diff options
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/search_phenotypes.py | 125 |
1 files changed, 0 insertions, 125 deletions
diff --git a/scripts/search_phenotypes.py b/scripts/search_phenotypes.py deleted file mode 100644 index 38b992b..0000000 --- a/scripts/search_phenotypes.py +++ /dev/null @@ -1,125 +0,0 @@ -""" -A script to do search for phenotype traits using the Xapian Search endpoint. -""" -import uuid -import json -import traceback -from urllib.parse import urljoin -from typing import Any, Iterable -from datetime import datetime, timedelta - -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 -from gn3.auth.authorisation.data.phenotypes import linked_phenotype_data - -class NoSearchResults(Exception): - """Raise when there are no results for a search.""" - -def do_search( - host: str, query: str, per_page: int, page: int = 1) -> Iterable[dict[str, Any]]: - """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) - results = response.json() - if len(results) > 0: - return (item for item in results) - raise NoSearchResults(f"No results for search '{query}'") - -def __filter_object__(search_item): - return (search_item["species"], search_item["group"], - search_item["dataset"], search_item["name"]) - -def remove_selected(search_results, selected: tuple): - """Remove any item that the user has selected.""" - return (item for item in search_results if __filter_object__(item) not in selected) - -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 update_status(redisconn: redis.Redis, redisname, status: str): - """Update the status of the search.""" - redisconn.hset(redisname, "status", json.dumps(status)) - -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 "[]")) - redisconn.hset(redisname, key, json.dumps(prev_results + results)) - -def expire_redis_results(redisconn: redis.Redis, redisname: str): - """Expire the results after a while to ensure they are cleaned up.""" - redisconn.expireat(redisname, datetime.now() + timedelta(minutes=30)) - -@click.command() -@click.argument("species") -@click.argument("query") -@click.argument("job-id", type=click.UUID) -@click.option( - "--host", default="http://localhost:8080/api/", help="The URI to GN3.") -@click.option("--per-page", default=10000, help="Number of results per page.") -@click.option("--selected", default="[]", help="Selected traits.") -@click.option( - "--auth-db-uri", default=AUTH_DB, help="The SQL URI to the auth database.") -@click.option( - "--gn3-db-uri", default=SQL_URI, - help="The SQL URI to the main GN3 database.") -@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] - 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): - """ - Search for phenotype traits, filtering out any linked and selected traits, - loading more and more pages until the `per_page` quota is fulfilled or the - search runs out of pages. - """ - 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): - update_status(redisconn, redisname, "started") - update_search_results(redisconn, redisname, tuple()) # init search results - try: - search_query = f"species:{species}" + ( - f" AND ({query})" if bool(query) else "") - selected_traits = tuple( - (item["species"], item["group"], item["dataset"], item["name"]) - for item in json.loads(selected)) - linked = tuple( - (row["SpeciesName"], row["InbredSetName"], row["dataset_name"], - str(row["PublishXRefId"])) - for row in linked_phenotype_data(authconn, gn3conn, species)) - page = 1 - count = 0 - while count < per_page: - results = tuple(remove_linked( - remove_selected( - do_search(host, search_query, per_page, page), - selected_traits), - linked))[0:per_page-count] - count = count + len(results) - page = page + 1 - update_search_results(redisconn, redisname, results) - except NoSearchResults as _nsr: - pass - except Exception as _exc: # pylint: disable=[broad-except] - update_status(redisconn, redisname, "failed") - redisconn.hset(redisname, "exception", json.dumps(traceback.format_exc())) - expire_redis_results(redisconn, redisname) - return 1 - update_status(redisconn, redisname, "completed") - expire_redis_results(redisconn, redisname) - return 0 - -if __name__ == "__main__": - search() # pylint: disable=[no-value-for-parameter] |