diff options
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/search_phenotypes.py | 10 |
1 files changed, 6 insertions, 4 deletions
diff --git a/scripts/search_phenotypes.py b/scripts/search_phenotypes.py index cdd1d96..4533cce 100644 --- a/scripts/search_phenotypes.py +++ b/scripts/search_phenotypes.py @@ -12,6 +12,7 @@ import click import redis import requests +from gn3 import jobs from gn3.auth import db as authdb from gn3 import db_utils as gn3db from gn3.settings import SQL_URI, AUTH_DB @@ -43,7 +44,8 @@ def remove_linked(search_results, linked: tuple): """Remove any item that has been already linked to a user group.""" return (item for item in search_results if __filter_object__(item) not in linked) -def save_to_redis(redisconn: redis.Redis, redisname: str, results: tuple[dict[str, Any], ...]): +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 "[]")) @@ -77,12 +79,12 @@ def search(# pylint: disable=[too-many-arguments, too-many-locals] loading more and more pages until the `per_page` quota is fulfilled or the search runs out of pages. """ - redisname = f"GN3:JOBS:{job_id}" + redisname = jobs.job_key(job_id) with (authdb.connection(auth_db_uri) as authconn, gn3db.database_connection(gn3_db_uri) as gn3conn, redis.Redis.from_url(redis_uri, decode_responses=True) as redisconn): redisconn.hset(redisname, "status", "started") - save_to_redis(redisconn, redisname, tuple()) + update_search_results(redisconn, redisname, tuple()) # init search results try: search_query = f"species:{species}" + ( f" AND ({query})" if bool(query) else "") @@ -103,7 +105,7 @@ def search(# pylint: disable=[too-many-arguments, too-many-locals] linked))[0:per_page-count] count = count + len(results) page = page + 1 - save_to_redis(redisconn, redisname, results) + update_search_results(redisconn, redisname, results) except NoSearchResults as _nsr: pass except Exception as _exc: # pylint: disable=[broad-except] |