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"""The views/routes for the resources package"""
import uuid
import json
import sqlite3
from functools import reduce
from flask import request, jsonify, Response, Blueprint, current_app as app
from gn_auth.auth.db.sqlite3 import with_db_connection
from .checks import authorised_for
from .models import (
Resource, save_resource, resource_data, resource_by_id, resource_categories,
assign_resource_user, link_data_to_resource, unassign_resource_user,
resource_category_by_id, unlink_data_from_resource,
create_resource as _create_resource)
from ..roles import Role
from ..errors import InvalidData, InconsistencyError, AuthorisationError
from ..groups.models import Group, GroupRole, group_role_by_id
from ... import db
from ...dictify import dictify
from ...authentication.oauth2.resource_server import require_oauth
from ...authentication.users import User, user_by_id, user_by_email
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:
try:
resource = _create_resource(
conn,
resource_name,
resource_category_by_id(conn, resource_category_id),
the_token.user,
(form.get("public") == "on"))
return jsonify(dictify(resource))
except sqlite3.IntegrityError as sql3ie:
if sql3ie.args[0] == ("UNIQUE constraint failed: "
"resources.resource_name"):
raise InconsistencyError(
"You cannot have duplicate resource names.") from sql3ie
app.logger.debug(
f"{type(sql3ie)=}: {sql3ie=}")
raise
@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)))
def __safe_get_requests_page__(key: str = "page") -> int:
"""Get the results page if it exists or default to the first page."""
try:
return abs(int(request.args.get(key, "1"), base=10))
except ValueError as _valerr:
return 1
def __safe_get_requests_count__(key: str = "count_per_page") -> int:
"""Get the results page if it exists or default to the first page."""
try:
count = request.args.get(key, "0")
if count != 0:
return abs(int(count, base=10))
return 0
except ValueError as _valerr:
return 0
@resources.route("/view/<uuid:resource_id>/data")
@require_oauth("profile group resource")
def view_resource_data(resource_id: uuid.UUID) -> Response:
"""Retrieve a particular resource's data."""
with require_oauth.acquire("profile group resource") as the_token:
db_uri = app.config["AUTH_DB"]
count_per_page = __safe_get_requests_count__("count_per_page")
offset = (__safe_get_requests_page__("page") - 1)
with db.connection(db_uri) as conn:
resource = resource_by_id(conn, the_token.user, resource_id)
return jsonify(resource_data(
conn,
resource,
((offset * count_per_page) if bool(count_per_page) else offset),
count_per_page))
@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 "data_link_id" in form, "Data Link 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"], uuid.UUID(form["data_link_id"]))
return jsonify(with_db_connection(__link__))
except AssertionError as aserr:
raise InvalidData(aserr.args[0]) from aserr
@resources.route("/data/unlink", methods=["POST"])
@require_oauth("profile group resource")
def unlink_data():
"""Unlink data bound to a specific resource."""
try:
form = request.form
assert "resource_id" in form, "Resource ID not provided."
assert "data_link_id" in form, "Data Link ID not provided."
with require_oauth.acquire("profile group resource") as the_token:
def __unlink__(conn: db.DbConnection):
return unlink_data_from_resource(
conn, the_token.user, uuid.UUID(form["resource_id"]),
uuid.UUID(form["data_link_id"]))
return jsonify(with_db_connection(__unlink__))
except AssertionError as aserr:
raise InvalidData(aserr.args[0]) from aserr
@resources.route("<uuid:resource_id>/user/list", methods=["GET"])
@require_oauth("profile group resource")
def resource_users(resource_id: uuid.UUID):
"""Retrieve all users with access to the given resource."""
