Fix bug related to missing params.

refinery/core/test_views.py

@@ -171,6 +171,14 @@ def test_get_data_set_pagination_limit_and_offset(self):
         self.assertEqual(get_response.data.get('data_sets')[0].get('uuid'),
                          self.data_set.uuid)
 
+    def test_total_data_sets_returned_correctly(self):
+        create_dataset_with_necessary_models(user=self.user)
+        get_request = self.factory.get(self.url_root)
+        get_request.user = self.user
+        get_response = self.view(get_request)
+        self.assertEqual(len(get_response.data.get('data_sets')),
+                         get_response.data.get('total_data_sets'))
+
     def test_dataset_delete_successful(self):
 
         self.assertEqual(DataSet.objects.all().count(), 2)

refinery/core/views.py

@@ -22,8 +22,8 @@
 
 import boto3
 import botocore
-from guardian.shortcuts import get_groups_with_perms, get_objects_for_user, \
-    get_perms
+from guardian.shortcuts import (get_groups_with_perms, get_objects_for_user,
+                                get_perms)
 
 from guardian.utils import get_anonymous_user
 from registration import signals
@@ -774,25 +774,26 @@ def get(self, request):
             request.user, 'dataset'
         ).order_by('-modification_date')
 
-        total_data_sets = len(user_data_sets)
-        if filters.get('is_owner') or filters.get('is_public') or \
-                filters.get('group'):
-            filtered_data_set = []
-            for data_set in user_data_sets:
-                if not data_set.is_valid:
-                    logger.warning(
-                        "DataSet with UUID: {} is invalid, and most likely is "
-                        "still being created".format(data_set.uuid)
-                    )
+        filtered_data_sets = []
+        filter_requested = filters.get('is_owner') \
+            or filters.get('is_public') \
+            or filters.get('group')
+        for data_set in user_data_sets:
+            if not data_set.is_valid:
+                logger.warning(
+                    "DataSet with UUID: {} is invalid, and most likely is "
+                    "still being created".format(data_set.uuid)
+                )
+            elif filter_requested:
                 if self.is_filtered_data_set(data_set, filters):
-                    filtered_data_set.append(data_set)
-
-            total_data_sets = len(filtered_data_set)
-            data_sets = paginator.paginate_queryset(filtered_data_set, request)
-        else:
-            data_sets = paginator.paginate_queryset(user_data_sets, request)
+                    filtered_data_sets.append(data_set)
+            else:
+                filtered_data_sets.append(data_set)
 
-        serializer = DataSetSerializer(data_sets, many=True,
+        total_data_sets = len(filtered_data_sets)
+        paged_data_sets = paginator.paginate_queryset(filtered_data_sets,
+                                                      request)
+        serializer = DataSetSerializer(paged_data_sets, many=True,
                                        context={'request': request})
 
         return Response({'data_sets': serializer.data,

refinery/data_set_manager/management/commands/process_isatab.py

@@ -25,23 +25,23 @@ class Command(BaseCommand):
     """
 
     def add_arguments(self, parser):
-        parser.add_argumenet(
+        parser.add_argument('username')
+        parser.add_argument('base_isa_dir')
+        parser.add_argument(
             '--base_pre_isa_dir',
             action='store',
-            type='string'
         )
-        parser.add_argumenet(
+        parser.add_argument(
             '--file_base_path',
             action='store',
-            type='string',
             default=None
         )
-        parser.add_argumenet(
+        parser.add_argument(
             '--public',
             action='store_true',
             default=False
         )
-        parser.add_argumenet(
+        parser.add_argument(
             '--overwrite',
             action='store_true',
             default=False
@@ -123,28 +123,22 @@ def handle(self, username, base_isa_dir, **options):
 
         task_num = 1
         total = len(isatab_dict)
-        for (uuid, filename, skipped) in result.iterate():
+        for uuid in result.iterate():
             try:
-                if not skipped:
-                    if uuid is not None:
-                        logger.info(
-                            "%s / %s: Successfully parsed %s into "
-                            "DataSet with UUID %s",
-                            task_num, total, filename, uuid)
-                    else:
-                        logger.info(
-                            "%s / %s: Import of %s failed. Please check "
-                            "Celery log files.",
-                            task_num, total, filename, uuid)
+                if uuid is not None:
+                    logger.info(
+                        "%s / %s: Successfully parsed file into "
+                        "DataSet with UUID %s",
+                        task_num, total, uuid)
                 else:
                     logger.info(
-                        "%s / %s: Skipped %s as it has been "
-                        "successfully parsed already. UUID %s",
-                        task_num, total, filename, uuid)
+                        "%s / %s: Import of %s failed. Please check "
+                        "Celery log files.",
+                        task_num, total, uuid)
                 task_num += 1
                 sys.stdout.flush()
             except:
-                logger.info("%s / %s: Unsuccessful parsed %s",
-                            task_num, total, filename)
+                logger.info("%s / %s: Unsuccessful parsed",
+                            task_num, total)
                 task_num += 1
                 sys.stdout.flush()