Merge pull request #402 from bento-platform/features/beacon-public-co…

…nfig-search

Beacon search endpoint

chord_metadata_service/patients/api_views.py

@@ -213,3 +213,71 @@ def get(self, request, *args, **kwargs):
                 "experiment_type": experiment_types
             }
         })
+
+
+class BeaconListIndividuals(APIView):
+    """
+    View to return lists of individuals filtered using search terms from katsu's config.json.
+    Uncensored equivalent of PublicListIndividuals.
+    """
+    def filter_queryset(self, queryset):
+        # Check query parameters validity
+        qp = self.request.query_params
+        if len(qp) > settings.CONFIG_PUBLIC["rules"]["max_query_parameters"]:
+            raise ValidationError(f"Wrong number of fields: {len(qp)}")
+
+        search_conf = settings.CONFIG_PUBLIC["search"]
+        field_conf = settings.CONFIG_PUBLIC["fields"]
+        queryable_fields = {
+            f: field_conf[f] for section in search_conf for f in section["fields"]
+        }
+
+        for field, value in qp.items():
+            if field not in queryable_fields:
+                raise ValidationError(f"Unsupported field used in query: {field}")
+
+            field_props = queryable_fields[field]
+            options = get_field_options(field_props)
+            if value not in options \
+                    and not (
+                        # case-insensitive search on categories
+                        field_props["datatype"] == "string"
+                        and value.lower() in [o.lower() for o in options]
+                    ) \
+                    and not (
+                        # no restriction when enum is not set for categories
+                        field_props["datatype"] == "string"
+                        and field_props["config"]["enum"] is None
+                    ):
+                raise ValidationError(f"Invalid value used in query: {value}")
+
+            # recursion
+            queryset = filter_queryset_field_value(queryset, field_props, value)
+
+        return queryset
+
+    def get(self, request, *args, **kwargs):
+        if not settings.CONFIG_PUBLIC:
+            return Response(settings.NO_PUBLIC_DATA_AVAILABLE, status=404)
+
+        base_qs = Individual.objects.all()
+        try:
+            filtered_qs = self.filter_queryset(base_qs)
+        except ValidationError as e:
+            return Response(errors.bad_request_error(
+                *(e.error_list if hasattr(e, "error_list") else e.error_dict.items())), status=400)
+
+        tissues_count, sampled_tissues = biosample_tissue_stats(filtered_qs)
+        experiments_count, experiment_types = experiment_type_stats(filtered_qs)
+
+        return Response({
+            "matches": filtered_qs.values_list("id", flat=True),
+            "biosamples": {
+                "count": tissues_count,
+                "sampled_tissue": sampled_tissues
+            },
+            "experiments": {
+                "count": experiments_count,
+                "experiment_type": experiment_types
+            }
+        })

chord_metadata_service/patients/tests/test_api.py

@@ -650,3 +650,43 @@ def test_public_filtering_age_range_min_and_max_no_config(self):
         self.assertIsInstance(response_obj, dict)
         self.assertIsInstance(response_obj, dict)
         self.assertEqual(response_obj, settings.NO_PUBLIC_DATA_AVAILABLE)
+
+
+class BeaconSearchTest(APITestCase):
+
+    random_range = 20
+
+    def setUp(self):
+        individuals = [c.generate_valid_individual() for _ in range(self.random_range)]
+        for individual in individuals:
+            Individual.objects.create(**individual)
+
+    # test beacon formatted response
+    @override_settings(CONFIG_PUBLIC=CONFIG_PUBLIC_TEST)
+    def test_beacon_search_response(self):
+        response = self.client.get('/api/beacon_search?sex=MALE')
+        male_count = Individual.objects.filter(sex="MALE").count()
+        self.assertEqual(response.status_code, status.HTTP_200_OK)
+        response_obj = response.json()
+        self.assertEqual(len(response_obj["matches"]), male_count)
+
+    @override_settings(CONFIG_PUBLIC={})
+    def test_beacon_search_response_no_config(self):
+        # test when config is not provided, returns NOT FOUND
+        response = self.client.get('/api/beacon_search?sex=MALE')
+        self.assertEqual(response.status_code, status.HTTP_404_NOT_FOUND)
+
+    @override_settings(CONFIG_PUBLIC=CONFIG_PUBLIC_TEST)
+    def test_beacon_search_response_invalid_search_key(self):
+        response = self.client.get('/api/beacon_search?birdwatcher=yes')
+        self.assertEqual(response.status_code, status.HTTP_400_BAD_REQUEST)
+
+    @override_settings(CONFIG_PUBLIC=CONFIG_PUBLIC_TEST)
+    def test_beacon_search_response_invalid_search_value(self):
+        response = self.client.get('/api/beacon_search?smoking=on_Sundays')
+        self.assertEqual(response.status_code, status.HTTP_400_BAD_REQUEST)
+
+    @override_settings(CONFIG_PUBLIC=CONFIG_PUBLIC_TEST)
+    def test_beacon_search_too_many_params(self):
+        response = self.client.get('/api/beacon_search?sex=MALE&smoking=Non-smoker&death_dc=Deceased')
+        self.assertEqual(response.status_code, status.HTTP_400_BAD_REQUEST)

chord_metadata_service/restapi/urls.py

@@ -102,4 +102,7 @@
     path('public_search_fields', public_search_fields, name='public-search-fields',),
     path('public_overview', public_overview, name='public-overview',),
     path('public_dataset', public_dataset, name='public-dataset'),
+
+    # uncensored endpoint for beacon search using fields from config.json
+    path('beacon_search', individual_views.BeaconListIndividuals.as_view(), name='beacon-search'),
 ]