with require_oauth.acquire("profile group resource") as the_token:
def __the_users__(conn: db.DbConnection):
resource = resource_by_id(conn, the_token.user, resource_id)
authorised = authorised_for(
conn, the_token.user, ("group:resource:edit-resource",),
(resource_id,))
if authorised.get(resource_id, False):
with db.cursor(conn) as cursor:
def __organise_users_n_roles__(users_n_roles, row):
user_id = uuid.UUID(row["user_id"])
user = users_n_roles.get(user_id, {}).get(
"user", User(user_id, row["email"], row["name"]))
role = GroupRole(
uuid.UUID(row["group_role_id"]),
resource.group,
Role(uuid.UUID(row["role_id"]), row["role_name"],
bool(int(row["user_editable"])), tuple()))
return {
**users_n_roles,
user_id: {
"user": user,
"user_group": Group(
uuid.UUID(row["group_id"]), row["group_name"],
json.loads(row["group_metadata"])),
"roles": users_n_roles.get(
user_id, {}).get("roles", tuple()) + (role,)
}
}
cursor.execute(
"SELECT g.*, u.*, r.*, gr.group_role_id "
"FROM groups AS g INNER JOIN "
"group_users AS gu ON g.group_id=gu.group_id "
"INNER JOIN users AS u ON gu.user_id=u.user_id "
"INNER JOIN group_user_roles_on_resources AS guror "
"ON u.user_id=guror.user_id INNER JOIN roles AS r "
"ON guror.role_id=r.role_id "
"INNER JOIN group_roles AS gr ON r.role_id=gr.role_id "
"WHERE guror.resource_id=?",
(str(resource_id),))
return reduce(__organise_users_n_roles__, cursor.fetchall(), {})
raise AuthorisationError(
"You do not have sufficient privileges to view the resource "
"users.")
results = (
{
"user": dictify(row["user"]),
"user_group": dictify(row["user_group"]),
"roles": tuple(dictify(role) for role in row["roles"])
} for row in (
user_row for user_id, user_row
in with_db_connection(__the_users__).items()))
return jsonify(tuple(results))
@resources.route("<uuid:resource_id>/user/assign", methods=["POST"])
@require_oauth("profile group resource role")
def assign_role_to_user(resource_id: uuid.UUID) -> Response:
"""Assign a role on the specified resource to a user."""
with require_oauth.acquire("profile group resource role") as the_token:
try:
form = request.form
group_role_id = form.get("group_role_id", "")
user_email = form.get("user_email", "")
assert bool(group_role_id), "The role must be provided."
assert bool(user_email), "The user email must be provided."
def __assign__(conn: db.DbConnection) -> dict:
resource = resource_by_id(conn, the_token.user, resource_id)
user = user_by_email(conn, user_email)
return assign_resource_user(
conn, resource, user,
group_role_by_id(conn, resource.group,
uuid.UUID(group_role_id)))
except AssertionError as aserr:
raise AuthorisationError(aserr.args[0]) from aserr
return jsonify(with_db_connection(__assign__))
@resources.route("<uuid:resource_id>/user/unassign", methods=["POST"])
@require_oauth("profile group resource role")
def unassign_role_to_user(resource_id: uuid.UUID) -> Response:
"""Unassign a role on the specified resource from a user."""
with require_oauth.acquire("profile group resource role") as the_token:
try:
form = request.form
group_role_id = form.get("group_role_id", "")
user_id = form.get("user_id", "")
assert bool(group_role_id), "The role must be provided."
assert bool(user_id), "The user id must be provided."
def __assign__(conn: db.DbConnection) -> dict:
resource = resource_by_id(conn, the_token.user, resource_id)
return unassign_resource_user(
conn, resource, user_by_id(conn, uuid.UUID(user_id)),
group_role_by_id(conn, resource.group,
uuid.UUID(group_role_id)))
except AssertionError as aserr:
raise AuthorisationError(aserr.args[0]) from aserr
return jsonify(with_db_connection(__assign__))
@resources.route("<uuid:resource_id>/toggle-public", methods=["POST"])
@require_oauth("profile group resource role")
def toggle_public(resource_id: uuid.UUID) -> Response:
"""Make a resource public if it is private, or private if public."""
with require_oauth.acquire("profile group resource") as the_token:
def __toggle__(conn: db.DbConnection) -> Resource:
old_rsc = resource_by_id(conn, the_token.user, resource_id)
return save_resource(
conn, the_token.user, Resource(
old_rsc.group, old_rsc.resource_id, old_rsc.resource_name,
old_rsc.resource_category, not old_rsc.public,
old_rsc.resource_data))
resource = with_db_connection(__toggle__)
return jsonify({
"resource": dictify(resource),
"description": (
"Made resource public" if resource.public
else "Made resource private")})
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