diff --git a/ippisite/ippidb/models.py b/ippisite/ippidb/models.py
index 977b0be8d4572fac2e3b4cc83923ed5e1c276027..43128034c806c1ea6bd92232fde803e4ba34c4d8 100644
--- a/ippisite/ippidb/models.py
+++ b/ippisite/ippidb/models.py
@@ -457,86 +457,24 @@ class PpiComplex(models.Model):
def __str__(self):
return 'PPI {}, Complex {} ({})'.format(self.ppi, self.complex, self.cc_nb)
-
-class CompoundManager(models.Manager):
+class ValidatedCompoundsManager(models.Manager):
"""
- CompoundManager adds automatically a number of annotations to the results
- of the database query, used for filters and compound card
+ ValidatedCompoundManager filters only compounds from validated
+ contributions (or not coming from contributions) in the results
+ of the database query
"""
- # def get_queryset(self):
- # return super().get_queryset().exclude(compoundaction__ppi__contribution__validated=False)
-
- def get_queryset_old(self):
- # @formatter:off
- qs = super().get_queryset()
- # with number of publications
- qs = qs.annotate(pubs=Count('refcompoundbiblio', distinct=True))
- # with best activity
- qs = qs.annotate(best_activity=Max('compoundactivityresult__activity'))
- # with LE
- qs = qs.annotate(le=Cast(1.37 * Max('compoundactivityresult__activity') / F('nb_atom_non_h'), FloatField()))
- # with LLE
- qs = qs.annotate(lle=Cast(Max('compoundactivityresult__activity') - F('a_log_p'), FloatField()))
- # Lipinsky MW (<=500)
- qs = qs.annotate(lipinsky_mw=Case(When(molecular_weight__lte=500, then=True), default=False, output_field=BooleanField()))
- # Lipinsky hba (<=10)
- qs = qs.annotate(lipinsky_hba=Case(When(nb_acceptor_h__lte=10, then=True), default=False, output_field=BooleanField()))
- # Lipinsky hbd (<5)
- qs = qs.annotate(lipinsky_hbd=Case(When(nb_donor_h__lte=5, then=True), default=False, output_field=BooleanField()))
- # Lipinsky a_log_p (<5)
- qs = qs.annotate(lipinsky_a_log_p=Case(When(a_log_p__lte=5, then=True), default=False, output_field=BooleanField()))
- # Lipinsky global
- qs = qs.annotate(lipinsky_score=Cast(F('lipinsky_mw'), IntegerField()) + Cast(F('lipinsky_hba'), IntegerField()) +
- Cast(F('lipinsky_hbd'), IntegerField()) + Cast(F('lipinsky_a_log_p'), IntegerField()))
- qs = qs.annotate(lipinsky=Case(When(lipinsky_score__gte=3, then=True), default=False, output_field=BooleanField()))
- # Veber hba_hbd (<=12)
- qs = qs.annotate(hba_hbd=F('nb_acceptor_h')+F('nb_donor_h'))
- qs = qs.annotate(veber_hba_hbd=Case(When(hba_hbd__lte=12, then=True), default=False, output_field=BooleanField()))
- # Veber TPSA (<=140)
- qs = qs.annotate(veber_tpsa=Case(When(tpsa__lte=140, then=True), default=False, output_field=BooleanField()))
- # Veber Rotatable Bonds (<=10)
- qs = qs.annotate(veber_rb=Case(When(nb_rotatable_bonds__lte=10, then=True), default=False, output_field=BooleanField()))
- # Veber global (Rotatable bonds and (hba_hbd or tpsa))
- qs = qs.annotate(veber=Case(When(Q(Q(nb_rotatable_bonds__lte=10) & (Q(hba_hbd__lte=12) | Q(tpsa__lte=140))), then=True), default=False, output_field=BooleanField()))
- # Pfizer AlogP (<=3)
- qs = qs.annotate(pfizer_a_log_p=Case(When(a_log_p__lte=3, then=True), default=False, output_field=BooleanField()))
- # Pfizer TPSA (>=75)
- qs = qs.annotate(pfizer_tpsa=Case(When(tpsa__gte=75, then=True), default=False, output_field=BooleanField()))
- # Pfizer global (AlogP and TPSA)
- qs = qs.annotate(pfizer=Case(When(Q(Q(a_log_p__lte=3) & Q(tpsa__gte=75)), then=True), default=False, output_field=BooleanField()))
- # PDB ligand available
- qs = qs.annotate(pdb_ligand_av=Cast(Max(Case(When(ligand_id__isnull=False, then=1), default=0, output_field=IntegerField())), BooleanField()))
- # inhibition role
- qs = qs.annotate(inhibition_role=Case(When(compoundactivityresult__modulation_type='I', then=True), default=False, output_field=BooleanField()))
- # binding role
