WIP: Use create mixin from resolwe (cluster speed test)

docs/CHANGELOG.rst

@@ -28,6 +28,7 @@ Fixed
 Added
 -----
 - Allow overriding docker image prefix via environment variable
+- Allow staff users to create new ``Variant`` objects through the API endpoint
 
 Changed
 -------

resolwe_bio/variants/serializers.py

@@ -27,6 +27,7 @@ class Meta:
         """Serializer configuration."""
 
         model = Variant
+        optional_fields = ["annotation"]
         fields = [
             "id",
             "species",
@@ -37,6 +38,7 @@ class Meta:
             "alternative",
             "annotation",
         ]
+        extra_kwargs = {"annotation": {"required": False}}
 
 
 class VariantTranscriptSerializer(SelectiveFieldMixin, serializers.ModelSerializer):

resolwe_bio/variants/tests/test_variant.py

@@ -562,9 +562,54 @@ def test_add_variant_annotations(self):
 
 class VariantTest(PrepareDataMixin, TestCase):
     def setUp(self) -> None:
-        self.view = VariantViewSet.as_view({"get": "list"})
+        self.view = VariantViewSet.as_view({"get": "list", "post": "create"})
         return super().setUp()
 
+    def test_create(self):
+        """Test the Variant creation.
+
+        Only users with staff status are allowed to create Variant objects.
+        """
+        variant_data = {
+            "species": "Homo Sapiens",
+            "genome_assembly": "test_create",
+            "chromosome": "CHR_test_create",
+            "position": 1,
+            "reference": "test_create",
+            "alternative": "alt_test_create",
+        }
+
+        # Test creation as unauthenticated user.
+        request = APIRequestFactory().post("/variant", variant_data, format="json")
+        response = self.view(request)
+        self.assertContains(
+            response,
+            "Authentication credentials were not provided.",
+            status_code=status.HTTP_403_FORBIDDEN,
+        )
+
+        # Test creation as non-staff user.
+        request = APIRequestFactory().post("/variant", variant_data, format="json")
+        force_authenticate(request, self.contributor)
+        response = self.view(request)
+        self.assertContains(
+            response,
+            "You do not have permission to perform this action.",
+            status_code=status.HTTP_403_FORBIDDEN,
+        )
+
+        # Test creation as staff user.
+        self.contributor.is_staff = True
+        self.contributor.save(update_fields=["is_staff"])
+        request = APIRequestFactory().post("/variant", variant_data, format="json")
+        force_authenticate(request, self.contributor)
+        response = self.view(request)
+        self.assertEqual(response.status_code, status.HTTP_201_CREATED)
+        # Check that the created object exists.
+        Variant.objects.get(**response.data)
+        self.contributor.is_staff = False
+        self.contributor.save(update_fields=["is_staff"])
+
     def test_filter(self):
         """Test the Variant filter."""
         request = APIRequestFactory().get("/variant")

resolwe_bio/variants/views.py

@@ -9,10 +9,6 @@
 import logging
 
 import django_filters as filters
-from rest_framework import mixins, viewsets
-
-from resolwe.flow.filters import OrderingFilter
-
 from resolwe_bio.variants.filters import (
     VariantAnnotationFilter,
     VariantCallFilter,
@@ -25,18 +21,26 @@
     VariantExperimentSerializer,
     VariantSerializer,
 )
+from rest_framework import mixins, viewsets
+
+from resolwe.flow.filters import OrderingFilter
+from resolwe.flow.views.mixins import ResolweCreateModelMixin
+from resolwe.flow.views.utils import IsStaffOrReadOnly
 
 from .models import Variant, VariantAnnotation, VariantCall, VariantExperiment
 
 logger = logging.getLogger(__name__)
 
 
-class VariantViewSet(mixins.ListModelMixin, viewsets.GenericViewSet):
+class VariantViewSet(
+    mixins.ListModelMixin, ResolweCreateModelMixin, viewsets.GenericViewSet
+):
     """Variant endpoint."""
 
     queryset = Variant.objects.all()
     serializer_class = VariantSerializer
     filter_backends = [filters.rest_framework.DjangoFilterBackend, OrderingFilter]
+    permission_classes = (IsStaffOrReadOnly,)
 
     filterset_class = VariantFilter
     ordering_fields = ("species", "genome_assembly", "position", "chromosome")