Remove protocol resource which is not used by client.

refinery/config/urls.py

@@ -20,8 +20,6 @@
 from core.views import CustomRegistrationView
 from data_set_manager.api import (AttributeResource,
                                   InvestigationResource, NodeResource,
-                                  ProtocolReferenceParameterResource,
-                                  ProtocolReferenceResource, ProtocolResource,
                                   PublicationResource, StudyResource)
 from data_set_manager.urls import data_set_manager_router
 from file_store.urls import file_store_router
@@ -43,9 +41,6 @@
 v1_api.register(UserAuthenticationResource())
 v1_api.register(InvitationResource())
 v1_api.register(InvestigationResource())
-v1_api.register(ProtocolResource())
-v1_api.register(ProtocolReferenceResource())
-v1_api.register(ProtocolReferenceParameterResource())
 v1_api.register(PublicationResource())
 v1_api.register(AttributeResource())
 v1_api.register(ExtendedGroupResource())

refinery/data_set_manager/api.py

@@ -16,9 +16,7 @@
 
 from file_store.models import FileStoreItem
 
-from .models import (Attribute, Investigation, Node, Protocol,
-                     ProtocolReference, ProtocolReferenceParameter,
-                     Publication, Study)
+from .models import Attribute, Investigation, Node, Publication, Study
 
 logger = logging.getLogger(__name__)
 
@@ -124,75 +122,6 @@ class Meta:
         }
 
 
-class ProtocolResource(ModelResource):
-    # Leads to to many "duplicated" references, i.e. many samples have the same
-    # protocol parameters but are regarded unique.
-    # references = fields.ToManyField(
-    #     'data_set_manager.api.ProtocolReferenceResource',
-    #     attribute=lambda bundle: (
-    #         ProtocolReference.objects.filter(
-    #             protocol=bundle.obj
-    #         ).distinct()
-    #     ),
-    #     full=True,
-    #     null=True
-    # )
-
-    class Meta:
-        queryset = Protocol.objects.all()
-        detail_uri_name = 'uuid'
-        allowed_methods = ['get']
-        resource_name = 'protocols'
-        filtering = {
-            'uuid': ALL
-        }
-        fields = [
-            'description',
-            'name'
-        ]
-
-
-class ProtocolReferenceResource(ModelResource):
-    parameters = fields.ToManyField(
-        'data_set_manager.api.ProtocolReferenceParameterResource',
-        attribute=lambda bundle: (
-            ProtocolReferenceParameter.objects.filter(
-                protocol_reference=bundle.obj
-            ).exclude(value__isnull=True).exclude(value__exact='').distinct()
-        ),
-        full=True,
-        null=True
-    )
-
-    class Meta:
-        queryset = ProtocolReference.objects.all()
-        allowed_methods = ['get']
-        resource_name = 'protocol-references'
-        fields = [
-            'id',
-            'parameters'
-        ]
-        include_resource_uri = False
-
-
-class ProtocolReferenceParameterResource(ModelResource):
-    class Meta:
-        queryset = (ProtocolReferenceParameter
-                    .objects
-                    .exclude(value__isnull=True)
-                    .exclude(value__exact=''))
-        allowed_methods = [
-            'get'
-        ]
-        resource_name = 'protocol-reference-parameters'
-        fields = [
-            'name',
-            'value',
-            'value_unit'
-        ]
-        include_resource_uri = False
-
-
 class PublicationResource(ModelResource):
     class Meta:
         queryset = Publication.objects.all()
@@ -205,12 +134,6 @@ class StudyResource(ModelResource):
         attribute='investigation__uuid',
         use_in='all'
     )
-    protocols = fields.ToManyField(
-        'data_set_manager.api.ProtocolResource',
-        'protocol_set',
-        full=True,
-        null=True
-    )
     publications = fields.ToManyField(
         'data_set_manager.api.PublicationResource',
         'publication_set',