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| author | Frederick Muriuki Muriithi | 2023-04-06 12:31:05 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2023-04-06 12:31:05 +0300 |
| commit | 17abad9300e4a96a14f94da486ef8307f7d27e06 (patch) | |
| tree | 38fe3bfd36be9a821adfc67b83fbbd587ceb8b5e /scripts | |
| parent | 3d873435f0d464864d4d691d6be4db40931fac05 (diff) | |
| download | genenetwork3-17abad9300e4a96a14f94da486ef8307f7d27e06.tar.gz | |
Remove deprecated `gn3.db_utils.database_connector` function
Remove the deprecated function and fix a myriad of bugs that arise from
removing the function.
Issue: https://issues.genenetwork.org/issues/bugfix_coupling_current_app_and_db_utils
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/partial_correlations.py | 8 |
1 files changed, 6 insertions, 2 deletions
diff --git a/scripts/partial_correlations.py b/scripts/partial_correlations.py index 1fbab78..aab8f08 100644 --- a/scripts/partial_correlations.py +++ b/scripts/partial_correlations.py @@ -4,7 +4,7 @@ import json import traceback from argparse import ArgumentParser -from gn3.db_utils import database_connector +from gn3.db_utils import database_connection from gn3.responses.pcorrs_responses import OutputEncoder from gn3.computations.partial_correlations import ( partial_correlations_with_target_db, @@ -108,6 +108,10 @@ def process_cli_arguments(): help="The correlation method to use", type=str, choices=("pearsons", "spearmans")) + parser.add_argument( + "sql_uri", + help="The uri to use to connect to the database", + type=str) against_db_parser(against_traits_parser( parser.add_subparsers( title="subcommands", @@ -119,7 +123,7 @@ def main(): """Entry point for the script""" args = process_cli_arguments() - with database_connector() as conn: + with database_connection(args.sql_uri) as conn: print(json.dumps(run_pcorrs(conn, args), cls=OutputEncoder)) |