Merge remote-tracking branch 'upstream/release_18.05' into dev

lib/galaxy/model/__init__.py

@@ -1987,6 +1987,9 @@ def set_extra_files_path(self, extra_files_path):
             self.external_extra_files_path = extra_files_path
     extra_files_path = property(get_extra_files_path, set_extra_files_path)
 
+    def extra_files_path_exists(self):
+        return self.object_store.exists(self, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id, dir_only=True)
+
     def _calculate_size(self):
         if self.external_filename:
             try:
@@ -2182,6 +2185,9 @@ def link_to(self, path):
     def extra_files_path(self):
         return self.dataset.extra_files_path
 
+    def extra_files_path_exists(self):
+        return self.dataset.extra_files_path_exists()
+
     @property
     def datatype(self):
         return datatype_for_extension(self.extension)

lib/galaxy/tools/data_manager/manager.py

@@ -326,7 +326,7 @@ def process_result(self, out_data):
             # moving a directory and the target already exists, we move the contents instead
             log.debug('Attempting to add entries for undeclared tables: %s.', ', '.join(data_tables_dict.keys()))
             for ref_file in out_data.values():
-                if os.path.exists(ref_file.extra_files_path):
+                if ref_file.extra_files_path_exists():
                     util.move_merge(ref_file.extra_files_path, self.data_managers.app.config.galaxy_data_manager_data_path)
             path_column_names = ['path']
             for data_table_name, data_table_values in data_tables_dict.items():