Move script to gn-auth

The script is not used in GN3.

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]