Remove rename() task and unnecessary code from rename_results() (#2725)

refinery/core/models.py

@@ -54,7 +54,6 @@
     add_annotated_nodes_selection, index_annotated_nodes_selection
 )
 from file_store.models import FileStoreItem, FileType
-from file_store.tasks import rename
 from galaxy_connector.models import Instance
 import tool_manager
 
@@ -1314,42 +1313,34 @@ def rename_results(self):
         logger.debug("Renaming analysis results")
         # rename file_store items to new name updated from galaxy file_ids
         for result in AnalysisResult.objects.filter(analysis_uuid=self.uuid):
-            # new name to load
-            new_file_name = result.file_name
-            # workaround for FastQC reports downloaded from Galaxy as zip
-            # archives
-            (root, ext) = os.path.splitext(new_file_name)
             try:
                 item = FileStoreItem.objects.get(uuid=result.file_store_uuid)
             except (FileStoreItem.DoesNotExist,
                     FileStoreItem.MultipleObjectsReturned) as exc:
-                logger.error("Error renaming HTML file '%s' to zip: %s",
-                             result.file_store_uuid, exc)
+                logger.error("Error renaming analysis result '%s': %s",
+                             result, exc)
+                break
+
+            # workaround for FastQC reports downloaded from Galaxy as zip
+            # archives
+            (root, ext) = os.path.splitext(result.file_name)
+            if ext == '.html':
+                try:
+                    zipfile = FileType.objects.get(name='ZIP')
+                except (FileType.DoesNotExist,
+                        FileType.MultipleObjectsReturned) as exc:
+                    logger.error("Error renaming HTML to zip: %s", exc)
+                else:
+                    if item.filetype == zipfile:
+                        item.rename_datafile(''.join([root, '.zip']))
             else:
-                if ext == '.html':
-                    try:
-                        zipfile = FileType.objects.get(name='ZIP')
-                    except (FileType.DoesNotExist,
-                            FileType.MultipleObjectsReturned) as exc:
-                        logger.error("Error renaming HTML to zip: %s", exc)
-                    else:
-                        if item.filetype == zipfile:
-                            new_file_name = ''.join([root, '.zip'])
-                renamed_file_store_item_uuid = rename(result.file_store_uuid,
-                                                      new_file_name)
-
-            # Try to generate an auxiliary node for visualization purposes
-            # NOTE: We have to do this after renaming happens because before
-            #  renaming, said FileStoreItems's datafile field does not point
-            #  to an actual file
-            file_store_item_uuid = (
-                renamed_file_store_item_uuid if
-                renamed_file_store_item_uuid else result.file_store_uuid
-            )
+                item.rename_datafile(result.file_name)
+
             try:
-                node = Node.objects.get(file_uuid=file_store_item_uuid)
-            except (Node.DoesNotExist, Node.MultipleObjectsReturned) as e:
-                logger.error("Error Fetching Node: %s", e)
+                node = Node.objects.get(file_uuid=item.uuid)
+            except (Node.DoesNotExist, Node.MultipleObjectsReturned) as exc:
+                logger.error("Error retrieving Node with file UUID '%s': %s",
+                             exc)
             else:
                 if node.is_derived():
                     node.run_generate_auxiliary_node_task()

refinery/file_store/tasks.py

@@ -302,30 +302,6 @@ def begin_auxiliary_node_generation(**kwargs):
         node.run_generate_auxiliary_node_task()
 
 
-@task()
-def rename(uuid, name):
-    """Change name of the file on disk and return the updated FileStoreItem
-    UUID.
-    :param uuid: UUID of a FileStoreItem.
-    :type uuid: str.
-    :param name: New name of the FileStoreItem specified by the UUID.
-    :type name: str.
-    :returns: FileStoreItem UUID or None if there was an error.
-    """
-    try:
-        item = FileStoreItem.objects.get(uuid=uuid)
-    except (FileStoreItem.DoesNotExist,
-            FileStoreItem.MultipleObjectsReturned) as exc:
-        logger.error("Failed to rename FileStoreItem with UUID '%s': %s",
-                     uuid, exc)
-        return None
-
-    if item.rename_datafile(name):
-        return item.uuid
-    else:
-        return None
-
-
 @task()
 def download_file(url, target_path, file_size=1):
     '''Download file to target_path from specified URL.