def test_unknown_frag_library(self):
"""
case where unknown fragment library is specified
"""
with self.assertRaisesRegex(InvalidCrystalsCSV,
r"^Unknown fragment library 'Wat'."):
parse_crystals_csv(BytesIO(UNKNOWN_FRAG_LIBRARY))
def test_unknown_frag_code(self):
"""
case where unknown fragment code is specified
"""
with self.assertRaisesRegex(InvalidCrystalsCSV,
r"^No fragment BT01 in 'MyLib' library."):
parse_crystals_csv(BytesIO(UNKNOW_FRAG_CODE))
def test_empty_sample_id(self):
"""
one of the crystals have an empty SampleID specified
"""
with self.assertRaisesRegex(InvalidCrystalsCSV,
r"Empty SampleID specified\."):
parse_crystals_csv(BytesIO(EMPTY_SAMPLE_ID))
def test_unexpected_column(self):
"""
unexpected column in the CSV
"""
with self.assertRaisesRegex(InvalidCrystalsCSV,
r"^Unexpected column: Suprise\."):
parse_crystals_csv(BytesIO(UNEXPECTED_COLUMN))
def test_missing_frag_code(self):
"""
case where fragment library is specified, by there is no fragment code
"""
with self.assertRaisesRegex(
InvalidCrystalsCSV,
r"^No fragment code specified for 'Cry2' crystal."):
parse_crystals_csv(BytesIO(MISSING_FRAG_CODE))
def test_missing_frag_library(self):
"""
case where fragment code is present, but no library is specified
"""
with self.assertRaisesRegex(
InvalidCrystalsCSV,
r"^No fragment library specified for 'Cry2' crystal."):
parse_crystals_csv(BytesIO(MISSING_FRAG_LIBRARY))
def test_ok(self):
crystals = parse_crystals_csv(BytesIO(VALID_CSV))
self.assertListEqual(
crystals.as_list(),
[
{
"SampleID": "MID2-x0017",
"FragmentLibrary": "FragMAXlib",
"FragmentCode": "VT00249",
},
{
"SampleID": "MID2-x0018",
"FragmentLibrary": "FragMAXlib",
"FragmentCode": "VT00249",
},
{
"SampleID": "MID2-x0019",
"FragmentLibrary": None,
"FragmentCode": None,
},
],
)
def test_missing_required_cols(self):
"""
required columns are missing
"""
with self.assertRaisesRegex(InvalidCrystalsCSV, "^Missing columns:.*"):
parse_crystals_csv(BytesIO(MISSING_REQ_COLUMS))
def test_csv_parse_error(self):
"""
unparsable CSV case
"""
with self.assertRaises(InvalidCrystalsCSV):
parse_crystals_csv(BytesIO(b'"'))
def clean_crystals_csv_file(self):
csv_file = self.cleaned_data["crystals_csv_file"]
try:
return parse_crystals_csv(csv_file)
except InvalidCrystalsCSV as e:
raise ValidationError(str(e))