diff options
| -rw-r--r-- | README.md | 2 | ||||
| -rw-r--r-- | gn3/api/correlation.py | 4 | ||||
| -rw-r--r-- | gn3/computations/partial_correlations.py | 8 | ||||
| -rw-r--r-- | scripts/pcorrs.py | 126 |
4 files changed, 133 insertions, 7 deletions
@@ -104,7 +104,7 @@ pytest -k unit_test Running pylint: ```bash -pylint *py tests gn3 +pylint *py tests gn3 scripts sheepdog ``` Running mypy(type-checker): diff --git a/gn3/api/correlation.py b/gn3/api/correlation.py index 5f2d486..3aadcb9 100644 --- a/gn3/api/correlation.py +++ b/gn3/api/correlation.py @@ -148,8 +148,8 @@ def partial_correlation(): trait_fullname(args["primary_trait"]), tuple( trait_fullname(trait) for trait in args["control_traits"]), + args["method"], tuple( - trait_fullname(trait) for trait in args["target_traits"]), - args["method"]) + trait_fullname(trait) for trait in args["target_traits"])) return build_response({"status": "success", "results": results}) diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py index 530dd71..f316f67 100644 --- a/gn3/computations/partial_correlations.py +++ b/gn3/computations/partial_correlations.py @@ -681,7 +681,7 @@ def partial_correlations_with_target_db(# pylint: disable=[R0913, R0914, R0911] check_res = check_for_common_errors( conn, primary_trait_name, control_trait_names, threshold) - if check_res.get("status") == "error": + if check_res.get("status") != "success": return check_res primary_trait = check_res["primary_trait"] @@ -819,15 +819,15 @@ def partial_correlations_with_target_db(# pylint: disable=[R0913, R0914, R0911] def partial_correlations_with_target_traits( conn: Any, primary_trait_name: str, - control_trait_names: Tuple[str, ...], - target_trait_names: Tuple[str, ...], method: str) -> dict: + control_trait_names: Tuple[str, ...], method: str, + target_trait_names: Tuple[str, ...]) -> dict: """ Compute partial correlation against a specific selection of traits. """ threshold = 0 check_res = check_for_common_errors( conn, primary_trait_name, control_trait_names, threshold) - if check_res.get("status") == "error": + if check_res.get("status") != "success": return check_res target_traits = { diff --git a/scripts/pcorrs.py b/scripts/pcorrs.py new file mode 100644 index 0000000..de364dc --- /dev/null +++ b/scripts/pcorrs.py @@ -0,0 +1,126 @@ +"""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() |