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# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# ----------------------------------------------------------------------------
import unittest
import tempfile
import shutil
import os
import numpy as np
import numpy.testing as npt
import h5py
from skbio import DistanceMatrix
from skbio.io.format.binary_dm import (_h5py_mat_to_skbio_mat,
_skbio_mat_to_h5py_mat, _get_header,
_parse_ids, _verify_dimensions,
_bytes_decoder, _passthrough_decoder,
_set_header,
_vlen_dtype,
_binary_dm_sniffer)
class BinaryMatrixTests(unittest.TestCase):
def setUp(self):
self.mat = np.array([[0, 0.1, 0.2],
[0.1, 0, 0.3],
[0.2, 0.3, 0]])
self.ids = ['a', 'b', 'c']
self.tempdir = tempfile.TemporaryDirectory()
self.basic_fname = os.path.join(self.tempdir.name, 'basic')
self.basic = h5py.File(self.basic_fname, 'a')
ids = self.basic.create_dataset('order', shape=(3, ),
dtype=_vlen_dtype)
ids[:] = self.ids
self.basic.create_dataset('matrix', data=self.mat)
_set_header(self.basic)
self.basic.close()
self.badids_fname = os.path.join(self.tempdir.name, 'badids')
self.badids = h5py.File(self.badids_fname, 'a')
ids = self.badids.create_dataset('order', shape=(2, ),
dtype=_vlen_dtype)
ids[:] = ['a', 'b']
self.badids.create_dataset('matrix', data=self.mat)
_set_header(self.badids)
self.badids.close()
self.noheader_fname = os.path.join(self.tempdir.name, 'noheader')
self.noheader = h5py.File(self.noheader_fname, 'a')
ids = self.noheader.create_dataset('order', shape=(3, ),
dtype=_vlen_dtype)
ids[:] = self.ids
self.noheader.create_dataset('matrix', data=self.mat)
def tearDown(self):
shutil.rmtree(self.tempdir.name)
def test_binary_dm_sniffer(self):
self.assertEqual((True, {}),
_binary_dm_sniffer(open(self.basic_fname, 'rb')))
self.assertEqual((False, {}),
_binary_dm_sniffer(open(self.badids_fname, 'rb')))
self.assertEqual((False, {}),
_binary_dm_sniffer(open(self.noheader_fname, 'rb')))
def test_h5py_mat_to_skbio_mat(self):
exp = DistanceMatrix(self.mat, self.ids)
obs = _h5py_mat_to_skbio_mat(DistanceMatrix,
h5py.File(self.basic_fname, 'r'))
self.assertEqual(obs, exp)
def test_skbio_mat_to_h5py_mat(self):
fh1 = h5py.File('f1', 'a', driver='core', backing_store=False)
mat = DistanceMatrix(self.mat, self.ids)
_skbio_mat_to_h5py_mat(mat, fh1)
npt.assert_equal(np.asarray(fh1['order'][:], dtype=str), mat.ids)
npt.assert_equal(fh1['matrix'], mat.data)
def test_get_header(self):
self.assertEqual(_get_header(h5py.File(self.basic_fname, 'r')),
{'format': b'BDSM', 'version': b'2020.06'})
self.assertEqual(_get_header(h5py.File(self.noheader_fname, 'r')),
None)
def test_parse_ids(self):
tests = [(['a', 'b', 'c'], ['a', 'b', 'c']),
([b'a', b'b', b'\xc3\xa9\xc3\xb8asd'],
['a', 'b', 'éøasd'])]
for test, exp in tests:
self.assertEqual(_parse_ids(test), exp)
def test_verify_dimensions(self):
self.assertTrue(_verify_dimensions(h5py.File(self.basic_fname, 'r')))
self.assertFalse(_verify_dimensions(h5py.File(self.badids_fname, 'r')))
def test_bytes_decoder(self):
test = [b'', b'a', b'\xc3\xa9\xc3\xb8asd']
exp = ['', 'a', 'éøasd']
self.assertEqual(_bytes_decoder(test), exp)
def test_passthrough_decoder(self):
tests = [('', ''), ('a', 'a'), ('éøasd', 'éøasd')]
for test, expected in tests:
self.assertEqual(_passthrough_decoder(test), expected)
def test_set_header(self):
def mock():
obj = h5py.File('bung', 'a', driver='core', backing_store=False)
return obj
m = mock()
_set_header(m)
if __name__ == '__main__':
unittest.main()
|
