Integrated copy h5 file into group functionality, imported from g5505_file_reader

src/hdf5_lib.py

@@ -223,6 +223,21 @@ def transfer_file_dict_to_hdf5(h5file, group_name, file_dict):
         print(inst) 
         logging.error('Failed to transfer data into HDF5: %s', inst)
 
+def copy_file_in_group(source_file_path, dest_file_obj : h5py.File, dest_group_name, work_with_copy : bool = True):
+    # Create copy of original file to avoid possible file corruption and work with it.
+
+    if work_with_copy:
+        tmp_file_path = utils.make_file_copy(source_file_path)
+    else:
+        tmp_file_path = source_file_path
+
+    # Open backup h5 file and copy complet filesystem directory onto a group in h5file
+    with h5py.File(tmp_file_path,'r') as src_file:
+        dest_file_obj.copy(source= src_file['/'], dest= dest_group_name)
+
+    if 'tmp_files' in tmp_file_path:
+        os.remove(tmp_file_path)
+
 def create_hdf5_file_from_filesystem_path(output_filename : str, 
                                           input_file_system_path : str, 
                                           select_dir_keywords = [], 
@@ -337,7 +352,8 @@ def create_hdf5_file_from_filesystem_path(output_filename : str,
                     dest_file_obj = h5file
                      #group_name +'/'+filename
                     #ext_to_reader_dict[file_ext](source_file_path, dest_file_obj, dest_group_name)
-                    g5505f_reader.select_file_reader(dest_group_name)(source_file_path, dest_file_obj, dest_group_name)
+                    #g5505f_reader.select_file_reader(dest_group_name)(source_file_path, dest_file_obj, dest_group_name)
+                    copy_file_in_group(source_file_path, dest_file_obj, dest_group_name, False)
 
             # Update the progress bar and log the end message
             utils.progressBar(dir_number, number_of_dirs, end_message)