def test_harmonize_undefined_smiles(metadata, aliases, undefined, expected):
spectrum_in = SpectrumBuilder().with_metadata(metadata).build()
spectrum = harmonize_undefined_smiles(spectrum_in,
aliases=aliases,
undefined=undefined)
assert spectrum.get("smiles") == expected
def test_harmonize_undefined_smiles_empty_string():
spectrum_in = Spectrum(mz=numpy.array([], dtype="float"),
intensities=numpy.array([], dtype="float"),
metadata={"smiles": ""})
spectrum = harmonize_undefined_smiles(spectrum_in)
assert spectrum.get("smiles") == ""
def test_harmonize_undefined_smiles_alias_nan_undefined_is_na():
spectrum_in = Spectrum(mz=numpy.array([], dtype="float"),
intensities=numpy.array([], dtype="float"),
metadata={"smiles": "nan"})
spectrum = harmonize_undefined_smiles(
spectrum_in, aliases=["nodata", "NaN", "Nan", "nan"], undefined="n/a")
assert spectrum.get("smiles") == "n/a"
def test_empty_spectrum():
spectrum_in = None
spectrum = harmonize_undefined_smiles(spectrum_in)
assert spectrum is None, "Expected different handling of None spectrum."
