def test_save_method_handles_no_cid_number_found(self, pcp_patch):
pcp_patch.side_effect = IndexError
data = deepcopy(self.cpd_data)
data.update({'cid_number': ''})
compound = Odorant(**data)
with self.assertRaises(ValidationError):
compound.save()
def test_supplier_clean_field_method(self, pcp_patch):
pcp_patch.return_value = [MockPubChemPyObject('synonyms', cid=5678)]
data = self.cpd_data.copy()
data.update({'supplier': Odorant.supplier_choices[0][0]})
compound = Odorant(**data)
with self.assertRaises(ValidationError):
compound.save()
def odorant_set(self):
qs = Odorant.substructure_matches(self.smiles) | Odorant.name_matches(
self.iupac_name_pattern, self.name)
if self.excludes:
chars = [i for i in self.excludes]
for s in chars:
qs = qs.exclude(smiles__icontains=s)
if self.includes:
chars = [i for i in self.includes]
for s in chars:
qs = qs.filter(smiles__icontains=s)
if self.max_carbons:
return [a for a in qs if a.carbon_count <= self.max_carbons]
return qs
def get_queryset(self):
notes_qs = UserOdorant.objects.filter(user=self.request.user.profile).values('compound')
if not notes_qs:
return Odorant.objects.none()
cpd_id_list = [a['compound'] for a in notes_qs]
queryset = Odorant.objects.filter(id__in=cpd_id_list)
return Odorant.substructure_matches(self.object.smiles, queryset)
def process_cas(request):
cas_no = request.GET.get('cas_number')
try:
obj = Odorant.objects.get(cas_number__exact=cas_no)
data = {
'object_exists': obj.get_absolute_url(),
'object_exists_name': str(obj),
}
return JsonResponse(data)
except ObjectDoesNotExist:
pass
try:
smiles = cirpy.query(cas_no, 'smiles')[0].value
pcp_query = pcp.get_compounds(smiles, 'smiles')[0]
cid_no = pcp_query.cid
except IndexError:
return JsonResponse({
'error': 'No compound found for this CAS number'
})
if smiles and cid_no:
data = {
'chemical_name': Odorant.scrape_compound_name(cid_no),
'iupac_name': pcp_query.iupac_name,
'structure_url': 'https://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid={}&t=l'.format(cid_no),
'hidden_cid': cid_no,
'smiles': smiles,
}
return JsonResponse(data)
def test_substructure_matches_for_valid_matching_smiles_string(self):
output = Odorant.substructure_matches('CCCCCC(O)')
self.assertIn(self.compound.id, [a.id for a in output])
self.assertIsNone(Odorant.substructure_matches('invalid_smiles'))
def test_save_method_raises_validation_error_if_incomplete_data(self):
compound = Odorant(cas_number='123-456-78')
with self.assertRaises(ValidationError):
compound.save()
def get_queryset(self):
unfiltered = super(ChemFilterSubstructureDetail, self).get_queryset
filter_method = getattr(Odorant.objects, self.kwargs['chem_type'], unfiltered)
return Odorant.substructure_matches(self.object.smiles, filter_method())