Run partial correlations with external script

Use new external script to run the partial correlations for both cases,
i.e.
- against an entire dataset, or
- against selected traits

1 files changed, 0 insertions, 126 deletions

diff --git a/scripts/pcorrs.py b/scripts/pcorrs.py
deleted file mode 100644
index de364dc..0000000
--- a/scripts/pcorrs.py
+++ /dev/null
@@ -1,126 +0,0 @@
-"""Script to run partial correlations"""
-
-import json
-import traceback
-from argparse import ArgumentParser
-
-from gn3.db_utils import database_connector
-from gn3.responses.pcorrs_responses import OutputEncoder
-from gn3.computations.partial_correlations import (
-    partial_correlations_with_target_db,
-    partial_correlations_with_target_traits)
-
-def cleanup_string(the_str):
-    "Remove tab, newline and carriage return characters."
-    return the_str.strip('"\t\n\r ')
-
-def process_common_args(args):
-    "Process the common CLI arguments to a form usable by the functions"
-    return {
-        "primary_trait_name": cleanup_string(args.primary_trait),
-        "control_trait_names": tuple(
-            cleanup_string(args.control_traits).split(",")),
-        "method": cleanup_string(args.method)
-    }
-
-def process_trait_args(args):
-    """Process arguments to a form usable by the
-    `partial_correlations_with_target_traits` function."""
-    return {
-        **process_common_args(args),
-        "target_trait_names": tuple(
-            cleanup_string(args.target_traits).split(","))
-    }
-
-def process_db_args(args):
-    """Process arguments for the `partial_correlations_with_target_db`
-    function."""
-    return {
-        **process_common_args(args),
-        "target_db_name": cleanup_string(args.target_database),
-        "criteria": args.criteria
-    }
-
-def pcorrs_against_traits(dbconn, args):
-    """Run partial correlations agaist selected traits."""
-    return partial_correlations_with_target_traits(
-        dbconn, **process_trait_args(args))
-
-def pcorrs_against_db(dbconn, args):
-    """Run partial correlations agaist the entire dataset provided."""
-    return partial_correlations_with_target_db(dbconn, **process_db_args(args))
-
-def run_pcorrs(dbconn, args):
-    """Run the selected partial correlations function."""
-    try:
-        return args.func(dbconn, args)
-    except Exception as exc: # pylint: disable=[broad-except,unused-variable]
-        return {
-            "status": "exception",
-            "message": traceback.format_exc()
-        }
-
-def against_traits_parser(parent_parser):
-    """Parser for command to run partial correlations against selected traits"""
-    parser = parent_parser.add_parser(
-        "against-traits",
-        help="Run partial correlations against a select list of traits")
-    parser.add_argument(
-        "target_traits",
-        help=(
-            "The target traits to run the partial correlations against. "
-            "This is a comma-separated list of traits' fullnames, in the "
-            "format <DATASET-NAME>::<TRAIT-NAME> e.g. "
-            "UCLA_BXDBXH_CARTILAGE_V2::ILM103710672"),
-        type=str)
-    parser.set_defaults(func=pcorrs_against_traits)
-    return parent_parser
-
-def against_db_parser(parent_parser):
-    """Parser for command to run partial correlations against entire dataset"""
-    parser = parent_parser.add_parser(
-        "against-db",
-        help="Run partial correlations against an entire dataset")
-    parser.add_argument(
-        "target_database",
-        help="The target database to run the partial correlations against",
-        type=str)
-    parser.add_argument(
-        "--criteria",
-        help="Number of results to return",
-        type=int, default=500)
-    parser.set_defaults(func=pcorrs_against_db)
-    return parent_parser
-
-def process_cli_arguments():
-    """Top level parser"""
-    parser = ArgumentParser()
-    parser.add_argument(
-        "primary_trait",
-        help="The primary trait's full name",
-        type=str)
-    parser.add_argument(
-        "control_traits",
-        help="A comma-separated list of traits' full names",
-        type=str)
-    parser.add_argument(
-        "method",
-        help="The correlation method to use",
-        type=str)
-    against_db_parser(against_traits_parser(
-        parser.add_subparsers(
-            title="subcommands",
-            description="valid subcommands",
-            required=True)))
-    return parser.parse_args()
-
-def main():
-    """Entry point for the script"""
-    args = process_cli_arguments()
-
-    with database_connector() as conn:
-        print(json.dumps(run_pcorrs(conn, args), cls=OutputEncoder))
-
-
-if __name__ == "__main__":
-    main()