "
"FROM linked_group_data "
f"{type_filter} "
f"EXCEPT {except_filter} ")
cursor.execute(ids_query)
ids = cursor.fetchall()
if ids:
clause = ", ".join(["(?, ?, ?)"] * len(ids))
data_query = (
"SELECT * FROM linked_group_data "
"WHERE (group_id, dataset_type, dataset_or_trait_id) "
f"IN (VALUES {clause})")
params = tuple(item for sublist in
((row[0], row[1], row[2]) for row in ids)
for item in sublist)
cursor.execute(data_query, params)
return jsonify(tuple(dict(row) for row in cursor.fetchall()))
return jsonify(tuple())
@resources.route("/<string:dataset_type>/ungrouped-data", methods=["GET"])
@require_oauth("profile group resource")
def ungrouped_data(dataset_type: str) -> Response:
"""View data not linked to any group."""
if dataset_type not in ("all", "mrna", "genotype", "phenotype"):
raise AuthorisationError(f"Invalid dataset type {dataset_type}")
with require_oauth.acquire("profile group resource") as _the_token:
with gn3dbutils.database_connection() as gn3conn:
return jsonify(with_db_connection(partial(
retrieve_ungrouped_data, gn3conn=gn3conn,
dataset_type=dataset_type)))
@resources.route("/data/link", methods=["POST"])
@require_oauth("profile group resource")
def link_data() -> Response:
"""Link selected data to specified group."""
with require_oauth.acquire("profile group resource") as _the_token:
form = request.form
group_id = uuid.UUID(form["group_id"])
dataset_id = form["dataset_id"]
dataset_type = form.get("dataset_type")
if dataset_type not in ("mrna", "genotype", "phenotype"):
raise InvalidData("Unexpected dataset type requested!")
def __link__(conn: db.DbConnection):
group = group_by_id(conn, group_id)
with gn3dbutils.database_connection() as gn3conn:
return link_data_to_group(
conn, gn3conn, dataset_type, dataset_id, group)
return jsonify(with_db_connection(__link__))
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