chore: remove ARGO code

chord_metadata_service/patients/api_views.py

@@ -43,7 +43,6 @@
     FHIRRenderer,
     PhenopacketsRenderer,
     IndividualCSVRenderer,
-    ARGORenderer,
     IndividualBentoSearchRenderer,
 )
 from chord_metadata_service.restapi.constants import MODEL_ID_PATTERN
@@ -69,9 +68,13 @@ class IndividualViewSet(viewsets.ModelViewSet):
     """
     serializer_class = IndividualSerializer
     pagination_class = LargeResultsSetPagination
-    renderer_classes = (*api_settings.DEFAULT_RENDERER_CLASSES, FHIRRenderer,
-                        PhenopacketsRenderer, IndividualCSVRenderer, ARGORenderer,
-                        IndividualBentoSearchRenderer)
+    renderer_classes = (
+        *api_settings.DEFAULT_RENDERER_CLASSES,
+        FHIRRenderer,
+        PhenopacketsRenderer,
+        IndividualCSVRenderer,
+        IndividualBentoSearchRenderer,
+    )
     filter_backends = [DjangoFilterBackend, filters.OrderingFilter]
     filterset_class = IndividualFilter
     ordering_fields = ["id"]
@@ -151,9 +154,13 @@ class IndividualBatchViewSet(BatchViewSet):
 
     serializer_class = IndividualSerializer
     pagination_class = BatchResultsSetPagination
-    renderer_classes = (*api_settings.DEFAULT_RENDERER_CLASSES, FHIRRenderer,
-                        PhenopacketsRenderer, IndividualCSVRenderer, ARGORenderer,
-                        IndividualBentoSearchRenderer)
+    renderer_classes = (
+        *api_settings.DEFAULT_RENDERER_CLASSES,
+        FHIRRenderer,
+        PhenopacketsRenderer,
+        IndividualCSVRenderer,
+        IndividualBentoSearchRenderer,
+    )
     # Override to infer the renderer based on a `format` argument from the POST request body
     content_negotiation_class = FormatInPostContentNegotiation
 

chord_metadata_service/patients/serializers.py

@@ -1,9 +1,12 @@
 from chord_metadata_service.phenopackets.serializers import BiosampleSerializer, SimplePhenopacketSerializer
 from chord_metadata_service.restapi.serializers import GenericSerializer
 from chord_metadata_service.restapi.fhir_utils import fhir_patient
-from chord_metadata_service.restapi.argo_utils import argo_donor
 from .models import Individual
 
+__all__ = [
+    "IndividualSerializer",
+]
+
 
 class IndividualSerializer(GenericSerializer):
     biosamples = BiosampleSerializer(read_only=True, many=True, exclude_when_nested=['individual'])
@@ -15,6 +18,3 @@ class Meta:
         # meta info for converting to FHIR
         fhir_datatype_plural = 'patients'
         class_converter = fhir_patient
-        # meta info for converting to ARGO
-        argo_profile_plural = 'donors'
-        argo_converter = argo_donor

chord_metadata_service/phenopackets/api_views.py

@@ -5,9 +5,12 @@
 from rest_framework.permissions import AllowAny
 from rest_framework.response import Response
 
-from chord_metadata_service.restapi.api_renderers import (PhenopacketsRenderer, FHIRRenderer,
-                                                          BiosamplesCSVRenderer, ARGORenderer,
-                                                          IndividualBentoSearchRenderer)
+from chord_metadata_service.restapi.api_renderers import (
+    PhenopacketsRenderer,
+    FHIRRenderer,
+    BiosamplesCSVRenderer,
+    IndividualBentoSearchRenderer,
+)
 from chord_metadata_service.restapi.constants import MODEL_ID_PATTERN
 from chord_metadata_service.restapi.pagination import LargeResultsSetPagination, BatchResultsSetPagination
 from chord_metadata_service.restapi.negociation import FormatInPostContentNegotiation
@@ -109,9 +112,13 @@ class BiosampleBatchViewSet(ExtendedPhenopacketsModelViewSet):
     filter_backends = [DjangoFilterBackend]
     filterset_class = f.BiosampleFilter
     pagination_class = BatchResultsSetPagination
-    renderer_classes = (*api_settings.DEFAULT_RENDERER_CLASSES, FHIRRenderer,
-                        PhenopacketsRenderer, BiosamplesCSVRenderer, ARGORenderer,
-                        IndividualBentoSearchRenderer)
+    renderer_classes = (
+        *api_settings.DEFAULT_RENDERER_CLASSES,
+        FHIRRenderer,
+        PhenopacketsRenderer,
+        BiosamplesCSVRenderer,
+        IndividualBentoSearchRenderer,
+    )
     content_negotiation_class = FormatInPostContentNegotiation
 
     def _get_filtered_queryset(self, ids_list=None):

chord_metadata_service/restapi/api_renderers.py

@@ -12,6 +12,18 @@
 from chord_metadata_service.phenopackets.utils import parse_onset
 from .jsonld_utils import dataset_to_jsonld
 
+__all__ = [
+    "FHIRRenderer",
+    "PhenopacketsRenderer",
+    "JSONLDDatasetRenderer",
+    "RDFDatasetRenderer",
+    "render_age",
+    "IndividualCSVRenderer",
+    "BiosamplesCSVRenderer",
+    "ExperimentCSVRenderer",
+    "IndividualBentoSearchRenderer",
+]
+
 OUTPUT_FORMAT_BENTO_SEARCH_RESULT = "bento_search_result"
 
 register('json-ld', Serializer, 'rdflib_jsonld.serializer', 'JsonLDSerializer')
@@ -45,26 +57,6 @@ def render(self, data, media_type=None, renderer_context=None):
         return super(FHIRRenderer, self).render(final_data, media_type, renderer_context)
 
 
-class ARGORenderer(JSONRenderer):
-    media_type = 'application/json'
-    format = 'argo'
-
-    def render(self, data, media_type=None, renderer_context=None):
-        argo_profile_plural = getattr(
-            renderer_context.get('view').get_serializer().Meta,
-            'argo_profile_plural', 'objects'
-        )
-        class_converter = getattr(
-            renderer_context.get('view').get_serializer().Meta,
-            'argo_converter', 'objects'
-        )
-        if 'results' in data:
-            final_data = {argo_profile_plural: [class_converter(item) for item in data['results']]}
-        else:
-            final_data = class_converter(data)
-        return super(ARGORenderer, self).render(final_data, media_type, renderer_context)
-
-
 class PhenopacketsRenderer(CamelCaseJSONRenderer):
     media_type = 'application/json'
     format = 'phenopackets'