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| author | Frederick Muriuki Muriithi | 2025-12-19 12:53:20 -0600 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2025-12-19 12:53:20 -0600 |
| commit | 56ed0f57b816b1023a97b7205268deed0a45c77e (patch) | |
| tree | 29bad7b0b2ff78230d80b5c5ec76eb2822b8d84b /scripts/rqtl2 | |
| parent | d04b7cb89b3fbaa1689f8f6525a2740eda7c3be3 (diff) | |
| download | gn-uploader-56ed0f57b816b1023a97b7205268deed0a45c77e.tar.gz | |
Fix issues caught by type-checker.
Diffstat (limited to 'scripts/rqtl2')
| -rw-r--r-- | scripts/rqtl2/install_genotypes.py | 6 | ||||
| -rw-r--r-- | scripts/rqtl2/install_phenos.py | 7 | ||||
| -rw-r--r-- | scripts/rqtl2/phenotypes_qc.py | 3 |
3 files changed, 9 insertions, 7 deletions
diff --git a/scripts/rqtl2/install_genotypes.py b/scripts/rqtl2/install_genotypes.py index 8762655..5e6abb0 100644 --- a/scripts/rqtl2/install_genotypes.py +++ b/scripts/rqtl2/install_genotypes.py @@ -20,7 +20,7 @@ from scripts.rqtl2.entry import build_main from scripts.rqtl2.cli_parser import add_common_arguments from scripts.cli_parser import init_cli_parser, add_global_data_arguments -__MODULE__ = "scripts.rqtl2.install_genotypes" +logger = getLogger(__name__) def insert_markers( dbconn: mdb.Connection, @@ -191,7 +191,7 @@ def install_genotypes(#pylint: disable=[too-many-locals] dbconn: mdb.Connection, fullyqualifiedjobid: str,#pylint: disable=[unused-argument] args: argparse.Namespace, - logger: Logger = getLogger(__name__) + logger: Logger = logger # pylint: disable=[redefined-outer-name] ) -> int: """Load any existing genotypes into the database.""" (speciesid, populationid, datasetid, rqtl2bundle) = ( @@ -257,5 +257,5 @@ if __name__ == "__main__": return parser.parse_args() - main = build_main(cli_args(), install_genotypes, __MODULE__) + main = build_main(cli_args(), install_genotypes, logger) sys.exit(main()) diff --git a/scripts/rqtl2/install_phenos.py b/scripts/rqtl2/install_phenos.py index 9059cd6..11ac8a4 100644 --- a/scripts/rqtl2/install_phenos.py +++ b/scripts/rqtl2/install_phenos.py @@ -19,7 +19,7 @@ from r_qtl import r_qtl2_qc as rqc from functional_tools import take -__MODULE__ = "scripts.rqtl2.install_phenos" +logger = getLogger(__name__) def insert_probesets(dbconn: mdb.Connection, platformid: int, @@ -101,7 +101,8 @@ def install_pheno_files(#pylint: disable=[too-many-locals] dbconn: mdb.Connection, fullyqualifiedjobid: str,#pylint: disable=[unused-argument] args: argparse.Namespace, - logger: Logger = getLogger()) -> int: + logger: Logger = logger # pylint: disable=[redefined-outer-name] +) -> int: """Load data in `pheno` files and other related files into the database.""" (speciesid, platformid, datasetid, rqtl2bundle) = ( args.speciesid, args.platformid, args.datasetid, args.rqtl2bundle) @@ -159,5 +160,5 @@ if __name__ == "__main__": return parser.parse_args() - main = build_main(cli_args(), install_pheno_files, __MODULE__) + main = build_main(cli_args(), install_pheno_files, logger) sys.exit(main()) diff --git a/scripts/rqtl2/phenotypes_qc.py b/scripts/rqtl2/phenotypes_qc.py index 9f11f57..72d6c83 100644 --- a/scripts/rqtl2/phenotypes_qc.py +++ b/scripts/rqtl2/phenotypes_qc.py @@ -376,7 +376,8 @@ def run_qc(# pylint: disable=[too-many-locals] rconn: Redis, dbconn: mdb.Connection, fullyqualifiedjobid: str, - args: Namespace + args: Namespace, + logger: Logger = logger # pylint: disable=[redefined-outer-name] ) -> int: """Run quality control checks on the bundle.""" print("Beginning the quality assurance checks.") |