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return warnings instead of exceptions & accept file handle #117

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f385983
Allow samplesheet to accept a file handle or a Path like object
dsommer Apr 4, 2022
efbc2bf
Merge pull request #1 from dsommer/ds_accept_string
dsommer Apr 10, 2022
989298c
replace exceptions with warnings
dsommer Apr 12, 2022
c8f599c
open samplesheets with universal newlines
dsommer Apr 12, 2022
a0f038e
Merge branch 'master' into ds_replace_exceptions_with_warnings
dsommer Apr 20, 2022
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66 changes: 33 additions & 33 deletions sample_sheet/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -120,7 +120,7 @@ class ReadStructure(object):

def __init__(self, structure: str) -> None:
if not bool(self._valid_pattern.match(structure)):
raise ValueError(f'Not a valid read structure: "{structure}"')
warnings.warn(f'Not a valid read structure: "{structure}"')
self.structure = structure

def _sum_cycles_from_tokens(self, tokens: List[str]) -> int:
Expand Down Expand Up @@ -294,15 +294,15 @@ def __init__(
if self._valid_index_key_pattern.match(key) and not bool(
self._valid_index_value_pattern.match(str(value))
):
raise ValueError(f'Not a valid index: {value}')
warnings.warn(f'Not a valid index: {value}')

self[key] = value
if (
self.Read_Structure is not None
and self.Read_Structure.is_single_indexed
and self.index is None
):
raise ValueError(
warnings.warn(
f'If a single-indexed read structure is defined then a '
f'sample `index` must be defined also: {self}'
)
Expand All @@ -312,7 +312,7 @@ def __init__(
and self.index is None
and self.index2 is None
):
raise ValueError(
warnings.warn(
f'If a dual-indexed read structure is defined then '
f'sample `index` and sample `index2` must be defined '
f'also: {self}'
Expand Down Expand Up @@ -418,7 +418,7 @@ def __init__(self, path: Optional[Union[Path, str, TextIO]] = None) -> None:

if self.path is not None:
if isinstance(self.path, (str, Path)):
with open(self.path, 'r') as f:
with open(self.path, 'rU') as f:
self._parse(f)
else:
self._parse(self.path)
Expand Down Expand Up @@ -456,7 +456,7 @@ def experimental_design(self) -> Any:

"""
if not self.samples:
raise ValueError('No samples in sample sheet')
warnings.warn('No samples in sample sheet')

markdown = tabulate(
[[getattr(s, h, '') for h in DESIGN_HEADER] for s in self.samples],
Expand Down Expand Up @@ -497,14 +497,14 @@ def _parse(self, handle: TextIO) -> None:
continue

# Raise exception if we encounter invalid characters.
if any(
character not in VALID_ASCII
for character in set(''.join(line))
):
raise ValueError(
f'Sample sheet contains invalid characters on line '
f'{i + 1}: {"".join(line)}'
)
# if any(
# character not in VALID_ASCII
# for character in set(''.join(line))
# ):
# warnings.warn(
# f'Sample sheet contains invalid characters on line '
# f'{i + 1}: {"".join(line)}'
# )

header_match = self._section_header_re.match(line[0])

Expand All @@ -527,11 +527,11 @@ def _parse(self, handle: TextIO) -> None:
elif section_name == 'Data':
if sample_header is not None:
self.add_sample(Sample(dict(zip(sample_header, line))))
elif any(key == '' for key in line):
raise ValueError(
f'Header for [Data] section is not allowed to '
f'have empty fields: {line}'
)
# elif any(key == '' for key in line):
# warnings.warn(
# f'Header for [Data] section is not allowed to '
# f'have empty fields: {line}'
# )
else:
sample_header = line
continue
Expand Down Expand Up @@ -584,7 +584,7 @@ def add_sample(self, sample: Sample) -> None:
"""
# Do not allow samples without Sample_ID defined.
if sample.Sample_ID is None:
raise ValueError('Sample must have "Sample_ID" defined.')
warnings.warn('Sample must have "Sample_ID" defined.')

