def test_require_precursor_mz_pass():
"""Test with correct precursor mz present."""
mz = numpy.array([10, 20, 30, 40], dtype="float")
intensities = numpy.array([0, 1, 10, 100], dtype="float")
spectrum_in = Spectrum(mz=mz, intensities=intensities)
spectrum_in.set("precursor_mz", 60.)
spectrum = require_precursor_mz(spectrum_in)
assert spectrum == spectrum_in, "Expected no changes."
def test_require_precursor_mz_fail_because_below_zero():
"""Test if spectrum is None when precursor_mz < 0"""
mz = numpy.array([10, 20, 30, 40], dtype="float")
intensities = numpy.array([0, 1, 10, 100], dtype="float")
spectrum_in = Spectrum(mz=mz, intensities=intensities)
spectrum_in.set("precursor_mz", -3.5)
spectrum = require_precursor_mz(spectrum_in)
assert spectrum is None, "Expected spectrum to be None."
def test_require_precursor_mz_without_precursor_mz():
"""Test if None is returned for missing precursor-mz."""
spectrum_in = Spectrum(mz=numpy.array([10, 20, 30, 40], dtype="float"),
intensities=numpy.array([0, 1, 10, 100],
dtype="float"),
metadata={})
spectrum = require_precursor_mz(spectrum_in)
assert spectrum is None, "Expected spectrum to be None."
def test_require_precursor_mz_with_wrong_precursor_mz():
"""Test if correct assert error is raised for precursor-mz as string."""
spectrum_in = SpectrumBuilder().with_metadata({
"precursor_mz": "445.0"
}).build()
with pytest.raises(AssertionError) as msg:
_ = require_precursor_mz(spectrum_in)
assert "Expected 'precursor_mz' to be a scalar number." in str(msg.value)
def test_require_precursor_mz_with_wrong_precursor_mz():
"""Test if correct assert error is raised for precursor-mz as string."""
spectrum_in = Spectrum(mz=numpy.array([10, 20, 30, 40], dtype="float"),
intensities=numpy.array([0, 1, 10, 100],
dtype="float"),
metadata={"precursor_mz": "445.0"})
with pytest.raises(AssertionError) as msg:
_ = require_precursor_mz(spectrum_in)
assert "Expected 'precursor_mz' to be a scalar number." in str(msg.value)
def test_if_spectrum_is_cloned():
"""Test if filter is correctly cloning the input spectrum."""
spectrum_in = SpectrumBuilder().with_metadata({
"precursor_mz": 100.
}).build()
spectrum = require_precursor_mz(spectrum_in)
spectrum.set("testfield", "test")
assert not spectrum_in.get("testfield"), \
"Expected input spectrum to remain unchanged."
def test_if_spectrum_is_cloned():
"""Test if filter is correctly cloning the input spectrum."""
mz = numpy.array([10, 20, 30, 40], dtype="float")
intensities = numpy.array([0, 1, 10, 100], dtype="float")
spectrum_in = Spectrum(mz=mz, intensities=intensities)
spectrum_in.set("precursor_mz", 1.)
spectrum = require_precursor_mz(spectrum_in)
spectrum.set("testfield", "test")
assert not spectrum_in.get("testfield"), \
"Expected input spectrum to remain unchanged."
def test_require_precursor_mz_fail_when_mz_too_small(precursor_mz):
"""Test if spectrum is None when precursor_mz <= minimum_accepted_mz"""
set_matchms_logger_level("INFO")
mz = numpy.array([10, 20, 30, 40], dtype="float")
intensities = numpy.array([0, 1, 10, 100], dtype="float")
spectrum_in = SpectrumBuilder().with_mz(mz).with_intensities(
intensities).build()
spectrum_in.set("precursor_mz", precursor_mz)
with LogCapture() as log:
spectrum = require_precursor_mz(spectrum_in)
assert spectrum is None, "Expected spectrum to be None."
log.check(
('matchms', 'INFO', 'Spectrum without precursor_mz was set to None.'))
reset_matchms_logger()
def test_require_precursor_mz_with_input_none():
"""Test if input spectrum is None."""
spectrum_in = None
spectrum = require_precursor_mz(spectrum_in)
assert spectrum is None
def test_require_precursor_mz(metadata, expected):
spectrum_in = SpectrumBuilder().with_metadata(metadata).build()
spectrum = require_precursor_mz(spectrum_in)
assert spectrum == expected, "Expected no changes."
