diff options
Diffstat (limited to 'quality_control/headers.py')
| -rw-r--r-- | quality_control/headers.py | 24 |
1 files changed, 14 insertions, 10 deletions
diff --git a/quality_control/headers.py b/quality_control/headers.py index f4f4dad..436ea5a 100644 --- a/quality_control/headers.py +++ b/quality_control/headers.py @@ -5,30 +5,34 @@ from typing import Union, Tuple, Sequence from quality_control.errors import InvalidValue, DuplicateHeading -def invalid_header( - line_number: int, headers: Sequence[str]) -> Union[InvalidValue, None]: +def invalid_header(filename: str, + line_number: int, + headers: Sequence[str]) -> Union[InvalidValue, None]: """Return an `InvalidValue` object if the header row has less than 2 items.""" if len(headers) < 2: return InvalidValue( - line_number, 0, "<TAB>".join(headers), + filename, line_number, 0, "<TAB>".join(headers), "The header MUST contain at least 2 columns") return None def invalid_headings( - line_number: int, strains: Sequence[str], + filename: str, line_number: int, strains: Sequence[str], headings: Sequence[str]) -> Union[Tuple[InvalidValue, ...], None]: """Return tuple of `InvalidValue` objects for each error found for every column heading.""" return tuple( - InvalidValue( - line_number, col, header, f"'{header}' not a valid strain.") + InvalidValue(filename, + line_number, + col, + header, + f"'{header}' not a valid strain.") for col, header in enumerate(headings, start=2) if header not in strains) -def duplicate_headings( - line_number: int, - headers: Sequence[str]) -> Tuple[DuplicateHeading, ...]: +def duplicate_headings(filename: str, + line_number: int, + headers: Sequence[str]) -> Tuple[DuplicateHeading, ...]: """Return a tuple of `DuplicateHeading` objects for each column heading that is a duplicate of another column heading.""" def __update_columns__(acc, item): @@ -42,7 +46,7 @@ def duplicate_headings( } return tuple( DuplicateHeading( - line_number, columns, heading, ( + filename, line_number, columns, heading, ( f"Heading '{heading}', is repeated in columns " f"{','.join(str(i) for i in columns)}")) for heading, columns in repeated.items()) |