# Set whether the samples will have ``index`` or ``index2``.
if len(self.samples) == 0:
Expand All @@ -607,7 +607,7 @@ def add_sample(self, sample: Sample) -> None:
or self.is_single_end # noqa
and not sample.Read_Structure.is_single_end
):
raise ValueError(
warnings.warn(
f'Sample sheet pairing has been set with '
f'Reads:"{self.Reads}" and is not compatible with sample '
f'read structure: {sample.Read_Structure}'
Expand All @@ -619,7 +619,7 @@ def add_sample(self, sample: Sample) -> None:
# Validate this sample against the ``SampleSheet.Read_Structure``
# attribute, which can be None, to ensure they are the same.
if self.Read_Structure != sample.Read_Structure:
raise ValueError(
warnings.warn(
f'Sample read structure ({sample.Read_Structure}) different '
f'than read structure in samplesheet ({self.Read_Structure}).'
)
Expand All @@ -637,12 +637,12 @@ def add_sample(self, sample: Sample) -> None:
# TODO: Look into if this is truly illegal or not.
warnings.warn(UserWarning(message))
if sample.index is None and self.samples_have_index:
raise ValueError(
warnings.warn(
f'Cannot add a sample without attribute `index` if a '
f'previous sample has `index` set: {sample})'
)
if sample.index2 is None and self.samples_have_index2:
raise ValueError(
warnings.warn(
f'Cannot add a sample without attribute `index2` if a '
f'previous sample has `index2` set: {sample})'
)
Expand All @@ -655,7 +655,7 @@ def add_sample(self, sample: Sample) -> None:
and sample.index2 == other.index2
and sample.Lane == other.Lane
):
raise ValueError(
warnings.warn(
f'Sample index combination for {sample} has already been '
f'added on this lane or flowcell: {other}'
)
Expand All @@ -667,7 +667,7 @@ def add_sample(self, sample: Sample) -> None:
and sample.index == other.index
and sample.Lane == other.Lane
):
raise ValueError(
warnings.warn(
f'First sample index for {sample} has already been '
f'added on this lane or flowcell: {other}'
)
Expand All @@ -679,7 +679,7 @@ def add_sample(self, sample: Sample) -> None:
and sample.index2 == other.index2
and sample.Lane == other.Lane
):
raise ValueError(
warnings.warn(
f'Second sample index for {sample} has already been '
f'added on this lane or flowcell: {other}'
)
Expand Down Expand Up @@ -748,21 +748,21 @@ def to_picard_basecalling_params(

"""
if len(self.samples) == 0:
raise ValueError('No samples in sample sheet')
warnings.warn('No samples in sample sheet')
if not (
isinstance(lanes, int)
or isinstance(lanes, (list, tuple))
and len(lanes) > 0
and all(isinstance(lane, int) for lane in lanes)
):
raise ValueError(f'Lanes must be an int or list of ints: {lanes}')
warnings.warn(f'Lanes must be an int or list of ints: {lanes}')
if len(set(len(sample.index or '') for sample in self.samples)) != 1:
raise ValueError('I7 indexes have differing lengths.')
warnings.warn('I7 indexes have differing lengths.')
if len(set(len(sample.index2 or '') for sample in self.samples)) != 1:
raise ValueError('I5 indexes have differing lengths.')
warnings.warn('I5 indexes have differing lengths.')
for attr in ('Sample_Name', 'Library_ID', 'index'):
if any(getattr(sample, attr) is None for sample in self.samples):
raise ValueError(
warnings.warn(
'Samples must have at least `Sample_Name`, '
'`Sample_Library`, and `index` attributes'
)
Expand Down Expand Up @@ -883,7 +883,7 @@ def write(self, handle: TextIO, blank_lines: int = 1) -> None:

"""
if not isinstance(blank_lines, int) or blank_lines <= 0:
raise ValueError('Number of blank lines must be a positive int.')
warnings.warn('Number of blank lines must be a positive int.')

writer = csv.writer(handle)
csv_width: int = max([len(self.all_sample_keys), 2])
Expand Down