def test_spectrum02():
with pytest.raises(traitlets.TraitError):
add_msms_ref.Spectrum(intensities=[1.2, 1], mzs=[123, 145, 256.04])
with pytest.raises(traitlets.TraitError):
add_msms_ref.Spectrum(intensities=[1.2, 1, 4], mzs=[123, 145])
with pytest.raises(traitlets.TraitError):
add_msms_ref.Spectrum(intensities=[1.2, 1, 4], mzs=[])
with pytest.raises(traitlets.TraitError):
add_msms_ref.Spectrum(intensities=[], mzs=[123])
with pytest.raises(traitlets.TraitError):
add_msms_ref.Spectrum(intensities=[1], mzs=[-123])
with pytest.raises(traitlets.TraitError):
add_msms_ref.Spectrum(intensities=[1, 1], mzs=[123, 22])
def test_has_missing_fields01():
ref = add_msms_ref.MsmsRef(
id="abcdefghijklmnop",
database="my_db",
name="2'-deoxyadenosine",
spectrum=add_msms_ref.Spectrum(intensities=[1, 1.4, 2],
mzs=[100, 101, 555]),
decimal=4,
precursor_mz=251.101839276,
polarity="negative",
adduct="[M-H]+",
fragmentation_method="CID",
collision_energy="60eV",
instrument="ThermoTOF-3000",
instrument_type="LC-ESI-QTOF",
formula="C10H13N5O3",
exact_mass=251.101839276,
inchi_key=INCHI_KEY,
inchi=INCHI,
)
assert not ref.has_missing_fields()
def tests_msms_ref01(mocker, compound):
mocker.patch("metatlas.datastructures.metatlas_objects.retrieve",
return_value=[compound])
add_msms_ref.MsmsRef(
database="my_db",
name="2'-deoxyadenosine",
spectrum=add_msms_ref.Spectrum(intensities=[1, 1.4, 2],
mzs=[100, 101, 555]),
decimal=4,
precursor_mz=251.101839276,
polarity="negative",
adduct="[M-H]+",
fragmentation_method="CID",
collision_energy="60eV",
instrument="ThermoTOF-3000",
instrument_type="LC-ESI-QTOF",
formula="C10H13N5O3",
exact_mass=251.101839276,
inchi_key=INCHI_KEY,
inchi=INCHI,
)
def test_spectrum01():
add_msms_ref.Spectrum(intensities=[1.2, 1, 4], mzs=[123, 145, 256.04])