Jkmarx/move node related to data set manager (#2911)

* Move node related to data_set_manager app

* Move node v1 api to data_set_manager.

* Update api v1 url dependency.

* Move node v1 api tests to correct directory.

refinery/config/urls.py

@@ -11,15 +11,15 @@
 from config.utils import RouterCombiner
 from core.api import (AnalysisResource, DataSetResource, ExtendedGroupResource,
                       GroupManagementResource, InvitationResource,
-                      NodeResource, ProjectResource, StatisticsResource,
+                      ProjectResource, StatisticsResource,
                       UserAuthenticationResource, UserProfileResource,
                       WorkflowResource)
 from core.forms import RegistrationFormWithCustomFields
 from core.models import AuthenticationFormUsernameOrEmail
 from core.urls import core_router
 from core.views import CustomRegistrationView
 from data_set_manager.api import (AssayResource, AttributeResource,
-                                  InvestigationResource,
+                                  InvestigationResource, NodeResource,
                                   ProtocolReferenceParameterResource,
                                   ProtocolReferenceResource, ProtocolResource,
                                   PublicationResource, StudyResource)

refinery/core/api.py

@@ -40,7 +40,7 @@
 
 from data_set_manager.api import (AssayResource, InvestigationResource,
                                   StudyResource)
-from data_set_manager.models import Attribute, Node, Study
+from data_set_manager.models import Study
 from file_store.models import FileStoreItem
 from .models import (Analysis, DataSet, ExtendedGroup, GroupManagement,
                      Invitation, Project, ResourceStatistics, Tutorials,
@@ -1056,71 +1056,6 @@ def alter_list_data_to_serialize(self, request, data):
         return data
 
 
-class NodeResource(ModelResource):
-    parents = fields.ToManyField('core.api.NodeResource', 'parents')
-    children = fields.ToManyField('core.api.NodeResource', 'children')
-    study = fields.ToOneField('data_set_manager.api.StudyResource', 'study')
-    assay = fields.ToOneField('data_set_manager.api.AssayResource', 'assay',
-                              null=True)
-    attributes = fields.ToManyField(
-        'data_set_manager.api.AttributeResource',
-        attribute=lambda bundle: (
-            Attribute.objects
-            .exclude(value__isnull=True)
-            .exclude(value__exact='')
-            .filter(node=bundle.obj, subtype='organism')
-        ), use_in='all', full=True, null=True
-    )
-
-    class Meta:
-        queryset = Node.objects.all()
-        resource_name = 'node'
-        detail_uri_name = 'uuid'  # for using UUIDs instead of pk in URIs
-        # required for public data set access by anonymous users
-        authentication = Authentication()
-        authorization = Authorization()
-        allowed_methods = ['get']
-        fields = ['analysis_uuid', 'assay', 'attributes', 'children',
-                  'file_url', 'file_uuid', 'name', 'parents', 'study',
-                  'subanalysis', 'type', 'uuid']
-        filtering = {
-            'uuid': ALL,
-            'study': ALL_WITH_RELATIONS,
-            'assay': ALL_WITH_RELATIONS,
-            'file_uuid': ALL,
-            'type': ALL
-        }
-        limit = 0
-        max_limit = 0
-
-    def prepend_urls(self):
-        return [
-            url((r"^(?P<resource_name>%s)/(?P<uuid>" + UUID_RE + r")/$") %
-                self._meta.resource_name,
-                self.wrap_view('dispatch_detail'),
-                name="api_dispatch_detail"),
-        ]
-
-    def dehydrate(self, bundle):
-        # return download URL of file if a file is associated with the node
-        try:
-            file_item = FileStoreItem.objects.get(uuid=bundle.obj.file_uuid)
-        except AttributeError:
-            logger.warning("No UUID provided")
-            bundle.data['file_url'] = None
-            bundle.data['file_import_status'] = None
-        except FileStoreItem.DoesNotExist:
-            logger.warning(
-                "Unable to find file store item with UUID '%s'",
-                bundle.obj.file_uuid)
-            bundle.data['file_url'] = None
-            bundle.data['file_import_status'] = None
-        else:
-            bundle.data['file_url'] = file_item.get_datafile_url()
-            bundle.data['file_import_status'] = file_item.get_import_status()
-        return bundle
-
-
 class StatisticsResource(Resource):
     user = fields.IntegerField(attribute='user')
     group = fields.IntegerField(attribute='group')

refinery/core/serializers.py

@@ -4,8 +4,6 @@
 from rest_framework import serializers
 from rest_framework.validators import UniqueValidator
 
-from data_set_manager.models import Node
-
 from .models import DataSet, Event, User, UserProfile, Workflow
 
 logger = logging.getLogger(__name__)
@@ -115,16 +113,6 @@ class Meta:
         model = Workflow
 
 
-class NodeSerializer(serializers.ModelSerializer):
-    file_uuid = serializers.CharField(max_length=36,
-                                      required=False,
-                                      allow_null=True)
-
-    class Meta:
-        model = Node
-        fields = ('uuid', 'file_uuid')
-
-
 class EventSerializer(serializers.ModelSerializer):
     data_set = DataSetSerializer()
     user = UserSerializer()

refinery/core/test_api.py

@@ -11,8 +11,10 @@
 from tastypie.exceptions import NotFound
 from tastypie.test import ResourceTestCase
 
