Fix BAM index file generation

refinery/core/serializers.py

@@ -96,12 +96,12 @@ def _get_aux_node_task_state(self, obj):
 
     def _get_file_extension(self, obj):
         try:
-            return FileStoreItem.objects.get(
-                    uuid=obj.file_uuid).get_file_extension()
+            file_store_item = FileStoreItem.objects.get(uuid=obj.file_uuid)
         except (FileStoreItem.DoesNotExist,
-                FileStoreItem.MultipleObjectsReturned) as e:
-            logger.debug(e)
+                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

refinery/core/tests.py

@@ -852,7 +852,7 @@ def setUp(self):
 
         self.node_filename = "{}.{}".format(
             self.node.name,
-            self.node.get_file_store_item().get_file_extension()
+            self.node.get_file_store_item().get_extension()
         )
 
         # Create AnalysisNodeConnections

refinery/data_set_manager/tasks.py

@@ -426,7 +426,7 @@ def generate_auxiliary_file(auxiliary_node, datafile_path,
         # Here we are checking for the FileExtension of the ParentNode's
         # FileStoreItem because we will create auxiliary files based on what
         # said value is
-        if parent_node_file_store_item.get_file_extension().lower() == "bam":
+        if parent_node_file_store_item.get_extension().lower() == "bam":
             generate_bam_index(auxiliary_file_store_item.uuid, datafile_path)
 
         generate_auxiliary_file.update_state(state=celery.states.SUCCESS)

refinery/file_store/models.py

@@ -226,11 +226,8 @@ def get_file_size(self, report_symlinks=False):
             return 0
 
     def get_file_extension(self):
-        """Return extension object based on datafile name or source"""
-        if self.datafile.name:
-            extension = _get_extension_from_string(self.datafile.name)
-        else:
-            extension = _get_extension_from_string(self.source)
+        """Return FileExtension object based on datafile name or source"""
+        extension = self.get_extension()
         try:
             return FileExtension.objects.get(name=extension)
         except FileExtension.DoesNotExist:
@@ -246,6 +243,13 @@ def get_file_extension(self):
         except FileExtension.MultipleObjectsReturned as exc:
             raise RuntimeError(exc)
 
+    def get_extension(self):
+        """Return extension of datafile name or file name in source"""
+        if self.datafile.name:
+            return _get_extension_from_string(self.datafile.name)
+        else:
+            return _get_extension_from_string(self.source)
+
     def get_file_object(self):
         """Return file object for the data file or None if failed to open"""
         try: