chore!: remove to-be-unused /overview endpoint

chord_metadata_service/restapi/api_views.py

@@ -2,19 +2,16 @@
 
 from adrf.decorators import api_view
 from bento_lib.responses import errors
-from django.db.models import QuerySet
-from drf_spectacular.utils import extend_schema, inline_serializer
-from rest_framework import serializers, status
+from rest_framework import status
 from rest_framework.decorators import permission_classes
 from rest_framework.request import Request as DrfRequest
 from rest_framework.response import Response
 
 from chord_metadata_service.authz.helpers import get_data_type_query_permissions
 from chord_metadata_service.authz.middleware import authz_middleware
 from chord_metadata_service.authz.permissions import BentoAllowAny
-from chord_metadata_service.authz.types import DataTypeDiscoveryPermissions
 from chord_metadata_service.chord.data_types import DATA_TYPE_PHENOPACKET, DATA_TYPE_EXPERIMENT
-from chord_metadata_service.discovery.scope import ValidatedDiscoveryScope, get_request_discovery_scope
+from chord_metadata_service.discovery.scope import get_request_discovery_scope
 from chord_metadata_service.experiments import models as experiments_models
 from chord_metadata_service.experiments.summaries import dt_experiment_summary
 from chord_metadata_service.metadata.service_info import get_service_info
@@ -37,54 +34,6 @@ async def service_info(_request: DrfRequest):
     return Response(await get_service_info())
 
 
-async def build_overview_response(
-    scope: ValidatedDiscoveryScope,
-    dt_permissions: DataTypeDiscoveryPermissions,
-    phenopackets: QuerySet | None = None,
-    experiments: QuerySet | None = None,
-) -> Response:
-    phenopackets_summary, experiments_summary = await asyncio.gather(
-        dt_phenopacket_summary(scope, dt_permissions[DATA_TYPE_PHENOPACKET], phenopackets),
-        dt_experiment_summary(scope, dt_permissions[DATA_TYPE_EXPERIMENT], experiments),
-    )
-
-    return Response({
-        DATA_TYPE_PHENOPACKET: phenopackets_summary,
-        DATA_TYPE_EXPERIMENT: experiments_summary,
-    })
-
-
-@extend_schema(
-    description="Overview of all Phenopackets in the database",
-    responses={
-        200: inline_serializer(
-            name='overview_response',
-            fields={
-                'phenopackets': serializers.IntegerField(),
-                'data_type_specific': serializers.JSONField(),
-            }
-        )
-    }
-)
-@api_view(["GET"])
-@permission_classes([BentoAllowAny])
-async def overview(request: DrfRequest):
-    """
-    get:
-    Overview of all Phenopackets and experiments in the database - private endpoint
-    """
-
-    # TODO: permissions based on project - this endpoint should be scrapped / completely rethought
-    # use node level discovery config for private overview
-    discovery_scope = ValidatedDiscoveryScope(project=None, dataset=None)
-
-    dt_permissions = await get_data_type_query_permissions(
-        request, [DATA_TYPE_PHENOPACKET, DATA_TYPE_EXPERIMENT], discovery_scope.as_authz_resource()
-    )
-
-    return await build_overview_response(discovery_scope, dt_permissions)
-
-
 @api_view(["GET"])
 @permission_classes([BentoAllowAny])
 def extra_properties_schema_types(_request: DrfRequest):
@@ -132,9 +81,12 @@ async def search_overview(request: DrfRequest):
         # If we don't have query:data on phenopackets, we cannot request a search overview
         return Response(errors.forbidden_error("Forbidden"), status=status.HTTP_403_FORBIDDEN)
 
-    return await build_overview_response(
-        scope,
-        dt_permissions,
-        phenopackets=phenopackets,
-        experiments=experiments,
+    phenopackets_summary, experiments_summary = await asyncio.gather(
+        dt_phenopacket_summary(scope, dt_permissions[DATA_TYPE_PHENOPACKET], phenopackets),
+        dt_experiment_summary(scope, dt_permissions[DATA_TYPE_EXPERIMENT], experiments),
     )
+
+    return Response({
+        DATA_TYPE_PHENOPACKET: phenopackets_summary,
+        DATA_TYPE_EXPERIMENT: experiments_summary,
+    })

chord_metadata_service/restapi/tests/test_api.py

@@ -73,46 +73,6 @@ def setUp(self) -> None:
         self.experiment_result = exp_m.ExperimentResult.objects.create(**exp_c.valid_experiment_result())
         self.experiment.experiment_results.set([self.experiment_result])
 
