def test_default_can_read():
F = DummyFormat('test', '', 'foobar')
# Prepare files
filename = join(DATA_PATH, 'data', 'spectra.foobar')
filename_wrong_ext = join(DATA_PATH, 'data', 'spectra.notavalidext')
# Test _can_read()
assert F.can_read(Request(filename))
assert not F.can_read(Request(filename_wrong_ext))
def test_reader():
filename = join(DATA_PATH, 'data', 'spectra.foobar')
F = MyFormat('test', '')
# Test using reader
n = 3
R = F.get_reader(Request(filename))
assert len(R) == n
specs = [spec for spec in R]
assert len(specs) == n
for i in range(3):
assert specs[i].spectrum[0, 0] == i
assert specs[i].wavelength[0] == i
assert specs[i].meta['index'] == i
for i in range(3):
assert R.get_meta_data(i)['index'] == i
# Read next
assert R.get_data(0).spectrum[0, 0] == 0
assert R.get_next_data().spectrum[0, 0] == 1
assert R.get_next_data().spectrum[0, 0] == 2
# Fail
R._failmode = 1
with pytest.raises(ValueError, message="Meta data be a dict"):
R.get_meta_data(0)
R._failmode = 2
with raises(IndexError):
[spec for spec in R]
def test_request_read_sources():
filename = join(DATA_PATH, 'data', 'spectra.foobar')
R = Request(filename)
first_bytes = R.firstbytes
all_bytes = open(filename, 'rb').read()
assert len(first_bytes) == 256
assert all_bytes.startswith(first_bytes)
def test_format_subclass():
filename = join(DATA_PATH, 'data', 'spectra.foobar')
F = MyFormat('test', '')
assert 'TEST DOCS' in F.doc
# Get and check reader and write classes
R = F.get_reader(Request(filename))
assert isinstance(R, MyFormat.Reader)
assert R.format is F
assert R.request.filename == filename
def test_get_reader():
filename = load_mzml_path()
R = Request(filename)
F = formats["MZML"]
assert F.can_read(R)
reader = F.get_reader(R)
assert reader.get_length() == 531
spec = reader.get_data(0)
assert spec.amplitudes.shape == (282,)
assert spec.wavelength.shape == (282,)
assert spec.meta['filename'] == basename(filename)
assert spec.amplitudes[0] == pytest.approx(37.384331)
def test_dummy_format():
filename = join(DATA_PATH, 'data', 'spectra.foobar')
R = Request(filename)
F = formats['FOOBAR']
assert F.can_read(R)
reader = F.get_reader(R)
assert reader.get_length() == 1
assert reader.get_meta_data() == {}
spec = reader.get_data(0)
assert spec.amplitudes.shape == (1, 801)
assert spec.wavelength.shape == (801, )
def test_format_context_manager():
filename = join(DATA_PATH, 'data', 'spectra.foobar')
F = MyFormat('test', '')
R = F.get_reader(Request(filename))
# Use as context manager
with R:
pass
# Objects are now closed, cannot be used
assert R.closed
with pytest.raises(RuntimeError,
message="I/O operation on closed Reader."):
R.__enter__()
with pytest.raises(RuntimeError,
message="I/O operation on closed Reader."):
R.get_data(0)
R = F.get_reader(Request(filename))
ids = id(R)
F._closed[:] = []
del R
gc.collect() # Invoke __del__
assert ids == F._closed[0]
def test_format_selection():
filename = join(DATA_PATH, 'data', 'spectra.foobar')
test_dir = mkdtemp()
fname2 = join(test_dir, 'test.selectext1')
fname3 = join(test_dir, 'test.haha')
open(fname2, 'wb')
open(fname3, 'wb')
try:
F = formats.search_read_format(Request(filename))
assert F is formats['DUMMY']
# Now with custom format
format = MyFormat('test_selection', 'xx', 'selectext1')
formats.add_format(format)
assert '.selectext1' in fname2
F = formats.search_read_format(Request(fname2))
assert F is format
assert '.haha' in fname3
F = formats.search_read_format(Request(fname3))
assert F is format
finally:
shutil.rmtree(test_dir)
def test_spc_format():
filename = load_spc_path()
R = Request(filename)
F = formats['SPC']
assert F.can_read(R)
reader = F.get_reader(R)
assert reader.get_length() == 1
assert reader.get_meta_data()['dat_fmt'] == 'x-y'
spec = reader.get_data()
assert spec.spectrum.shape == (1911, )
assert spec.wavelength.shape == (1911, )
spec = reader.get_data(0)
assert spec.spectrum.shape == (1911, )
assert spec.wavelength.shape == (1911, )
def test_get_reader(filename, filename_cmp, format_spec, len_spectrum,
spectrum_shape, wavelength_shape, first_value):
R = Request(filename)
F = formats[format_spec]
assert F.can_read(R)
reader = F.get_reader(R)
assert reader.get_length() == len_spectrum
spec = reader.get_data()
if isinstance(spec, Spectrum):
_check_get_spectra(spec, filename, filename_cmp, spectrum_shape,
wavelength_shape)
spec = reader.get_data(0)
assert spec.amplitudes.size == spectrum_shape[-1]
assert spec.wavelength.size == wavelength_shape[-1]
assert spec.amplitudes[0] == pytest.approx(first_value)
def test_fsm_format():
filename = load_fsm_path()
R = Request(filename)
F = formats['FSM']
assert F.can_read(R)
reader = F.get_reader(R)
assert reader.get_length() == 7998
assert reader.get_meta_data()['signature'] == b'PEPE'
spec = reader.get_data()
assert spec.spectrum.shape == (7998, 1641)
assert spec.wavelength.shape == (1641, )
spec = reader.get_data(0)
assert spec.spectrum.shape == (1641, )
assert spec.wavelength.shape == (1641, )
assert spec.spectrum[0] == pytest.approx(38.656551)
def test_request_file_no_seek():
R = Request(File())
with raises(IOError):
R.firstbytes
def test_request_error(type_error, msg, params):
with pytest.raises(type_error, message=msg):
Request(params)
def test_request():
filename = 'file://' + join(DATA_PATH, 'data', 'spectra.foobar')
R = Request(filename)
assert R._uri_type == core.request.URI_FILENAME
assert R.get_local_filename() == filename[7:]
file_obj = R.get_file()
assert file_obj.name == filename[7:]
filename = join(DATA_PATH, 'data', 'spectra.foobar')
R = Request(filename)
assert R._uri_type == core.request.URI_FILENAME
assert R.get_local_filename() == filename
file_obj = R.get_file()
assert file_obj.name == filename
filename = join(DATA_PATH, 'data', 'spectra.foobar')
file_obj = open(filename, 'rb')
R = Request(file_obj)
assert R.get_local_filename() == filename
assert R.get_file().name == filename
shutil.copy(filename, expanduser('~/'))
filename = '~/spectra.foobar'
R = Request(filename)
assert R.filename == expanduser('~/spectra.foobar').replace('/', sep)
os.remove(expanduser(filename))
filename = join(DATA_PATH, 'data', 'spectra.foobar')
R = Request(filename, some_kwarg='something')
assert R.kwargs == {'some_kwarg': 'something'}