class MoleculeViewSet(
FilterToUserMixIn,
mixins.RetrieveModelMixin,
# mixins.DestroyModelMixin,
GenericViewSet):
queryset = Molecule.objects.order_by('id')
serializer_class = MoleculeSerializer
pagination_class = MoleculePagination
owner_relation = 'providers__project__owner'
def get_queryset(self):
ret = super().get_queryset().distinct()
if self.action in ('retrieve', 'list') and 'properties' in self.request.query_params:
for prop in self.request.query_params['properties'].split(','):
lookup = f"rdkit_prop_{prop}"
prop_calculator = getattr(djrdkit, prop)
ret = ret.annotate(**{ lookup: prop_calculator('entity__rdMol')})
return ret
properties = openapi.Parameter('properties', openapi.IN_QUERY, description="Attach specified physchem properties to the response. You should be able to use all properties listed here: https://django-rdkit.readthedocs.io/en/latest/functions.html", type=openapi.TYPE_ARRAY, items=openapi.Items(type=openapi.TYPE_STRING))
@swagger_auto_schema(
manual_parameters=[properties]
)
def retrieve(self, request, *args, **kwargs):
return super().retrieve(request, *args, **kwargs)
molset_id_param = openapi.Parameter('activity_set', openapi.IN_QUERY, description="Return only activities that belong to a certain activity set.", type=openapi.TYPE_NUMBER)
@swagger_auto_schema(
methods=['GET']
, responses={200: ActivitySerializer(many=True)}
, manual_parameters=[molset_id_param]
)
@action(detail=True, methods=['get'])
def activities(self, request, pk=None):
try:
molecule = self.get_queryset().get(pk=pk)
except Molecule.DoesNotExist:
return Response({"error" : f"No molecule found: {pk}"}, status=status.HTTP_404_NOT_FOUND)
activities = molecule.activities.filter(source__project__owner=self.request.user).distinct().order_by('id')
activity_set = self.request.query_params.get('activity_set', None)
if activity_set is not None:
activities = activities.filter(source__pk=int(activity_set))
# paginator = ActivityPagination()
# page = paginator.paginate_queryset(activities, self.request, view=self)
# if page is not None:
# serializer = ActivitySerializer(page, many=True)
# return paginator.get_paginated_response(serializer.data)
# else:
# return Response({"error" : "You need to specify a valid page number."}, status=status.HTTP_400_BAD_REQUEST)
return Response(ActivitySerializer(activities, many=True).data, status=status.HTTP_200_OK)
def activities(self, request, pk=None):
try:
molecule = self.get_queryset().get(pk=pk)
except Molecule.DoesNotExist:
return Response({"error" : f"No molecule found: {pk}"}, status=status.HTTP_404_NOT_FOUND)
activities = molecule.activities.filter(source__project__owner=self.request.user).distinct().order_by('id')
activity_set = self.request.query_params.get('activity_set', None)
if activity_set is not None:
activities = activities.filter(source__pk=int(activity_set))
# paginator = ActivityPagination()
# page = paginator.paginate_queryset(activities, self.request, view=self)
# if page is not None:
# serializer = ActivitySerializer(page, many=True)
# return paginator.get_paginated_response(serializer.data)
# else:
# return Response({"error" : "You need to specify a valid page number."}, status=status.HTTP_400_BAD_REQUEST)
return Response(ActivitySerializer(activities, many=True).data, status=status.HTTP_200_OK)
def activities(self, request, pk=None):
try:
activity_set = self.get_queryset().get(pk=pk)
except ActivitySet.DoesNotExist:
return Response({"error" : f"No such set: {pk}"}, status=status.HTTP_404_NOT_FOUND)
activities = Activity.objects.filter(source=activity_set)
mols = self.request.query_params.get('mols', [])
if mols:
mols = mols.split(',')
activities = activities.filter(molecule__in=mols)
activities = activities.order_by('id')
paginator = ActivityPagination()
page = paginator.paginate_queryset(activities, self.request, view=self)
if page is not None:
serializer = ActivitySerializer(page, many=True)
return paginator.get_paginated_response(serializer.data)
else:
return Response({"error" : "You need to specify a valid page number."}, status=status.HTTP_400_BAD_REQUEST)
class ActivitySetViewSet(FilterToProjectMixIn, FilterToUserMixIn,
mixins.ListModelMixin, mixins.RetrieveModelMixin,
mixins.DestroyModelMixin, viewsets.GenericViewSet):
queryset = ActivitySet.objects.order_by('-created')
serializer_class = ActivitySetSerializer
owner_relation = "project__owner"
project_id_param = openapi.Parameter(
'project_id',
openapi.IN_QUERY,
description="Return activity sets related to just this project.",
type=openapi.TYPE_NUMBER)
@swagger_auto_schema(
operation_description=
"List all activity sets. Can give a project ID to filter on."
# , methods=['GET']
,
manual_parameters=[project_id_param],
responses={200: ActivitySetSerializer(many=True)})
def list(self, request, *args, **kwargs):
return super().list(request, *args, **kwargs)
mols_param = openapi.Parameter(
'mols',
openapi.IN_QUERY,
description="Only return activities for the given molecule IDs.",
type=openapi.TYPE_ARRAY,
items=openapi.Items(type=openapi.TYPE_INTEGER))
@swagger_auto_schema(methods=['GET'],
manual_parameters=[mols_param],
responses={200: ActivitySerializer(many=True)})
@action(detail=True, methods=['get'])
def activities(self, request, pk=None):
try:
activity_set = self.get_queryset().get(pk=pk)
except ActivitySet.DoesNotExist:
return Response({"error": f"No such set: {pk}"},
status=status.HTTP_404_NOT_FOUND)
activities = Activity.objects.filter(source=activity_set)
mols = self.request.query_params.get('mols', [])
if mols:
mols = mols.split(',')
activities = activities.filter(molecule__in=mols)
activities = activities.order_by('id')
paginator = ActivityPagination()
page = paginator.paginate_queryset(activities, self.request, view=self)
if page is not None:
serializer = ActivitySerializer(page, many=True)
return paginator.get_paginated_response(serializer.data)
else:
return Response(
{"error": "You need to specify a valid page number."},
status=status.HTTP_400_BAD_REQUEST)
@swagger_auto_schema(
methods=['GET'],
responses={200: ActivitySetSummarySerializer(many=False)})
@action(detail=True, methods=['get'])
def summary(self, request, pk):
try:
activity_set = self.get_queryset().get(pk=pk)
except ActivitySet.DoesNotExist:
return Response({"error": f"No such set: {pk}"},
status=status.HTTP_404_NOT_FOUND)
summary = activity_set.getSummary()
serializer = ActivitySetSummarySerializer(summary)
data = serializer.data
return Response(data, status=status.HTTP_200_OK)