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| author | Frederick Muriuki Muriithi | 2024-02-15 05:32:37 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2024-02-15 05:32:37 +0300 |
| commit | 8afa048a8dce9df6b03dfd5868c0dd0952eaec44 (patch) | |
| tree | 8b9a5965811aefcf3159a26af59ea9c42453c993 | |
| parent | 962e33e97116fd18ee166d49aa3b573ed4ce6378 (diff) | |
| download | gn-uploader-8afa048a8dce9df6b03dfd5868c0dd0952eaec44.tar.gz | |
Only log out information if the check is actually run.
| -rw-r--r-- | scripts/qc_on_rqtl2_bundle.py | 12 |
1 files changed, 6 insertions, 6 deletions
diff --git a/scripts/qc_on_rqtl2_bundle.py b/scripts/qc_on_rqtl2_bundle.py index dd5e73e..d77b6c2 100644 --- a/scripts/qc_on_rqtl2_bundle.py +++ b/scripts/qc_on_rqtl2_bundle.py @@ -111,9 +111,9 @@ def retrieve_errors_with_progress(rconn: Redis,#pylint: disable=[too-many-locals def qc_geno_errors(rconn, fqjobid, zfile, logger) -> bool: """Check for errors in `geno` file(s).""" - logger.info("Checking for errors in the 'geno' file…") cdata = rqtl2.control_data(zfile) if "geno" in cdata: + logger.info("Checking for errors in the 'geno' file…") gerrs = tuple(retrieve_errors_with_progress( rconn, fqjobid, zfile, "geno", (rqc.make_genocode_checker(cdata.get("genotypes", {})),))) @@ -124,15 +124,15 @@ def qc_geno_errors(rconn, fqjobid, zfile, logger) -> bool: if len(gerrs) > 0: logger.error("The 'geno' file has errors.") return True + logger.info("No errors found in the 'geno' file.") - logger.info("No errors found in the 'geno' file.") return False def qc_pheno_errors(rconn, fqjobid, zfile, logger) -> bool: """Check for errors in `pheno` file(s).""" - logger.info("Checking for errors in the 'pheno' file…") cdata = rqtl2.control_data(zfile) if "pheno" in cdata: + logger.info("Checking for errors in the 'pheno' file…") perrs = tuple(retrieve_errors_with_progress( rconn,fqjobid, zfile, "pheno", (partial(decimal_points_error, mini=3),))) @@ -143,15 +143,15 @@ def qc_pheno_errors(rconn, fqjobid, zfile, logger) -> bool: if len(perrs) > 0: logger.error("The 'pheno' file has errors.") return True + logger.info("No errors found in the 'pheno' file.") - logger.info("No errors found in the 'pheno' file.") return False def qc_phenose_errors(rconn, fqjobid, zfile, logger) -> bool: """Check for errors in `phenose` file(s).""" - logger.info("Checking for errors in the 'phenose' file…") cdata = rqtl2.control_data(zfile) if "phenose" in cdata: + logger.info("Checking for errors in the 'phenose' file…") perrs = tuple(retrieve_errors_with_progress( rconn,fqjobid, zfile, "phenose", (partial(decimal_points_error, mini=6),))) @@ -162,8 +162,8 @@ def qc_phenose_errors(rconn, fqjobid, zfile, logger) -> bool: if len(perrs) > 0: logger.error("The 'phenose' file has errors.") return True + logger.info("No errors found in the 'phenose' file.") - logger.info("No errors found in the 'phenose' file.") return False def qc_phenocovar_errors(_rconn, _fqjobid, _zfile, _logger) -> bool: |