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."