def test_write(self):
for fp, obj in zip(self.valid_fps, self.ordination_results_objs):
fh = StringIO()
_ordination_results_to_ordres(obj, fh)
obs = fh.getvalue()
fh.close()
with open(fp, 'U') as fh:
exp = fh.read()
npt.assert_equal(obs, exp)
def test_roundtrip_read_write(self):
for fp in self.valid_fps:
# Read.
obj1 = _ordres_to_ordination_results(fp)
# Write.
fh = StringIO()
_ordination_results_to_ordres(obj1, fh)
fh.seek(0)
# Read.
obj2 = _ordres_to_ordination_results(fh)
fh.close()
assert_ordination_results_equal(obj1, obj2)
def test_to_file(self):
"""Should serialize a DissimilarityMatrix to file."""
for dm_f_line, dm in zip(self.dm_f_lines, self.dms):
for file_type in ('file like', 'file name'):
if file_type == 'file like':
obs_f = StringIO()
dm.to_file(obs_f)
obs = obs_f.getvalue()
obs_f.close()
elif file_type == 'file name':
with tempfile.NamedTemporaryFile('r+') as temp_file:
dm.to_file(temp_file.name)
temp_file.flush()
temp_file.seek(0)
obs = temp_file.read()
self.assertEqual(obs, dm_f_line)
def test_to_file(self):
"""Should serialize a DissimilarityMatrix to file."""
for dm_f_line, dm in zip(self.dm_f_lines, self.dms):
for file_type in ('file like', 'file name'):
if file_type == 'file like':
obs_f = StringIO()
dm.to_file(obs_f)
obs = obs_f.getvalue()
obs_f.close()
elif file_type == 'file name':
with tempfile.NamedTemporaryFile('r+') as temp_file:
dm.to_file(temp_file.name)
temp_file.flush()
temp_file.seek(0)
obs = temp_file.read()
self.assertEqual(obs, dm_f_line)
def test_to_file(self):
for scores, test_path in zip(self.scores, self.test_paths):
for file_type in ('file like', 'file name'):
if file_type == 'file like':
obs_f = StringIO()
scores.to_file(obs_f)
obs = obs_f.getvalue()
obs_f.close()
elif file_type == 'file name':
with tempfile.NamedTemporaryFile('r+') as temp_file:
scores.to_file(temp_file.name)
temp_file.flush()
temp_file.seek(0)
obs = temp_file.read()
with open(get_data_path(test_path), 'U') as f:
exp = f.read()
yield npt.assert_equal, obs, exp
def test_to_file(self):
for scores, test_path in zip(self.scores, self.test_paths):
for file_type in ('file like', 'file name'):
if file_type == 'file like':
obs_f = StringIO()
scores.to_file(obs_f)
obs = obs_f.getvalue()
obs_f.close()
elif file_type == 'file name':
with tempfile.NamedTemporaryFile('r+') as temp_file:
scores.to_file(temp_file.name)
temp_file.flush()
temp_file.seek(0)
obs = temp_file.read()
with open(get_data_path(test_path), 'U') as f:
exp = f.read()
yield npt.assert_equal, obs, exp
def test_roundtrip_read_write(self):
for reader_fn, writer_fn, fhs in ((_dm_to_dissimilarity_matrix,
_dissimilarity_matrix_to_dm,
self.dissim_fhs),
(_dm_to_distance_matrix,
_distance_matrix_to_dm,
self.dist_fhs)):
for fh in fhs:
# Read.
dm1 = reader_fn(fh)
# Write.
out_fh = StringIO()
writer_fn(dm1, out_fh)
out_fh.seek(0)
# Read.
dm2 = reader_fn(out_fh)
out_fh.close()
self.assertEqual(dm1, dm2)
def test_write(self):
for fn, objs, strs in ((_dissimilarity_matrix_to_dm, self.dissim_objs,
self.dissim_strs),
(_distance_matrix_to_dm, self.dist_objs,
self.dist_strs)):
for obj, str_ in zip(objs, strs):
fh = StringIO()
fn(obj, fh)
obs = fh.getvalue()
fh.close()
self.assertEqual(obs, str_)
# Test writing CSV (TSV is written above).
for fn, cls in ((_dissimilarity_matrix_to_dm, DissimilarityMatrix),
(_distance_matrix_to_dm, DistanceMatrix)):
obj = cls(self.dm_3x3_data, ['a', 'b', 'c'])
fh = StringIO()
fn(obj, fh, delimiter=',')
obs = fh.getvalue()
fh.close()
self.assertEqual(obs, DM_3x3_CSV)