diff options
Diffstat (limited to 'gn3/auth/authorisation/resources/views.py')
| -rw-r--r-- | gn3/auth/authorisation/resources/views.py | 108 |
1 files changed, 21 insertions, 87 deletions
diff --git a/gn3/auth/authorisation/resources/views.py b/gn3/auth/authorisation/resources/views.py index e373182..b2773a8 100644 --- a/gn3/auth/authorisation/resources/views.py +++ b/gn3/auth/authorisation/resources/views.py @@ -1,19 +1,15 @@ """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) + resource_by_id, resource_categories, link_data_to_resource, + 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 ..errors import InvalidData from ... import db from ...dictify import dictify @@ -56,86 +52,24 @@ def view_resource(resource_id: uuid.UUID) -> Response: 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: +def link_data(): + """Link group data to a specific resource.""" + try: 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__)) + 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 |