-    def test_overview(self):
-        response = self.dt_authz_full_get('/api/overview')
-        response_obj = response.json()
-        self.assertEqual(response.status_code, status.HTTP_200_OK)
-        self.assertIsInstance(response_obj, dict)
-        # phenopackets
-        phenopacket_res = response_obj['phenopacket']
-        self.assertEqual(phenopacket_res['count'], 2)
-        self.assertEqual(phenopacket_res['data_type_specific']['individuals']['count'], 2)
-        self.assertIsInstance(phenopacket_res['data_type_specific']['individuals']['age'], dict)
-        self.assertEqual(
-            phenopacket_res['data_type_specific']['individuals']['age'],
-            {**{'40': 1, '30': 1}, **phenopacket_res['data_type_specific']['individuals']['age']})
-        self.assertEqual(phenopacket_res['data_type_specific']['biosamples']['count'], 2)
-        self.assertEqual(phenopacket_res['data_type_specific']['phenotypic_features']['count'], 1)
-        self.assertEqual(phenopacket_res['data_type_specific']['diseases']['count'], 1)
-        # experiments
-        experiment_res = response_obj['experiment']
-        self.assertEqual(experiment_res['count'], 2)
-        self.assertEqual(
-            experiment_res['data_type_specific']['experiments']['study_type']['Whole genome Sequencing'], 2)
-        self.assertEqual(
-            experiment_res['data_type_specific']['experiments']['experiment_type']['DNA Methylation'], 2
-        )
-        self.assertEqual(experiment_res['data_type_specific']['experiments']['molecule']['total RNA'], 2)
-        self.assertEqual(experiment_res['data_type_specific']['experiments']['library_strategy']['Bisulfite-Seq'], 2)
-        self.assertEqual(experiment_res['data_type_specific']['experiments']['library_source']['Genomic'], 2)
-        self.assertEqual(experiment_res['data_type_specific']['experiments']['library_selection']['PCR'], 2)
-        self.assertEqual(experiment_res['data_type_specific']['experiments']['library_layout']['Single'], 2)
-        self.assertEqual(experiment_res['data_type_specific']['experiments']['extraction_protocol']['NGS'], 2)
-        self.assertEqual(experiment_res['data_type_specific']['experiment_results']['count'], 1)
-        self.assertEqual(experiment_res['data_type_specific']['experiment_results']['file_format']['VCF'], 1)
-        self.assertEqual(
-            experiment_res['data_type_specific']['experiment_results']['data_output_type']['Derived data'], 1
-        )
-        self.assertEqual(experiment_res['data_type_specific']['experiment_results']['usage']['download'], 1)
-        self.assertEqual(experiment_res['data_type_specific']['instruments']['count'], 1)
-        self.assertEqual(experiment_res['data_type_specific']['instruments']['platform']['Illumina'], 2)
-        self.assertEqual(experiment_res['data_type_specific']['instruments']['model']['Illumina HiSeq 4000'], 2)
-
     def test_search_overview(self):
         payload = json.dumps({'id': [ph_c.VALID_INDIVIDUAL_1['id']]})
         response = self.dt_authz_full_post(reverse('search-overview'), data=payload, content_type='application/json')

chord_metadata_service/restapi/urls.py

@@ -12,7 +12,7 @@
 from chord_metadata_service.patients import api_views as individual_views
 from chord_metadata_service.phenopackets import api_views as phenopacket_views
 from chord_metadata_service.resources import api_views as resources_views
-from chord_metadata_service.restapi.api_views import overview, search_overview, extra_properties_schema_types
+from chord_metadata_service.restapi.api_views import search_overview, extra_properties_schema_types
 from chord_metadata_service.restapi.routers import BatchListRouter
 
 __all__ = ["router", "batch_router", "urlpatterns"]
@@ -61,7 +61,6 @@
     path('extra_properties_schema_types', extra_properties_schema_types, name="extra-properties-schema-types"),
 
     # overviews (statistics)
-    path('overview', overview, name="overview"),
     path('search_overview', search_overview, name="search-overview"),
 
     # public endpoints (no confidential information leak)