diff options
Diffstat (limited to 'scripts/search_phenotypes.py')
| -rw-r--r-- | scripts/search_phenotypes.py | 8 |
1 files changed, 4 insertions, 4 deletions
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): """ |