def test_floating_point():
compound = mo.Compound(name='foo', mono_isotopic_molecular_weight=1.0)
mo.store(compound)
compound.mono_isotopic_molecular_weight = 1.000007
mo.store(compound)
test = mo.retrieve('compound', name='foo')[-1]
assert test.mono_isotopic_molecular_weight == 1.000007, test.mono_isotopic_molecular_weight
def test_get_latest():
test = mo.Compound(name='hello')
mo.store(test)
test.name = 'goodbye'
mo.store(test)
test = mo.retrieve('compound', creation_time=test.creation_time)
assert len(test) == 1, len(test)
assert test[0].name == 'goodbye'
def test_remove_objects():
compound = mo.Compound(name='foo',
MonoIsotopic_molecular_weight=1.0,
reference_xrefs=[mo.ReferenceDatabase(name='baz')])
sub_id = compound.reference_xrefs[0].unique_id
mo.store(compound)
db = mo.retrieve('referencedatabase', unique_id=sub_id)[0]
assert db.unique_id == sub_id
mo.remove_objects(compound, _override=True)
test = mo.retrieve('compound', name='foo')
assert not test
test_sub = mo.retrieve('compounds_reference_xrefs', target_id=sub_id)
assert not test_sub
def make_atlas_df(atlas):
mz = []
rt = []
atlas_compound = []
label = []
for compound in atlas.compound_identifications:
label.append(compound.name)
if compound.mz_references:
mz.append(compound.mz_references[0])
else:
mz.append(metob.MzReference())
if compound.rt_references:
rt.append(compound.rt_references[0])
else:
rt.append(metob.RtReference())
if compound.compound:
atlas_compound.append(compound.compound[0])
else:
atlas_compound.append(metob.Compound())
compound_df = metob.to_dataframe(atlas_compound)
compound_df.rename(columns={
'name': 'compound_name',
'description': 'compound_description'
},
inplace=True)
#.rename(columns = {'name':'compound_name'}, inplace = True)
atlas_df = pd.concat(
[metob.to_dataframe(rt),
metob.to_dataframe(mz), compound_df], axis=1)
# atlas_df['label'] = label
atlas_keys = [
u'inchi_key', 'compound_name', u'rt_max', u'rt_min', u'rt_peak',
u'rt_units', u'detected_polarity', u'mz', u'mz_tolerance',
u'mz_tolerance_units', 'mono_isotopic_molecular_weight',
'pubchem_compound_id', 'synonyms', 'inchi', 'adduct'
]
# atlas_keys = [u'label','compound_name','compound_description',u'synonyms', u'num_free_radicals', u'number_components', u'permanent_charge', u'rt_max', u'rt_min', u'rt_peak',
# u'rt_units', u'detected_polarity', u'mz', u'mz_tolerance',u'mz_tolerance_units',
# u'inchi', u'inchi_key', u'neutralized_2d_inchi', u'neutralized_2d_inchi_key', u'neutralized_inchi',
# u'neutralized_inchi_key',u'chebi_id', u'hmdb_id', u'img_abc_id', u'kegg_id',u'lipidmaps_id', u'metacyc_id',
# u'mono_isotopic_molecular_weight', u'pubchem_compound_id', u'kegg_url', u'chebi_url', u'hmdb_url', u'lipidmaps_url', u'pubchem_url',u'wikipedia_url', u'source']
atlas_df = atlas_df[atlas_keys]
print(atlas_df.shape, len(label))
atlas_df['label'] = label
return atlas_df