diff --git a/data_management/services/dlu_filesystem.py b/data_management/services/dlu_filesystem.py index f1b9d44..fcaff53 100644 --- a/data_management/services/dlu_filesystem.py +++ b/data_management/services/dlu_filesystem.py @@ -126,13 +126,16 @@ def rename_and_move_files(self, file_list: list[DLUFile], slide_name_map, packag source_package_directory = self.globus_data_directory + '/' + self.globus_dir_prefix + package_id for file in file_list: - dest_file = os.path.join(dest_package_directory, slide_name_map[file.name]) - logger.info("Copying file " + os.path.join(source_package_directory, file.name) + " to " - + os.path.join(dest_package_directory, slide_name_map[file.name])) - shutil.copy(os.path.join(source_package_directory, file.name), - dest_file) - file = DLUFile(name=slide_name_map[file.name], path=dest_package_directory, - checksum=calculate_checksum(dest_file), size=os.path.getsize(dest_file)) + dest_file_name = slide_name_map[file.name] + renamed_src_path = os.path.join(source_package_directory, dest_file_name) + dest_path = os.path.join(dest_package_directory, dest_file_name) + + logger.info("Renaming file " + os.path.join(source_package_directory, file.name) + " to " + renamed_src_path) + os.rename(os.path.join(source_package_directory, file.name), renamed_src_path) + logger.info("Copying file " + renamed_src_path + " to " + dest_path) + shutil.copy(renamed_src_path, dest_path) + file = DLUFile(name=dest_file_name, path=dest_package_directory, + checksum=calculate_checksum(dest_path), size=os.path.getsize(dest_path)) dluFiles.append(file) return dluFiles