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| author | Frederick Muriuki Muriithi | 2022-06-28 09:32:14 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2022-06-28 09:32:14 +0300 |
| commit | d8d590cbc0a427c2f508c66bc91cd8af97aba606 (patch) | |
| tree | c35b06930f37a208d90f0996a66434ea4137e3eb | |
| parent | b4e81dd5cba130f0a2f47771bb2fd4d289ef745d (diff) | |
| download | genenetwork3-d8d590cbc0a427c2f508c66bc91cd8af97aba606.tar.gz | |
Parse the method from UI before passing it to external process
To reduce the chances of the system failing due to the external process being
launched with the wrong parameters, add a parsing stage that converts the
method from the UI into a form acceptable by the CLI script.
* gn3/commands.py: parse the method from UI
* scripts/partial_correlations.py: simplify the acceptable methods
| -rw-r--r-- | gn3/commands.py | 10 | ||||
| -rw-r--r-- | scripts/partial_correlations.py | 2 |
2 files changed, 10 insertions, 2 deletions
diff --git a/gn3/commands.py b/gn3/commands.py index 0a74b7d..0b8db5b 100644 --- a/gn3/commands.py +++ b/gn3/commands.py @@ -67,9 +67,17 @@ def compose_pcorrs_command( primary_trait: str, control_traits: Tuple[str, ...], method: str, **kwargs): """Compose the command to run partias correlations""" + def __parse_method__(method): + mthd = method.lower().replace("'", "") + if "pearsons" in mthd: + return "pearsons" + if "spearmans" in mthd: + return "spearmans" + raise Exception(f"Invalid method '{method}'") + prefix_cmd = ( f"{sys.executable}", "-m", "scripts.partial_correlations", - primary_trait, ",".join(control_traits), method) + primary_trait, ",".join(control_traits), __parse_method__(method)) if ( kwargs.get("target_database") is not None and kwargs.get("target_traits") is None): diff --git a/scripts/partial_correlations.py b/scripts/partial_correlations.py index d28a17a..1fbab78 100644 --- a/scripts/partial_correlations.py +++ b/scripts/partial_correlations.py @@ -107,7 +107,7 @@ def process_cli_arguments(): "method", help="The correlation method to use", type=str, - choices=("Pearson's r", "Spearman's rho")) + choices=("pearsons", "spearmans")) against_db_parser(against_traits_parser( parser.add_subparsers( title="subcommands", |