diff options
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/assign_data_to_default_admin.py | 10 | ||||
| -rw-r--r-- | scripts/batch_assign_data_to_default_admin.py | 2 | ||||
| -rw-r--r-- | scripts/link_inbredsets.py | 3 | ||||
| -rw-r--r-- | scripts/register_sys_admin.py | 2 | ||||
| -rw-r--r-- | scripts/search_phenotypes.py | 8 |
5 files changed, 12 insertions, 13 deletions
diff --git a/scripts/assign_data_to_default_admin.py b/scripts/assign_data_to_default_admin.py index 0ae209a..69fc50c 100644 --- a/scripts/assign_data_to_default_admin.py +++ b/scripts/assign_data_to_default_admin.py @@ -11,10 +11,9 @@ from pathlib import Path from uuid import UUID, uuid4 import click +from gn_libs import mysqldb as biodb from MySQLdb.cursors import DictCursor -from gn_auth.auth.db import mariadb as biodb - import gn_auth.auth.db.sqlite3 as authdb from gn_auth.auth.authentication.users import User from gn_auth.auth.authorisation.roles.models import ( @@ -22,8 +21,8 @@ from gn_auth.auth.authorisation.roles.models import ( from gn_auth.auth.authorisation.resources.groups.models import ( Group, save_group, add_resources_to_group) -from gn_auth.auth.authorisation.resources.models import ( - Resource, ResourceCategory, __assign_resource_owner_role__) +from gn_auth.auth.authorisation.resources.common import assign_resource_owner_role +from gn_auth.auth.authorisation.resources.models import Resource, ResourceCategory class DataNotFound(Exception): @@ -412,7 +411,8 @@ def entry(authdbpath, mysqldburi): assign_data_to_resource( authconn, bioconn, resource, the_admin_group) with authdb.cursor(authconn) as cursor: - __assign_resource_owner_role__(cursor, resource, admin) + assign_resource_owner_role( + cursor, resource.resource_id, admin.user_id) except DataNotFound as dnf: print(dnf.args[0], file=sys.stderr) sys.exit(1) diff --git a/scripts/batch_assign_data_to_default_admin.py b/scripts/batch_assign_data_to_default_admin.py index 3df123d..a468019 100644 --- a/scripts/batch_assign_data_to_default_admin.py +++ b/scripts/batch_assign_data_to_default_admin.py @@ -7,10 +7,10 @@ import logging from pathlib import Path import click +from gn_libs import mysqldb as biodb from pymonad.maybe import Just, Maybe, Nothing from pymonad.tools import monad_from_none_or_value -from gn_auth.auth.db import mariadb as biodb from gn_auth.auth.db import sqlite3 as authdb from gn_auth.auth.authentication.users import User from gn_auth.auth.authorisation.resources.groups.models import ( diff --git a/scripts/link_inbredsets.py b/scripts/link_inbredsets.py index 5db7ea8..c78a050 100644 --- a/scripts/link_inbredsets.py +++ b/scripts/link_inbredsets.py @@ -6,11 +6,10 @@ import uuid from pathlib import Path import click +from gn_libs import mysqldb as biodb import gn_auth.auth.db.sqlite3 as authdb -from gn_auth.auth.db import mariadb as biodb - from scripts.assign_data_to_default_admin import ( sys_admins, admin_group, select_sys_admin) diff --git a/scripts/register_sys_admin.py b/scripts/register_sys_admin.py index dfd4d59..06aa845 100644 --- a/scripts/register_sys_admin.py +++ b/scripts/register_sys_admin.py @@ -16,7 +16,7 @@ def fetch_email() -> str: try: user_input = input("Enter the administrator's email: ") email = validate_email(user_input.strip(), check_deliverability=True) - return email["email"] + return email["email"] # type: ignore except EmailNotValidError as _enve: print("You did not provide a valid email address. Try again...", file=sys.stderr) diff --git a/scripts/search_phenotypes.py b/scripts/search_phenotypes.py index 20d91c9..eee112d 100644 --- a/scripts/search_phenotypes.py +++ b/scripts/search_phenotypes.py @@ -11,9 +11,9 @@ from datetime import datetime, timedelta import click import redis import requests +from gn_libs import mysqldb as gn3db from gn_auth import jobs -from gn_auth.auth.db import mariadb as gn3db from gn_auth.auth.db import sqlite3 as authdb from gn_auth.settings import SQL_URI, AUTH_DB from gn_auth.auth.authorisation.data.phenotypes import linked_phenotype_data @@ -26,7 +26,7 @@ def do_search( """Do the search and return the results""" search_uri = urljoin(host, (f"search/?page={page}&per_page={per_page}" f"&type=phenotype&query={query}")) - response = requests.get(search_uri) + response = requests.get(search_uri, timeout=300) results = response.json() if len(results) > 0: return (item for item in results) @@ -52,7 +52,7 @@ def update_search_results(redisconn: redis.Redis, redisname: str, results: tuple[dict[str, Any], ...]): """Save the results to redis db.""" key = "search_results" - prev_results = tuple(json.loads(redisconn.hget(redisname, key) or "[]")) + prev_results = tuple(json.loads(redisconn.hget(redisname, key) or "[]")) # type: ignore redisconn.hset(redisname, key, json.dumps(prev_results + results)) def expire_redis_results(redisconn: redis.Redis, redisname: str): @@ -75,7 +75,7 @@ def expire_redis_results(redisconn: redis.Redis, redisname: str): @click.option( "--redis-uri", default="redis://:@localhost:6379/0", help="The URI to the redis server.") -def search(# pylint: disable=[too-many-arguments, too-many-locals] +def search(# pylint: disable=[too-many-arguments, too-many-positional-arguments, too-many-locals] species: str, query: str, job_id: uuid.UUID, host: str, per_page: int, selected: str, auth_db_uri: str, gn3_db_uri: str, redis_uri: str): """ |