Add filtering Variant by VariantCall and VariantExperiment

docs/CHANGELOG.rst

@@ -13,6 +13,7 @@ Unreleased
 
 Added
 -----
+- Add filtering ``Variant`` by ``VariantExperiment`` and ``VariantCall``
 
 Changed
 -------

docs/conf.py

@@ -14,9 +14,9 @@
     INSTALLED_APPS=(
         "django.contrib.auth",
         "django.contrib.contenttypes",
-        "resolwe.observers",
         "resolwe.permissions",
         "resolwe.flow",
+        "resolwe.observers",
         "resolwe.storage",
         "resolwe_bio",
     ),

resolwe_bio/variants/filters.py

@@ -52,10 +52,12 @@ class Meta:
             "annotation__dbsnp_id": TEXT_LOOKUPS,
             "annotation__clinvar_id": TEXT_LOOKUPS,
             "annotation__data": RELATED_LOOKUPS,
+            "variant_calls": RELATED_LOOKUPS,
             "variant_calls__quality": NUMBER_LOOKUPS,
             "variant_calls__depth": NUMBER_LOOKUPS,
             "variant_calls__sample__slug": TEXT_LOOKUPS,
             "variant_calls__sample": RELATED_LOOKUPS,
+            "variant_calls__experiment": RELATED_LOOKUPS,
             "variant_calls__filter": TEXT_LOOKUPS,
             "variant_calls__genotype": TEXT_LOOKUPS,
             "variant_calls__genotype_quality": NUMBER_LOOKUPS,
@@ -112,7 +114,7 @@ class Meta:
             "variant__position": NUMBER_LOOKUPS,
             "variant__reference": TEXT_LOOKUPS,
             "variant__alternative": TEXT_LOOKUPS,
-            "experiment__id": NUMBER_LOOKUPS,
+            "experiment": RELATED_LOOKUPS,
             "quality": NUMBER_LOOKUPS,
             "depth": NUMBER_LOOKUPS,
             "filter": TEXT_LOOKUPS,

resolwe_bio/variants/tests/test_variant.py

@@ -799,6 +799,7 @@ def test_filter(self):
             status_code=status.HTTP_400_BAD_REQUEST,
         )
 
+        # Filter by sample.
         request = APIRequestFactory().get(
             "/variant", {"variant_calls__sample__in": [self.sample.pk]}
         )
@@ -826,29 +827,47 @@ def test_filter(self):
         self.assertEqual(response.status_code, status.HTTP_200_OK)
         self.assertCountEqual(response.data, expected)
 
+        # Filter by variant call
+        request = APIRequestFactory().get(
+            "/variant", {"variant_calls": self.calls[0].pk}
+        )
+        response = self.view(request)
+        expected = VariantSerializer(self.variants[:1], many=True).data
+        self.assertEqual(response.status_code, status.HTTP_200_OK)
+        self.assertCountEqual(response.data, expected)
+
+        # Filter by experiment
+        request = APIRequestFactory().get(
+            "/variant", {"variant_calls__experiment": self.experiments[0].pk}
+        )
+        response = self.view(request)
+        expected = VariantSerializer(self.variants[:1], many=True).data
+        self.assertEqual(response.status_code, status.HTTP_200_OK)
+        self.assertCountEqual(response.data, expected)
+
     def test_filter_sample_by_variant(self):
         client = APIClient()
         path = reverse("resolwebio-api:entity-list")
 
         # Anonymous user, no perms.
         response = response = client.get(
-            path, {"variant_calls__variant": self.calls[0].pk}
+            path, {"variant_calls__variant": self.variants[0].pk}
         )
         self.assertEqual(response.status_code, status.HTTP_200_OK)
         self.assertEqual(response.data, [])
 
         # Contributor, no perms.
         client.force_authenticate(user=self.contributor)
         response = response = client.get(
-            path, {"variant_calls__variant": self.calls[0].pk}
+            path, {"variant_calls__variant": self.variants[0].pk}
         )
         self.assertEqual(response.status_code, status.HTTP_200_OK)
         self.assertEqual(response.data, [])
 
         # Permission granted.
         self.sample.set_permission(Permission.VIEW, self.contributor)
         response = response = client.get(
-            path, {"variant_calls__variant": self.calls[0].pk}
+            path, {"variant_calls__variant": self.variants[0].pk}
         )
         self.assertEqual(response.status_code, status.HTTP_200_OK)
         response.data[0].pop("current_user_permissions")
@@ -1225,7 +1244,7 @@ def test_filter(self):
 
         # Filter by experiment id.
         request = APIRequestFactory().get(
-            "/variantcall", {"experiment__id": self.experiments[0].id}
+            "/variantcall", {"experiment": self.experiments[0].id}
         )
         force_authenticate(request, self.contributor)
         expected = VariantCallSerializer(self.calls[:1], many=True).data