diff options
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/search_phenotypes.py | 19 |
1 files changed, 14 insertions, 5 deletions
diff --git a/scripts/search_phenotypes.py b/scripts/search_phenotypes.py index 38b992b..1e8d0fc 100644 --- a/scripts/search_phenotypes.py +++ b/scripts/search_phenotypes.py @@ -22,10 +22,16 @@ 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]]: + dataset_type: str, host: str, query: str, per_page: int, + page: int = 1) -> Iterable[dict[str, Any]]: """Do the search and return the results""" + search_types = { + "phenotype": "phenotype", + "genotype": "gene" + } search_uri = urljoin(host, (f"search/?page={page}&per_page={per_page}" - f"&type=phenotype&query={query}")) + f"&type={search_types[dataset_type]}" + f"&query={query}")) response = requests.get(search_uri) results = response.json() if len(results) > 0: @@ -61,6 +67,7 @@ def expire_redis_results(redisconn: redis.Redis, redisname: str): @click.command() @click.argument("species") +@click.argument("dataset_type") @click.argument("query") @click.argument("job-id", type=click.UUID) @click.option( @@ -76,8 +83,9 @@ def expire_redis_results(redisconn: redis.Redis, redisname: str): "--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): + species: str, dataset_type: 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 @@ -104,7 +112,8 @@ def search(# pylint: disable=[too-many-arguments, too-many-locals] while count < per_page: results = tuple(remove_linked( remove_selected( - do_search(host, search_query, per_page, page), + do_search( + dataset_type, host, search_query, per_page, page), selected_traits), linked))[0:per_page-count] count = count + len(results) |