def test_from_file_with_file_path(self):
"""Should identify the filepath correctly and parse from it."""
# should fail with the expected exception
with self.assertRaises(DissimilarityMatrixFormatError):
DissimilarityMatrix.from_file(self.bad_dm_fp)
obs = DissimilarityMatrix.from_file(self.dm_2x2_asym_fp)
self.assertEqual(self.dm_2x2_asym, obs)
self.assertTrue(isinstance(obs, DissimilarityMatrix))
obs = DissimilarityMatrix.from_file(self.dm_3x3_fp)
self.assertEqual(self.dm_3x3, obs)
self.assertTrue(isinstance(obs, DissimilarityMatrix))
def test_round_trip_read_write(self):
"""Test reading, writing, and reading again works as expected."""
for dm_f in self.dm_fs:
# Read.
dm1 = DissimilarityMatrix.from_file(dm_f)
# Write.
out_f = StringIO()
dm1.to_file(out_f)
out_f.seek(0)
# Read.
dm2 = DissimilarityMatrix.from_file(out_f)
self.assertEqual(dm1, dm2)
def test_from_file_real_file(self):
"""Should correctly parse a real on-disk file."""
with tempfile.TemporaryFile(mode='r+',
prefix='skbio.tests.test_distance',
suffix='.txt') as fh:
fh.write('\n'.join(DM_3x3_WHITESPACE_F))
fh.seek(0)
obs = DissimilarityMatrix.from_file(fh)
self.assertEqual(obs, self.dm_3x3)
def test_from_file_invalid_input(self):
"""Raises error on ill-formatted dissimilarity matrix file."""
# Empty dm.
with self.assertRaises(DissimilarityMatrixFormatError):
DissimilarityMatrix.from_file([])
# Number of values don't match number of IDs.
with self.assertRaises(DissimilarityMatrixFormatError):
DissimilarityMatrix.from_file(self.bad_dm_f1)
# Mismatched IDs.
with self.assertRaises(DissimilarityMatrixFormatError):
DissimilarityMatrix.from_file(self.bad_dm_f2)
# Extra data at end.
with self.assertRaises(DissimilarityMatrixFormatError):
DissimilarityMatrix.from_file(self.bad_dm_f3)
# Missing data.
with self.assertRaises(DissimilarityMatrixFormatError):
DissimilarityMatrix.from_file(self.bad_dm_f4)
# Header, but no data.
with self.assertRaises(DissimilarityMatrixFormatError):
DissimilarityMatrix.from_file(self.bad_dm_f5)
# Non-hollow.
with self.assertRaises(DissimilarityMatrixError):
DissimilarityMatrix.from_file(self.bad_dm_f6)
def test_from_file_list_of_strings(self):
"""Should correctly parse a list of strings."""
obs = DissimilarityMatrix.from_file(DM_3x3_WHITESPACE_F)
self.assertEqual(obs, self.dm_3x3)
def test_from_file_extra_junk(self):
"""Should correctly parse a file with extra whitespace and comments."""
obs = DissimilarityMatrix.from_file(self.dm_3x3_whitespace_f)
self.assertEqual(obs, self.dm_3x3)
def test_from_file(self):
"""Should parse and return a valid DissimilarityMatrix given a file."""
for dm_f, dm in zip(self.dm_fs, self.dms):
obs = DissimilarityMatrix.from_file(dm_f)
self.assertEqual(obs, dm)