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| author | Frederick Muriuki Muriithi | 2024-10-14 13:18:56 -0500 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2024-10-14 13:27:43 -0500 |
| commit | 57fa9c35d25a7ca5e8d7e3fc021f12cecef06a60 (patch) | |
| tree | 90684ed9f5d976c3d4a9b870dcbf9f4e74b679f1 /r_qtl | |
| parent | 3062921c9436a351a34f7ebe523c5f4fa2bac856 (diff) | |
| download | gn-uploader-57fa9c35d25a7ca5e8d7e3fc021f12cecef06a60.tar.gz | |
Improve error messages for R/qtl2 code.
Diffstat (limited to 'r_qtl')
| -rw-r--r-- | r_qtl/r_qtl2.py | 13 |
1 files changed, 8 insertions, 5 deletions
diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py index 9da4081..d7d81d1 100644 --- a/r_qtl/r_qtl2.py +++ b/r_qtl/r_qtl2.py @@ -18,6 +18,10 @@ FILE_TYPES = ( "geno", "founder_geno", "pheno", "covar", "phenocovar", "gmap", "pmap", "phenose") +__CONTROL_FILE_ERROR_MESSAGE__ = ( + "The zipped bundle that was provided does not contain a valid control file " + "in either JSON or YAML format.") + def __special_file__(filename): """ @@ -112,7 +116,7 @@ def __control_data_from_zipfile__(zfile: ZipFile) -> dict: or filename.endswith(".json")))) num_files = len(files) if num_files == 0: - raise InvalidFormat("Expected a json or yaml control file.") + raise InvalidFormat(__CONTROL_FILE_ERROR_MESSAGE__) if num_files > 1: raise InvalidFormat("Found more than one possible control file.") @@ -129,7 +133,6 @@ def __control_data_from_zipfile__(zfile: ZipFile) -> dict: else yaml.safe_load(zfile.read(files[0]))) } - def __control_data_from_dirpath__(dirpath: Path): """Load control data from a given directory path.""" files = tuple(path for path in dirpath.iterdir() @@ -137,7 +140,7 @@ def __control_data_from_dirpath__(dirpath: Path): and (path.suffix in (".yaml", ".json")))) num_files = len(files) if num_files == 0: - raise InvalidFormat("Expected a json or yaml control file.") + raise InvalidFormat(__CONTROL_FILE_ERROR_MESSAGE__) if num_files > 1: raise InvalidFormat("Found more than one possible control file.") @@ -200,8 +203,8 @@ def control_data(control_src: Union[Path, ZipFile]) -> dict: if control_src.is_dir(): return __cleanup__(__control_data_from_dirpath__(control_src)) raise InvalidFormat( - "Expects either a zipfile.ZipFile object or a pathlib.Path object " - "pointing to a directory containing the R/qtl2 bundle.") + "Expects either a zipped bundle of files or a path-like object " + "pointing to the zipped R/qtl2 bundle.") def replace_na_strings(cdata, val): |