- qs = qs.annotate(binding_role=Case(When(compoundactivityresult__modulation_type='B', then=True), default=False, output_field=BooleanField()))
- # stabilisation role
- qs = qs.annotate(stabilisation_role=Case(When(compoundactivityresult__modulation_type='S', then=True), default=False, output_field=BooleanField()))
- # cellular tests performed
- qs = qs.annotate(celltest_av=Cast(Max(Case(When(compoundactivityresult__test_activity_description__test_type='CELL', then=1), default=0, output_field=IntegerField())), BooleanField()))
- # inhibition tests performed
- qs = qs.annotate(inhitest_av=Cast(Max(Case(When(compoundactivityresult__test_activity_description__test_modulation_type='I', then=1), default=0, output_field=IntegerField())), BooleanField()))
- # stabilisation tests performed
- qs = qs.annotate(stabtest_av=Cast(Max(Case(When(compoundactivityresult__test_activity_description__test_modulation_type='S', then=1), default=0, output_field=IntegerField())), BooleanField()))
- # binding tests performed
- qs = qs.annotate(bindtest_av=Cast(Max(Case(When(compoundactivityresult__test_activity_description__test_modulation_type='B', then=1), default=0, output_field=IntegerField())), BooleanField()))
- # pharmacokinetic tests performed
- qs = qs.annotate(pktest_av=Cast(Max(Case(When(refcompoundbiblio__bibliography__pharmacokinetic=True, then=1), default=0, output_field=IntegerField())), BooleanField()))
- # cytotoxicity tests performedudy
- qs = qs.annotate(cytoxtest_av=Cast(Max(Case(When(refcompoundbiblio__bibliography__cytotox=True, then=1), default=0, output_field=IntegerField())), BooleanField()))
- # in silico st performed
- qs = qs.annotate(insilico_av=Cast(Max(Case(When(refcompoundbiblio__bibliography__in_silico=True, then=1), default=0, output_field=IntegerField())), BooleanField()))
- # number of tests available
- qs = qs.annotate(tests_av=Count('compoundactivityresult', distinct=True))
- # @formatter:on
- return qs
+ def get_queryset(self):
+ return super().get_queryset().exclude(compoundaction__ppi__contribution__validated=False)
class Compound(AutoFillableModel):
"""
Chemical compound
"""
- objects = CompoundManager()
+
+ objects = models.Manager()
+ validated = ValidatedCompoundsManager()
+
canonical_smile = models.TextField(
verbose_name='Canonical Smiles',
unique=True,
@@ -888,6 +826,7 @@ class Compound(AutoFillableModel):
models.Index(fields=['le']),
models.Index(fields=['lle']),
]
+ #default_manager_name = 'ippidb.models.ValidatedCompoundsManager'
# indexes = [
# models.Index(fields=['lipinsky']),
# models.Index(fields=['veber']),
diff --git a/ippisite/ippidb/tests_contribute.py b/ippisite/ippidb/tests_contribute.py
index a0a280f60f3e364c53e44a5c3bcfe69a7c614f24..537852443ced19dc6f0af4806939ebb16e3398c9 100644
--- a/ippisite/ippidb/tests_contribute.py
+++ b/ippisite/ippidb/tests_contribute.py
@@ -53,6 +53,11 @@ class ContributionViewsTestCase(TestCase):
models.Compound.objects.count() + len(entry_data["compounds"]),
"Compounds count",
),
+ (
+ models.Compound.validated.count,
+ models.Compound.validated.count(),
+ "Validated Compounds count",
+ ),
(
models.CompoundAction.objects.count,
models.CompoundAction.objects.count() + len(entry_data["compounds"]),
@@ -77,6 +82,19 @@ class ContributionViewsTestCase(TestCase):
self._process_contribution_wizard_without_sanity_check(entry_data)
for fcn, results, msg in future_expected_equals:
self.assertEqual(fcn(), results, msg=msg)
+ post_validation_expected_equals = [
+ (
+ models.Compound.validated.count,
+ models.Compound.objects.count(),
+ "Validated Compounds count",
+ ),
+ ]
+ contribution_to_be_validated = models.Contribution.objects.get(validated=False)
+ contribution_to_be_validated.validated = True
+ contribution_to_be_validated.save()
+ for fcn, results, msg in post_validation_expected_equals:
+ self.assertEqual(fcn(), results, msg=msg)
+
def _process_contribution_wizard_without_sanity_check(self, entry_data):
"""