Check whether h5 file being written exists. If so, we do not overwrite it because it may be underdoing refinement, changes or updates, for archiving, sharing, or publishing.

src/hdf5_writer.py

@@ -162,7 +162,15 @@ def create_hdf5_file_from_filesystem_path(path_to_input_directory: str,
     print(start_message)
     logging.info(start_message)
 
-    
+    # Check if the .h5 file already exists
+    if os.path.exists(path_to_output_file) and mode in ['w']:
+        message = (
+            f"[Notice] The file '{path_to_output_file}' already exists and will not be overwritten.\n"
+            "If you wish to replace it, please delete the existing file first and rerun the program."
+        )
+        print(message)
+        logging.error(message)
+    else:
         with h5py.File(path_to_output_file, mode=mode, track_order=True) as h5file:
 
             number_of_dirs = len(path_to_filenames_dict.keys())