Jkmarx/remove unused igv stuff (#2844)

* Remove unused igv template.

* Revise node api to remove igv related features.

* Fix typo

* Add get method.

* Add patch.

* Add patch

* Refactor duplicate code to seperate method.

* Add auth.

* Fix node object.

* Remove irrelevant unit tests.

* Fix yaml for swagger.

* Fix spacing.

* Remove datafile and update index.

* Remove unneccessary variable.

* Avoid string conversion.

* Specify None.

* Jkmarx/remove file ui (#2845)

* Add service for removing file.

* Add method to view.

* Seperate the add and remove features.

* Add file name.

* Add remove for owners only.

* Fix download for nonowners.

refinery/core/serializers.py

@@ -1,12 +1,10 @@
 import logging
 
-import celery
 from django.conf import settings
 from rest_framework import serializers
 from rest_framework.validators import UniqueValidator
 
 from data_set_manager.models import Node
-from file_store.models import FileStoreItem
 
 from .models import DataSet, Event, User, UserProfile, Workflow
 
@@ -117,100 +115,32 @@ class Meta:
         model = Workflow
 
 
-class NodeSerializer(serializers.HyperlinkedModelSerializer):
-    assay = serializers.StringRelatedField()
-    study = serializers.StringRelatedField()
-    child_nodes = serializers.SerializerMethodField('_get_children')
-    parent_nodes = serializers.SerializerMethodField('_get_parents')
-    auxiliary_nodes = serializers.SerializerMethodField('_get_aux_nodes')
-    auxiliary_file_generation_task_state = serializers.SerializerMethodField(
-                '_get_aux_node_task_state'
-            )
-    file_extension = serializers.SerializerMethodField(
-        '_get_file_extension')
-    relative_file_store_item_url = serializers.SerializerMethodField(
-        '_get_relative_url')
-    ready_for_igv_detail_view = serializers.SerializerMethodField(
-     '_ready_for_igv_detail_view')
-    is_auxiliary_node = serializers.SerializerMethodField(
-     '_is_auxiliary_node')
-
-    def _get_children(self, obj):
-        return obj.get_children()
-
-    def _get_parents(self, obj):
-        return obj.get_parents()
-
-    def _get_aux_nodes(self, obj):
-        aux_nodes = obj.get_auxiliary_nodes()
-        urls = []
-        for uuid in aux_nodes:
-            try:
-                node = Node.objects.get(uuid=uuid)
-                urls.append(node.get_relative_file_store_item_url())
-            except (Node.DoesNotExist,
-                    Node.MultipleObjectsReturned) as e:
-                logger.debug(e)
-        return urls
-
-    def _get_aux_node_task_state(self, obj):
-        return obj.get_auxiliary_file_generation_task_state()
-
-    def _get_file_extension(self, obj):
-        try:
-            file_store_item = FileStoreItem.objects.get(uuid=obj.file_uuid)
-        except (FileStoreItem.DoesNotExist,
-                FileStoreItem.MultipleObjectsReturned) as exc:
-            logger.debug(exc)
-            return None
-        return file_store_item.get_extension()
-
-    def _get_relative_url(self, obj):
-        return obj.get_relative_file_store_item_url() or None
-
-    def _ready_for_igv_detail_view(self, obj):
-        if not obj.is_auxiliary_node:
-            ready_for_igv_detail_view = True
-            for item in obj.get_auxiliary_nodes():
-                try:
-                    node = Node.objects.get(uuid=item)
-                except (Node.DoesNotExist,
-                        Node.MultipleObjectsReturned) \
-                        as e:
-                    logger.error(e)
-                    return False
-
-                state = node.get_auxiliary_file_generation_task_state()
-                if not state == celery.states.SUCCESS:
-                    ready_for_igv_detail_view = False
-
-            return ready_for_igv_detail_view
-        else:
-            return None
-
-    def _is_auxiliary_node(self, obj):
-        return obj.is_auxiliary_node
+class NodeSerializer(serializers.ModelSerializer):
+    file_uuid = serializers.CharField(max_length=36,
+                                      required=False,
+                                      allow_null=True)
 
