fixing test.

pynxtools/dataconverter/helpers.py

@@ -17,21 +17,20 @@
 #
 """Helper functions commonly used by the convert routine."""
 
-from typing import List, Optional, Any
-from typing import Tuple, Callable, Union
+import json
 import re
 import xml.etree.ElementTree as ET
 from datetime import datetime, timezone
-import json
+from typing import Any, Callable, List, Optional, Tuple, Union
 
+import h5py
 import numpy as np
 from ase.data import chemical_symbols
-import h5py
 
 from pynxtools import get_nexus_version, get_nexus_version_hash
+from pynxtools.dataconverter.logger import logger as pynx_logger
 from pynxtools.nexus import nexus
 from pynxtools.nexus.nexus import NxdlAttributeError
-from pynxtools.dataconverter.logger import logger as pynx_logger
 
 
 def is_a_lone_group(xml_element) -> bool:
@@ -510,8 +509,8 @@ def ensure_all_required_fields_exist(template, data, nxdl_root, logger=pynx_logg
                     )
                 continue
             if not does_group_exist(renamed_path, data):
-                raise ValueError(f"The required group, {path}, hasn't been supplied.")
-            continue
+                logger.warning(f"The required group, {path}, hasn't been supplied.")
+                continue
         if not is_path_in_data_dict or data[renamed_path] is None:
             logger.warning(
                 f"The data entry corresponding to {path} is required "

tests/dataconverter/test_helpers.py

@@ -17,12 +17,13 @@
 #
 """Test cases for the helper functions used by the DataConverter."""
 
-import xml.etree.ElementTree as ET
-import os
 import logging
-from setuptools import distutils
-import pytest
+import os
+import xml.etree.ElementTree as ET
+
 import numpy as np
+import pytest
+from setuptools import distutils
 
 from pynxtools.dataconverter import helpers
 from pynxtools.dataconverter.logger import logger as pynx_logger
@@ -351,21 +352,8 @@ def fixture_filled_test_data(template, tmp_path):
             id="missing-empty-yet-required-group2",
         ),
         pytest.param(
-            alter_dict(
-                remove_from_dict(
-                    TEMPLATE, "/ENTRY[my_entry]/required_group/description"
-                ),
-                "The required group, /ENTRY[entry]/required_group, hasn't been supplied.",
-                id="missing-empty-yet-required-group",
-            ),
-            pytest.param(
-                remove_from_dict(
-                    TEMPLATE, "/ENTRY[my_entry]/required_group2/description"
-                ),
-                "The required group, /ENTRY[entry]/required_group2, hasn't been supplied.",
-                id="missing-empty-yet-required-group2",
-            ),
-            (""),
+            remove_from_dict(TEMPLATE, "/ENTRY[my_entry]/required_group/description"),
+            "The required group, /ENTRY[entry]/required_group, hasn't been supplied.",
             id="allow-required-and-empty-group",
         ),
         pytest.param(
@@ -388,7 +376,7 @@ def fixture_filled_test_data(template, tmp_path):
 def test_validate_data_dict(
     caplog, data_dict, error_message, template, nxdl_root, request
 ):
-    """Unit test for the data validation routine"""
+    """Unit test for the data validation routine."""
     if request.node.callspec.id in (
         "valid-data-dict",
         "lists",
@@ -398,15 +386,19 @@ def test_validate_data_dict(
         "no-child-provided-optional-parent",
         "int-instead-of-chars",
         "link-dict-instead-of-bool",
-        "allow-required-and-empty-group",
         "opt-group-completely-removed",
     ):
         helpers.validate_data_dict(template, data_dict, nxdl_root, logger=pynx_logger)
-    # Missing required fields
+    # Missing required fields caught by logger with warning
     elif request.node.callspec.id in (
         "empty-required-field",
+        "allow-required-and-empty-group",
         "req-group-in-opt-parent-removed",
+        "missing-empty-yet-required-group",
+        "missing-empty-yet-required-group2",
     ):
+        assert "" == caplog.text
+        # logger records
         captured_logs = caplog.records
         helpers.validate_data_dict(template, data_dict, nxdl_root, pynx_logger)
         assert any(error_message in rec.message for rec in captured_logs)