diff options
| author | Frederick Muriuki Muriithi | 2024-02-20 10:57:56 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2024-02-20 10:57:56 +0300 |
| commit | ce243a57b24d6adecb169487e706290d91b22d19 (patch) | |
| tree | 6b0b06a444c16ffb8be1c65fa4e5b78ced6a0615 /scripts | |
| parent | a4324cd24b5a14fbcf19a6e04d2b76fb2838038e (diff) | |
| download | gn-uploader-ce243a57b24d6adecb169487e706290d91b22d19.tar.gz | |
Track filename in the errors
R/qtl2 bundles can contain more than one file, of the same type. When
errors are encountered in any of the files, we need to be able to
inform the user which file it is, in addition to the line and column
number.
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/qc_on_rqtl2_bundle.py | 2 |
1 files changed, 1 insertions, 1 deletions
diff --git a/scripts/qc_on_rqtl2_bundle.py b/scripts/qc_on_rqtl2_bundle.py index d77b6c2..027f387 100644 --- a/scripts/qc_on_rqtl2_bundle.py +++ b/scripts/qc_on_rqtl2_bundle.py @@ -116,7 +116,7 @@ def qc_geno_errors(rconn, fqjobid, zfile, logger) -> bool: 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", {})),))) + (rqc.make_genocode_checker(cdata.get("genotypes", {}), "geno"),))) add_to_errors(rconn, fqjobid, "errors-generic", tuple( err for err in gerrs if isinstance(err, rqfe.MissingFile))) add_to_errors(rconn, fqjobid, "errors-geno", tuple( |