def test_derive_formula_from_name_examples(string_addition, expected_formula):
spectrum_in = Spectrum(mz=numpy.array([], dtype="float"),
intensities=numpy.array([], dtype="float"),
metadata={"compound_name": "peptideXYZ [M+H+K] "+string_addition})
spectrum = derive_formula_from_name(spectrum_in)
assert spectrum.get("formula") == expected_formula, "Expected different formula."
def test_derive_formula_from_name_no_name_given():
spectrum_in = Spectrum(mz=numpy.array([], dtype="float"),
intensities=numpy.array([], dtype="float"),
metadata={})
spectrum = derive_formula_from_name(spectrum_in)
assert spectrum.get("formula", None) is None, "Expected None for adduct."
assert spectrum.get("compound_name", None) is None, "Expected None for name."
def test_derive_formula_from_name_default():
spectrum_in = Spectrum(mz=numpy.array([], dtype="float"),
intensities=numpy.array([], dtype="float"),
metadata={"compound_name": "peptideXYZ [M+H+K] C5H12NO2"})
spectrum = derive_formula_from_name(spectrum_in)
assert spectrum.get("formula") == "C5H12NO2", "Expected different formula."
assert spectrum.get("compound_name") == "peptideXYZ [M+H+K]", "Expected different cleaned name."
def test_derive_formula_from_name_remove_formula_false():
spectrum_in = Spectrum(mz=numpy.array([], dtype="float"),
intensities=numpy.array([], dtype="float"),
metadata={"compound_name": "peptideXYZ [M+H+K] C5H12NO2"})
spectrum = derive_formula_from_name(spectrum_in, remove_formula_from_name=False)
assert spectrum.get("formula") == "C5H12NO2", "Expected different formula."
assert spectrum.get("compound_name") == spectrum_in.get("compound_name"), "Expected no name change."
def test_derive_formula_from_name_dont_overwrite_present_adduct():
spectrum_in = Spectrum(mz=numpy.array([], dtype="float"),
intensities=numpy.array([], dtype="float"),
metadata={"compound_name": "peptideXYZ C5H12NO2",
"formula": "totallycorrectformula"})
spectrum = derive_formula_from_name(spectrum_in)
assert spectrum.get("formula") == "totallycorrectformula", "Expected different adduct."
assert spectrum.get("compound_name") == "peptideXYZ", "Expected different cleaned name."
def test_derive_formula_from_name_examples(string_addition, expected_formula):
spectrum_in = SpectrumBuilder().with_metadata({
"compound_name":
"peptideXYZ [M+H+K] " + string_addition
}).build()
spectrum = derive_formula_from_name(spectrum_in)
assert spectrum.get(
"formula") == expected_formula, "Expected different formula."
def test_derive_formula_from_name(metadata, remove_formula_from_name,
expected_formula, expected_compound_name):
spectrum_in = SpectrumBuilder().with_metadata(metadata).build()
spectrum = derive_formula_from_name(
spectrum_in, remove_formula_from_name=remove_formula_from_name)
assert spectrum.get(
"formula") == expected_formula, "Expected different formula."
assert spectrum.get(
"compound_name"
) == expected_compound_name, "Expected different cleaned name."
def test_empty_spectrum():
spectrum_in = None
spectrum = derive_formula_from_name(spectrum_in)
assert spectrum is None, "Expected different handling of None spectrum."
