def test_samplesheet_to_old_style_json():
output = samplesheet_to_json(COMPLETE_CSV,
old_style_json=True,
file_presence_check=False)
correct_output = output_conversions.samplegroup_to_biowdl_old_json(
input_conversions.samplesheet_csv_to_samplegroup(COMPLETE_CSV))
assert output == correct_output
def test_samplesheet_md5_checks(correct_md5sum_samplesheet):
samplesheet_to_json(correct_md5sum_samplesheet,
file_presence_check=True,
file_md5_check=True)
def test_unknown_samplesheet_format():
samplesheet = Path("bla.customformat")
with pytest.raises(NotImplementedError) as error:
samplesheet_to_json(samplesheet)
error.match("Unsupported extension: .customformat")
def test_nosuffix():
samplesheet = FILESDIR / Path("804935870934875")
output = samplesheet_to_json(samplesheet, fileformat='yaml')
correct_output = output_conversions.samplegroup_to_biowdl_new_json(
input_conversions.biowdl_yaml_to_samplegroup(samplesheet))
assert output == correct_output
def test_yaml_samplesheet_to_json():
samplesheet = FILESDIR / Path("complete.yml")
output = samplesheet_to_json(samplesheet, file_presence_check=False)
correct_output = output_conversions.samplegroup_to_biowdl_new_json(
input_conversions.biowdl_yaml_to_samplegroup(samplesheet))
assert output == correct_output
def test_samplesheet_to_json_no_checks():
output = samplesheet_to_json(COMPLETE_CSV, file_presence_check=False)
correct_output = output_conversions.samplegroup_to_biowdl_new_json(
input_conversions.samplesheet_csv_to_samplegroup(COMPLETE_CSV))
assert output == correct_output