def test_str(self):
assert str(Score(7)) == "7.0"
assert str(Score(7, flag_string="Hello", flag_severity=8)) == "7.0"
assert repr(Score(7)) == "Score(7.0)"
assert repr(
Score(7, flag_string="Hello",
flag_severity=8)) == "Score(7.0, Flag('Hello', severity=8))"
def test_repr():
molecule = Molecule(
name="Dimethyl Phthalate",
formula="C10 H10 O4",
matches={
"overall": Score(62.90),
"tgt": Score(62.90, flag_string="low score", flag_severity=2),
},
)
assert str(molecule) == "Molecule(Dimethyl Phthalate, C10H10O4)"
assert repr(molecule) == "<Molecule(Dimethyl Phthalate, Formula({'C': 10, 'H': 10, 'O': 4}))>"
def test_matches(self):
molecule = Molecule(
name="Dimethyl Phthalate",
matches={
"overall": Score(62.90),
"tgt": Score(62.90, flag_string="low score", flag_severity=2),
},
)
assert molecule.matches == {
"overall": Score(62.90),
"tgt": Score(62.90, flag_string="low score", flag_severity=2),
}
with pytest.raises(TypeError, match="'matches' must be a dictionary, not"):
Molecule(name="Dimethyl Phthalate", matches="Hello World") # type: ignore
def compound(spectrum, molecule):
return Compound(
algo="FindByFormula",
location={'m': 169.0893, "rt": 13.649, 'a': 29388223, 'y': 3377289},
results=[molecule],
spectra=[spectrum],
compound_scores={"fbf": Score(62.90, flag_string="low score", flag_severity=2)},
)
def test_dict():
assert dict(
Molecule(
name="Dimethyl Phthalate",
formula="C10 H10 O4",
matches={
"overall": Score(62.90),
"tgt": Score(62.90, flag_string="low score", flag_severity=2),
},
)
) == {
"name": "Dimethyl Phthalate",
"formula": Formula({'C': 10, 'H': 10, 'O': 4}),
"matches": {
"overall": Score(62.90),
"tgt": Score(62.90, flag_string="low score", flag_severity=2),
},
}
def test_dict(spectrum, molecule, compound):
as_dict = {
"algo": "FindByFormula",
"location": {'m': 169.0893, "rt": 13.649, 'a': 29388223, 'y': 3377289},
"results": [molecule],
"spectra": [spectrum],
"compound_scores": {"fbf": Score(62.90, flag_string="low score", flag_severity=2)},
}
assert dict(compound) == as_dict
class TestCreation:
def test_algo(self):
assert Compound(algo="FindByFormula").algo == "FindByFormula"
def test_location(self):
assert Compound(
algo="FindByFormula", location={'m': 169.0893, "rt": 13.649, 'a': 29388223, 'y': 3377289}
).location == {'m': 169.0893, "rt": 13.649, 'a': 29388223, 'y': 3377289}
assert Compound(
algo="FindByFormula", location={'m': 169.0893, "rt": 13.649, 'a': 29388223, 'y': 3377289}
).location == {'m': 169.0893, "rt": 13.649, 'a': 29388223, 'y': 3377289}
assert Compound(algo="FindByFormula").location == {}
@pytest.mark.parametrize(
"scores",
[
{"fbf": Score(56.24, flag_string="low score; No H adduct", flag_severity=2)},
{"fbf": Score(82.53, flag_string="No H adduct", flag_severity=2)},
{"fbf": Score(60.62, flag_string="low score", flag_severity=2)},
{"fbf": Score(62.90, flag_string="low score", flag_severity=2)},
]
)
def test_compound_scores(self, scores):
assert Compound(algo="FindByFormula", compound_scores=scores).compound_scores == copy.deepcopy(scores)
assert Compound(algo="FindByFormula").compound_scores == {}
def test_results(self, molecule):
results = [molecule, molecule]
assert Compound(algo="FindByFormula", results=results).results == copy.deepcopy(results)
assert Compound(algo="FindByFormula", results=()).results == []
assert Compound(algo="FindByFormula", results=[]).results == []
assert Compound(algo="FindByFormula").results == []
def test_spectra(self, spectrum):
assert Compound(algo="FindByFormula", spectra=[spectrum]).spectra == [spectrum]
assert Compound(algo="FindByFormula", spectra=(spectrum, )).spectra == [spectrum]
assert Compound(algo="FindByFormula", spectra=()).spectra == []
