add "!" notation to remove optional groups with missing required chil…

…dren (#22)

* add "!" notation to remove optional groups with missing required children

* Implement suggestions

---------

Co-authored-by: domna <[email protected]>

pynxtools_mpes/reader.py

@@ -18,6 +18,7 @@
 """MPES reader implementation for the DataConverter."""
 
 import errno
+import logging
 import os
 from functools import reduce
 from typing import Any, Tuple, Union
@@ -33,6 +34,9 @@
     parse_flatten_json,
 )
 
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.INFO)
+
 DEFAULT_UNITS = {
     "X": "step",
     "Y": "step",
@@ -330,7 +334,13 @@ def read(  # pylint: disable=too-many-branches
 
         fill_data_indices_in_config(config_file_dict, x_array_loaded)
 
+        optional_groups_to_remove = []
+
         for key, value in config_file_dict.items():
+            if isinstance(value, str) and value.startswith("!"):
+                optional_groups_to_remove.append(key)
+                value = value[1:]
+
             if isinstance(value, str) and ":" in value:
                 precursor = value.split(":")[0]
                 value = value[value.index(":") + 1 :]
@@ -384,6 +394,18 @@ def read(  # pylint: disable=too-many-branches
         for key, value in eln_data_dict.items():
             template[key] = value
 
+        # remove groups that have required children missing
+        for key in optional_groups_to_remove:
+            if template.get(key) is None:
+                group_to_delete = key.rsplit("/", 1)[0]
+                logger.info(
+                    f"[info]: Required element {key} not provided. "
+                    f"Removing the parent group {group_to_delete}.",
+                )
+                for temp_key in template.keys():
+                    if temp_key.startswith(group_to_delete):
+                        del template[temp_key]
+
         return template