diff options
Diffstat (limited to 'scripts/rqtl2/phenotypes_qc.py')
| -rw-r--r-- | scripts/rqtl2/phenotypes_qc.py | 40 |
1 files changed, 20 insertions, 20 deletions
diff --git a/scripts/rqtl2/phenotypes_qc.py b/scripts/rqtl2/phenotypes_qc.py index 5c89ca0..98b855f 100644 --- a/scripts/rqtl2/phenotypes_qc.py +++ b/scripts/rqtl2/phenotypes_qc.py @@ -41,15 +41,15 @@ logging.basicConfig( "(%(pathname)s: %(lineno)d) %(message)s")) logger = logging.getLogger(__MODULE__) -def validate(phenobundle: Path, logger: Logger) -> dict: +def validate(phenobundle: Path, alogger: Logger) -> dict: """Check that the bundle is generally valid""" try: rqc.validate_bundle(phenobundle) except rqe.RQTLError as rqtlerr: - # logger.error("Bundle file validation failed!", exc_info=True) + # alogger.error("Bundle file validation failed!", exc_info=True) return { "skip": True, - "logger": logger, + "logger": alogger, "phenobundle": phenobundle, "errors": (" ".join(rqtlerr.args),) } @@ -57,20 +57,20 @@ def validate(phenobundle: Path, logger: Logger) -> dict: "errors": tuple(), "skip": False, "phenobundle": phenobundle, - "logger": logger + "logger": alogger } def check_for_mandatory_pheno_keys( phenobundle: Path, - logger: Logger, + alogger: Logger, **kwargs ) -> dict: """Check that the mandatory keys exist for phenotypes.""" if kwargs.get("skip", False): return { **kwargs, - "logger": logger, + "logger": alogger, "phenobundle": phenobundle } @@ -81,7 +81,7 @@ def check_for_mandatory_pheno_keys( for key in _mandatory_keys if key not in _cdata.keys()) return { **kwargs, - "logger": logger, + "logger": alogger, "phenobundle": phenobundle, "errors": _errors, "skip": len(_errors) > 0 @@ -90,14 +90,14 @@ def check_for_mandatory_pheno_keys( def check_for_averages_files( phenobundle: Path, - logger: Logger, + alogger: Logger, **kwargs ) -> dict: """Check that averages files appear together""" if kwargs.get("skip", False): return { **kwargs, - "logger": logger, + "logger": alogger, "phenobundle": phenobundle } @@ -110,7 +110,7 @@ def check_for_averages_files( if ((first in _cdata.keys()) and (second not in _cdata.keys()))) return { **kwargs, - "logger": logger, + "logger": alogger, "phenobundle": phenobundle, "errors": _errors, "skip": len(_errors) > 0 @@ -144,15 +144,15 @@ 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 +179,7 @@ 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 +199,7 @@ 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, @@ -240,7 +240,7 @@ 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 +271,7 @@ 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 +287,7 @@ 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 +314,7 @@ 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, |