     class Meta:
         model = Node
-        fields = [
-            'uuid',
-            'name',
-            'type',
-            'analysis_uuid',
-            'subanalysis',
-            'assay',
-            'study',
-            'relative_file_store_item_url',
-            'parent_nodes',
-            'child_nodes',
-            'auxiliary_nodes',
-            'is_auxiliary_node',
-            'file_extension',
-            'auxiliary_file_generation_task_state',
-            'ready_for_igv_detail_view',
-            'file_uuid'
-        ]
+        fields = ['uuid', 'file_uuid']
+
+    def validate_file_uuid(self, file_uuid):
+        if file_uuid is not None:
+            raise serializers.ValidationError(
+                'API does not support adding file store uuids.'
+            )
+        pass
+
+    def partial_update(self, instance, validated_data):
+        """
+        Update and return an existing `Node` instance, given the
+        validated data.
+        """
+        instance.file_uuid = validated_data.get('file_uuid',
+                                                instance.file_uuid)
+
+        instance.save()
+        return instance
 
 
 class EventSerializer(serializers.ModelSerializer):

refinery/core/urls.py

@@ -74,7 +74,6 @@
 
 # DRF url routing
 core_router = DefaultRouter()
-core_router.register(r'nodes', NodeViewSet)
 core_router.register(r'workflows', WorkflowViewSet)
 core_router.register(r'events', EventViewSet)
 core_router.urls.extend([
@@ -85,6 +84,8 @@
         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

@@ -12,7 +12,7 @@
 from django.core.mail import EmailMessage
 from django.core.urlresolvers import reverse
 from django.db import transaction
-from django.http import (HttpResponse, HttpResponseBadRequest,
+from django.http import (Http404, HttpResponse, HttpResponseBadRequest,
                          HttpResponseForbidden, HttpResponseNotFound,
                          HttpResponseRedirect, HttpResponseServerError,
                          JsonResponse)
@@ -32,13 +32,16 @@
 from requests.exceptions import HTTPError
 from rest_framework import authentication, status, viewsets
 from rest_framework.decorators import detail_route
+from rest_framework.exceptions import APIException
 from rest_framework.permissions import IsAuthenticated
 from rest_framework.renderers import JSONRenderer
 from rest_framework.response import Response
 from rest_framework.views import APIView
 import xmltodict
 
 from data_set_manager.models import Node
+from data_set_manager.search_indexes import NodeIndex
+from file_store.models import FileStoreItem
 
 from .forms import ProjectForm, UserForm, UserProfileForm, WorkflowForm
 from .models import (Analysis, CustomRegistrationProfile, DataSet, Event,
@@ -693,13 +696,80 @@ def graph(self, request, *args, **kwargs):
         )
 
 
-class NodeViewSet(viewsets.ModelViewSet):
-    """API endpoint that allows Nodes to be viewed"""
-    queryset = Node.objects.all()
-    serializer_class = NodeSerializer
-    lookup_field = 'uuid'
-    http_method_names = ['get']
-    # permission_classes = (IsAuthenticated,)
+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 update_file_store(self, old_uuid, new_uuid):
+        if new_uuid is None:
+            try:
+                FileStoreItem.objects.get(uuid=old_uuid).delete_datafile()
+            except (FileStoreItem.DoesNotExist,
+                    FileStoreItem.MultipleObjectsReturned) as e:
+                logger.error(e)
+
+    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(node, status=status.HTTP_401_UNAUTHORIZED)
+
+    def patch(self, request, uuid):
+        node = self.get_object(uuid)
+        old_file_uuid = node.file_uuid
+        data_set_owner = node.study.get_dataset().get_owner()
+
+        if data_set_owner == request.user:
+            serializer = NodeSerializer(node, data=request.data, partial=True)
+            if serializer.is_valid():
+                serializer.save()
+                self.update_file_store(old_file_uuid, node.file_uuid)
+                NodeIndex().update_object(node, using="data_set_manager")
+                return Response(
+                    serializer.data, status=status.HTTP_202_ACCEPTED
+                )
+            return Response(
+                serializer.errors, status=status.HTTP_400_BAD_REQUEST
+            )
+
+        return Response(uuid, status=status.HTTP_401_UNAUTHORIZED)
 
 
 class EventViewSet(viewsets.ModelViewSet):
@@ -800,12 +870,10 @@ def get_object(self, uuid):
             return DataSet.objects.get(uuid=uuid)
         except DataSet.DoesNotExist as e:
             logger.error(e)
-            return Response(uuid, status=status.HTTP_404_NOT_FOUND)
+            raise Http404
         except DataSet.MultipleObjectsReturned as e:
             logger.error(e)
-            return Response(
-                uuid, status=status.HTTP_500_INTERNAL_SERVER_ERROR
-            )
+            raise APIException("Multiple objects returned.")
 
     def is_user_authorized(self, user, data_set):
         if (not user.is_authenticated() or