+from data_set_manager.api import NodeResource
 from data_set_manager.models import Investigation, Study
-from .api import AnalysisResource, DataSetResource, NodeResource
+
+from .api import AnalysisResource, DataSetResource
 from .models import (Analysis, Node, Project, UserProfile, Workflow,
                      WorkflowEngine)
 

refinery/core/urls.py

@@ -10,8 +10,7 @@
 from rest_framework.routers import DefaultRouter
 
 from .views import (AnalysesViewSet, DataSetsViewSet, EventViewSet,
-                    NodeViewSet, OpenIDToken, UserProfileViewSet,
-                    WorkflowViewSet)
+                    OpenIDToken, UserProfileViewSet, WorkflowViewSet)
 
 urlpatterns = patterns(
     'core.views',
@@ -84,8 +83,6 @@
         DataSetsViewSet.as_view()),
     url(r'^analyses/(?P<uuid>' + UUID_RE + r')/$',
         AnalysesViewSet.as_view()),
-    url(r'^nodes/(?P<uuid>' + UUID_RE + r')/$',
-        NodeViewSet.as_view()),
     url(r'^openid_token/$',
         OpenIDToken.as_view(), name="openid-token")
 ])

refinery/core/views.py

@@ -39,14 +39,11 @@
 from rest_framework.views import APIView
 import xmltodict
 
-from data_set_manager.models import Node
-from file_store.models import FileStoreItem
-
 from .forms import ProjectForm, UserForm, UserProfileForm, WorkflowForm
 from .models import (Analysis, CustomRegistrationProfile, DataSet, Event,
                      ExtendedGroup, Invitation, Ontology, Project,
                      UserProfile, Workflow, WorkflowEngine)
-from .serializers import (DataSetSerializer, EventSerializer, NodeSerializer,
+from .serializers import (DataSetSerializer, EventSerializer,
                           UserProfileSerializer, WorkflowSerializer)
 from .utils import (api_error_response, get_data_sets_annotations,
                     get_resources_for_user)
@@ -698,87 +695,6 @@ def graph(self, request, *args, **kwargs):
         )
 
 
-class NodeViewSet(APIView):
-    """API endpoint that allows Nodes to be viewed".
-     ---
-    #YAML
-
-    PATCH:
-        parameters_strategy:
-        form: replace
-        query: merge
-
-        parameters:
-            - name: uuid
-              description: User profile uuid used as an identifier
-              type: string
-              paramType: path
-              required: true
-            - name: file_uuid
-              description: uuid for file store item
-              type: string
-              paramType: form
-              required: false
-    ...
-    """
-    http_method_names = ['get', 'patch']
-
-    def get_object(self, uuid):
-        try:
-            return Node.objects.get(uuid=uuid)
-        except Node.DoesNotExist as e:
-            logger.error(e)
-            raise Http404
-        except Node.MultipleObjectsReturned as e:
-            logger.error(e)
-            raise APIException("Multiple objects returned.")
-
-    def get(self, request, uuid):
-        node = self.get_object(uuid)
-        data_set = node.study.get_dataset()
-        public_group = ExtendedGroup.objects.public_group()
-
-        if request.user.has_perm('core.read_dataset', data_set) or \
-                'read_dataset' in get_perms(public_group, data_set):
-            serializer = NodeSerializer(node)
-            return Response(serializer.data)
-
-        return Response(uuid, status=status.HTTP_401_UNAUTHORIZED)
-
-    def patch(self, request, uuid):
-        node = self.get_object(uuid)
-        new_file_uuid = request.data.get('file_uuid')
-        data_set = node.study.get_dataset()
-
-        if not data_set.is_clean():
-            return Response(
-                'Files cannot be removed once an analysis or visualization '
-                'has ran on a data set ',
-                status=status.HTTP_400_BAD_REQUEST
-            )
-
-        if data_set.get_owner() == request.user:
-            # to remove the data file, we need to delete it and update index,
-            #  the file store item uuid should remain
-            if new_file_uuid is None:
-                try:
-                    file_store_item = FileStoreItem.objects.get(
-                        uuid=node.file_uuid
-                    )
-                except (FileStoreItem.DoesNotExist,
-                        FileStoreItem.MultipleObjectsReturned) as e:
-                    logger.error(e)
-                else:
-                    file_store_item.delete_datafile()
-
-            node.update_solr_index()
-            return Response(
-                NodeSerializer(node).data, status=status.HTTP_200_OK
-            )
-
-        return Response(uuid, status=status.HTTP_401_UNAUTHORIZED)
-
-
 class EventViewSet(viewsets.ModelViewSet):
     """API endpoint that allows Events to be viewed"""
     queryset = Event.objects.all()

refinery/data_set_manager/api.py

@@ -3,15 +3,25 @@
 
 @author: nils
 '''
+import logging
 
+from django.conf.urls import url
+
+from constants import UUID_RE
 from tastypie import fields
+from tastypie.authentication import Authentication
+from tastypie.authorization import Authorization
 from tastypie.constants import ALL, ALL_WITH_RELATIONS
 from tastypie.resources import ModelResource
 