assert Compound(algo="FindByFormula", spectra=[]).spectra == []
assert Compound(algo="FindByFormula").spectra == []
def test_repr(compound, spectrum, molecule, file_regression: FileRegressionFixture):
assert str(compound) == "Compound([Molecule(Dimethyl Phthalate, C10H10O4)])"
assert repr(compound) == "<Compound([<Molecule(Dimethyl Phthalate, Formula({'C': 10, 'H': 10, 'O': 4}))>])>"
compound = Compound(
algo="FindByFormula",
location={'m': 169.0893, "rt": 13.649, 'a': 29388223, 'y': 3377289},
results=[molecule, molecule, molecule, molecule, molecule],
spectra=[spectrum],
compound_scores={"fbf": Score(62.90, flag_string="low score", flag_severity=2)},
)
file_regression.check(str(compound), encoding="UTF-8", extension="_str.txt")
file_regression.check(repr(compound), encoding="UTF-8", extension="_repr.txt")
def expected_compound(fbf_spectrum, tof_spectrum):
score = Score(99.79)
return Compound(
algo="FindByFormula",
location={'m': 169.0893, "rt": 13.649, 'a': 29388223, 'y': 3377289},
compound_scores={"fbf": score},
results=[
Molecule(
name="Diphenylamine", formula="C12 H11 N", matches={
"overall": score,
"tgt": score,
}
)
],
spectra=[fbf_spectrum, tof_spectrum],
)
raw_xml = """
<Molecule name="Dimethyl Phthalate" formula="C10 H10 O4">
<MatchScores>
<Match algo="overall" score="62.90" />
<Match algo="tgt" score="62.90" tgtFlagsString="low score" tgtFlagsSeverity="2" />
</MatchScores>
</Molecule>
"""
expects = Molecule(
name="Dimethyl Phthalate",
formula="C10 H10 O4",
matches={
"overall": Score(62.90),
"tgt": Score(62.90, flag_string="low score", flag_severity=2),
},
)
@pytest.mark.parametrize("raw_xml, expects", [(raw_xml, expects)])
def test_from_xml(raw_xml, expects):
tree = lxml.objectify.fromstring(raw_xml)
spec = Molecule.from_xml(tree)
assert spec == expects
raw_xml_1 = '<MatchScores><Match algo="fbf" score="86.30" /></MatchScores>'
raw_xml_2 = '<MatchScores><Match algo="fbf" score="56.24" tgtFlagsString="low score; No H adduct" tgtFlagsSeverity="2" /></MatchScores>'
raw_xml_3 = '<MatchScores><Match algo="fbf" score="82.53" tgtFlagsString="No H adduct" tgtFlagsSeverity="2" /></MatchScores>'
def test_equals(self):
assert Score(7) == Score(7)
assert Score(7) != Score(8)
assert Score(7, flag_string="Hello") != Score(8)
assert Score(7, flag_string="Hello", flag_severity=3) != Score(8)
assert Score(7, flag_string="Hello") == Score(7, flag_string="Hello")
assert Score(7, flag_string="Hello",
flag_severity=3) == Score(7,
flag_string="Hello",
flag_severity=3)
assert Score(7.5, flag_string="Hello",
flag_severity=3) == Score(7.5,
flag_string="Hello",
flag_severity=3)
assert Score(7, flag_string="Hello") != Score(7, flag_string="World")
assert Score(7, flag_string="Hello", flag_severity=2) != Score(
7, flag_string="Hello", flag_severity=3)
score = Score(56.24, Flag("low score; No H adduct", severity=2))
assert score == Score(56.24, Flag("low score; No H adduct",
severity=2))
def test_creation(self):
assert Score(7) == 7
assert Score(7, flag_string="Hello") == 7
assert Score(7, flag_string="Hello", flag_severity=3) == 7
def test_float(self):
assert float(Score(7)) == 7.0
assert float(Score(7, flag_string="Hello", flag_severity=8)) == 7.0
}),
(raw_xml_3, {
"fbf": 82.53
}),
(raw_xml_4, {
"fbf": 60.62
}),
(raw_xml_5, {
"fbf": 62.90
}),
(raw_xml_multiline, {
"fbf": 62.90,
"abc": 12.34
}),
(raw_xml_1, {
"fbf": Score(86.3)
}),
(raw_xml_2, {
"fbf":
Score(56.24, flag_string="low score; No H adduct", flag_severity=2)
}),
(raw_xml_3, {
"fbf": Score(82.53, flag_string="No H adduct", flag_severity=2)
}),
(raw_xml_4, {
"fbf": Score(60.62, flag_string="low score", flag_severity=2)
}),
(raw_xml_5, {
"fbf": Score(62.90, flag_string="low score", flag_severity=2)
}),
(raw_xml_multiline, {