def test_biom_open_gz(self):
with biom_open(get_data_path('test.json.gz')) as f:
self.assertTrue(isinstance(f, gzip.GzipFile))
with biom_open(get_data_path('test_writing.json.gz'), 'w') as f:
self.assertTrue(isinstance(f, gzip.GzipFile))
remove(get_data_path('test_writing.json.gz'))
def test_biom_open_hdf5(self):
with biom_open(get_data_path('test.biom')) as f:
self.assertTrue(isinstance(f, h5py.File))
with biom_open(get_data_path('test_writing.biom'), 'w') as f:
self.assertTrue(isinstance(f, h5py.File))
remove(get_data_path('test_writing.biom'))
def test_biom_open_hdf5(self):
with biom_open(get_data_path('test.biom')) as f:
self.assertTrue(isinstance(f, h5py.File))
with biom_open(get_data_path('test_writing.biom'), 'w') as f:
self.assertTrue(isinstance(f, h5py.File))
remove(get_data_path('test_writing.biom'))
def test_biom_open_gz(self):
with biom_open(get_data_path('test.json.gz')) as f:
self.assertTrue(isinstance(f, gzip.GzipFile))
with biom_open(get_data_path('test_writing.json.gz'), 'w') as f:
self.assertTrue(isinstance(f, gzip.GzipFile))
remove(get_data_path('test_writing.json.gz'))
def test_load_classic(self):
tab = load_table(get_data_path('test.json'))
with NamedTemporaryFile(mode='w') as fp:
fp.write(str(tab))
fp.flush()
obs = load_table(fp.name)
npt.assert_equal(obs.ids(), tab.ids())
npt.assert_equal(obs.ids(axis='observation'),
tab.ids(axis='observation'))
npt.assert_equal(obs.matrix_data.toarray(), tab.matrix_data.toarray())
def test_biom_open_json(self):
with biom_open(get_data_path('test.json')) as f:
self.assertTrue(isinstance(f, file))
def test_is_hdf5_file(self):
self.assertTrue(is_hdf5_file(get_data_path('test.biom')))
self.assertFalse(is_hdf5_file(get_data_path('test.json')))
def test_load_table_unicode(self):
t = load_table(get_data_path('bad_table.txt'))
self.assertEqual(u's__Cortinarius grosmornënsis',
t.metadata('otu1', 'observation')['taxonomy'])
def test_biom_open_json(self):
with biom_open(get_data_path('test.json')) as f:
self.assertTrue(hasattr(f, 'read'))
def test_biom_open_hdf5_no_h5py(self):
with self.assertRaises(RuntimeError):
with biom_open(get_data_path('test.biom')) as f:
pass
def test_biom_open_empty(self):
with self.assertRaises(ValueError) as e:
with biom_open(get_data_path('no-contents.biom'), 'r') as f:
pass
self.assertTrue("is empty and can't be parsed" in str(e.exception))
def test_is_hdf5_file(self):
self.assertTrue(is_hdf5_file(get_data_path('test.biom')))
self.assertFalse(is_hdf5_file(get_data_path('test.json')))
def test_biom_open_hdf5_no_h5py(self):
with self.assertRaises(RuntimeError):
with biom_open(get_data_path('test.biom')) as f:
pass
def test_biom_open_json(self):
with biom_open(get_data_path("test.json")) as f:
self.assertTrue(hasattr(f, "read"))
def test_biom_open_empty(self):
with self.assertRaises(ValueError) as e:
with biom_open(get_data_path("no-contents.biom"), "r") as f:
pass
self.assertTrue("is empty and can't be parsed" in str(e.exception))
def test_biom_open_json(self):
with biom_open(get_data_path('test.json')) as f:
self.assertTrue(isinstance(f, file))