+from file_store.models import FileStoreItem
+
 from .models import (Assay, Attribute, Investigation, Node, Protocol,
                      ProtocolReference, ProtocolReferenceParameter,
                      Publication, Study)
 
+logger = logging.getLogger(__name__)
+
 
 class AttributeResource(ModelResource):
     node = fields.ForeignKey('core.api.NodeResource', 'node', use_in='all')
@@ -37,6 +47,71 @@ class Meta:
         ]
 
 
+class NodeResource(ModelResource):
+    parents = fields.ToManyField('core.api.NodeResource', 'parents')
+    children = fields.ToManyField('core.api.NodeResource', 'children')
+    study = fields.ToOneField('data_set_manager.api.StudyResource', 'study')
+    assay = fields.ToOneField('data_set_manager.api.AssayResource', 'assay',
+                              null=True)
+    attributes = fields.ToManyField(
+        'data_set_manager.api.AttributeResource',
+        attribute=lambda bundle: (
+            Attribute.objects
+            .exclude(value__isnull=True)
+            .exclude(value__exact='')
+            .filter(node=bundle.obj, subtype='organism')
+        ), use_in='all', full=True, null=True
+    )
+
+    class Meta:
+        queryset = Node.objects.all()
+        resource_name = 'node'
+        detail_uri_name = 'uuid'  # for using UUIDs instead of pk in URIs
+        # required for public data set access by anonymous users
+        authentication = Authentication()
+        authorization = Authorization()
+        allowed_methods = ['get']
+        fields = ['analysis_uuid', 'assay', 'attributes', 'children',
+                  'file_url', 'file_uuid', 'name', 'parents', 'study',
+                  'subanalysis', 'type', 'uuid']
+        filtering = {
+            'uuid': ALL,
+            'study': ALL_WITH_RELATIONS,
+            'assay': ALL_WITH_RELATIONS,
+            'file_uuid': ALL,
+            'type': ALL
+        }
+        limit = 0
+        max_limit = 0
+
+    def prepend_urls(self):
+        return [
+            url((r"^(?P<resource_name>%s)/(?P<uuid>" + UUID_RE + r")/$") %
+                self._meta.resource_name,
+                self.wrap_view('dispatch_detail'),
+                name="api_dispatch_detail"),
+        ]
+
+    def dehydrate(self, bundle):
+        # return download URL of file if a file is associated with the node
+        try:
+            file_item = FileStoreItem.objects.get(uuid=bundle.obj.file_uuid)
+        except AttributeError:
+            logger.warning("No UUID provided")
+            bundle.data['file_url'] = None
+            bundle.data['file_import_status'] = None
+        except FileStoreItem.DoesNotExist:
+            logger.warning(
+                "Unable to find file store item with UUID '%s'",
+                bundle.obj.file_uuid)
+            bundle.data['file_url'] = None
+            bundle.data['file_import_status'] = None
+        else:
+            bundle.data['file_url'] = file_item.get_datafile_url()
+            bundle.data['file_import_status'] = file_item.get_import_status()
+        return bundle
+
+
 class InvestigationResource(ModelResource):
     class Meta:
         queryset = Investigation.objects.all()

refinery/data_set_manager/serializers.py

@@ -1,6 +1,6 @@
 from rest_framework import serializers
 
-from .models import Assay, AttributeOrder
+from .models import Assay, AttributeOrder, Node
 
 
 class AssaySerializer(serializers.ModelSerializer):
@@ -35,3 +35,13 @@ def update(self, instance, validated_data):
                                                 instance.is_active)
         instance.save()
         return instance
+
+
+class NodeSerializer(serializers.ModelSerializer):
+    file_uuid = serializers.CharField(max_length=36,
+                                      required=False,
+                                      allow_null=True)
+
+    class Meta:
+        model = Node
+        fields = ('uuid', 'file_uuid')

refinery/data_set_manager/urls.py

@@ -14,8 +14,9 @@
 from .views import (AddFileToNodeView, Assays, AssaysAttributes,
                     AssaysFiles, CheckDataFilesView,
                     ChunkedFileUploadCompleteView, ChunkedFileUploadView,
-                    DataSetImportView, ImportISATabView, ProcessISATabView,
-                    ProcessMetadataTableView, TakeOwnershipOfPublicDatasetView)
+                    DataSetImportView, ImportISATabView, NodeViewSet,
+                    ProcessISATabView, ProcessMetadataTableView,
+                    TakeOwnershipOfPublicDatasetView)
 
 urlpatterns = patterns(
     'data_set_manager.views',
@@ -56,4 +57,6 @@
         AssaysAttributes.as_view()),
     url(r'^data_set_manager/add-file/$',
         AddFileToNodeView.as_view()),
+    url(r'^nodes/(?P<uuid>' + UUID_RE + r')/$',
+        NodeViewSet.as_view()),
 ])