diff options
Diffstat (limited to 'scripts/rqtl2')
| -rw-r--r-- | scripts/rqtl2/entry.py | 2 | ||||
| -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 | 36 |
4 files changed, 28 insertions, 23 deletions
diff --git a/scripts/rqtl2/entry.py b/scripts/rqtl2/entry.py index e0e00e7..7423a4b 100644 --- a/scripts/rqtl2/entry.py +++ b/scripts/rqtl2/entry.py @@ -26,7 +26,7 @@ def build_main( def main(): with (Redis.from_url(args.redisuri, decode_responses=True) as rconn, database_connection(args.databaseuri) as dbconn): - logger.setLevel(args.loglevel.upper()) + logger.setLevel(args.log_level.upper()) fqjobid = jobs.job_key(args.redisprefix, args.jobid) try: 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 699c291..72d6c83 100644 --- a/scripts/rqtl2/phenotypes_qc.py +++ b/scripts/rqtl2/phenotypes_qc.py @@ -41,7 +41,10 @@ logging.basicConfig( "(%(pathname)s: %(lineno)d) %(message)s")) logger = logging.getLogger(__MODULE__) -def validate(phenobundle: Path, logger: Logger) -> dict: +def validate( + phenobundle: Path, + logger: Logger# pylint: disable=[redefined-outer-name] +) -> dict: """Check that the bundle is generally valid""" try: rqc.validate_bundle(phenobundle) @@ -63,7 +66,7 @@ def validate(phenobundle: Path, logger: Logger) -> dict: def check_for_mandatory_pheno_keys( phenobundle: Path, - logger: Logger, + logger: Logger,# pylint: disable=[redefined-outer-name] **kwargs ) -> dict: """Check that the mandatory keys exist for phenotypes.""" @@ -90,7 +93,7 @@ def check_for_mandatory_pheno_keys( def check_for_averages_files( phenobundle: Path, - logger: Logger, + logger: Logger,# pylint: disable=[redefined-outer-name] **kwargs ) -> dict: """Check that averages files appear together""" @@ -144,15 +147,15 @@ def redis_logger( ) -> Iterator[logging.Logger]: """Build a Redis message-list logger.""" rconn = Redis.from_url(redisuri, decode_responses=True) - logger = logging.getLogger(loggername) - logger.propagate = False + _logger = logging.getLogger(loggername) + _logger.propagate = False handler = RedisMessageListHandler( rconn, fullyqualifiedkey(fqkey, filename))#type: ignore[arg-type] handler.setFormatter(logging.getLogger().handlers[0].formatter) - logger.addHandler(handler) + _logger.addHandler(handler) try: - yield logger + yield _logger finally: rconn.close() @@ -179,7 +182,7 @@ def qc_phenocovar_file( redisuri, f"{__MODULE__}.qc_phenocovar_file", filepath.name, - f"{fqkey}:logs") as logger, + f"{fqkey}:logs") as _logger, Redis.from_url(redisuri, decode_responses=True) as rconn): print("Running QC on file: ", filepath.name) _csvfile = rqtl2.read_csv_file(filepath, separator, comment_char) @@ -199,7 +202,7 @@ def qc_phenocovar_file( def collect_errors(errors_and_linecount, line): _errs, _lc = errors_and_linecount - logger.info("Testing record '%s'", line[0]) + _logger.info("Testing record '%s'", line[0]) if len(line) != len(_headings): _errs = _errs + (save_error(InvalidValue( filepath.name, @@ -209,12 +212,12 @@ def qc_phenocovar_file( (f"Record {_lc} in file {filepath.name} has a different " "number of columns than the number of headings"))),) _line = dict(zip(_headings, line)) - if not bool(_line["description"]): + if not bool(_line.get("description")): _errs = _errs + ( save_error(InvalidValue(filepath.name, _line[_headings[0]], "description", - _line["description"], + _line.get("description"), "The description is not provided!")),) rconn.hset(file_fqkey(fqkey, "metadata", filepath), @@ -240,7 +243,7 @@ def merge_dicts(*dicts): return reduce(lambda merged, dct: {**merged, **dct}, dicts, {}) -def decimal_points_error(# pylint: disable=[too-many-arguments] +def decimal_points_error(# pylint: disable=[too-many-arguments,too-many-positional-arguments] filename: str, rowtitle: str, coltitle: str, @@ -271,7 +274,7 @@ def integer_error( return InvalidValue(filename, rowtitle, coltitle, cellvalue, message) -def qc_pheno_file(# pylint: disable=[too-many-locals, too-many-arguments] +def qc_pheno_file(# pylint: disable=[too-many-locals, too-many-arguments, too-many-positional-arguments] filepath: Path, redisuri: str, fqkey: str, @@ -287,7 +290,7 @@ def qc_pheno_file(# pylint: disable=[too-many-locals, too-many-arguments] redisuri, f"{__MODULE__}.qc_pheno_file", filepath.name, - f"{fqkey}:logs") as logger, + f"{fqkey}:logs") as _logger, Redis.from_url(redisuri, decode_responses=True) as rconn): print("Running QC on file: ", filepath.name) save_error = partial( @@ -314,7 +317,7 @@ def qc_pheno_file(# pylint: disable=[too-many-locals, too-many-arguments] def collect_errors(errors_and_linecount, line): _errs, _lc = errors_and_linecount - logger.debug("Checking row %s", line[0]) + _logger.debug("Checking row %s", line[0]) if line[0] not in samples: _errs = _errs + (save_error(InvalidValue( filepath.name, @@ -373,7 +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.") |