FAIRmat-NFDI · domna · Apr 18, 2024 · Apr 18, 2024 · Apr 18, 2024 · Apr 18, 2024
diff --git a/pynxtools/dataconverter/helpers.py b/pynxtools/dataconverter/helpers.py
@@ -264,14 +264,12 @@ def convert_data_dict_path_to_hdf5_path(path) -> str:
     return hdf5path
 
 
-def is_value_valid_element_of_enum(value, elem) -> Tuple[bool, list]:
+def is_value_valid_element_of_enum(value, elist) -> Tuple[bool, list]:
     """Checks whether a value has to be specific from the NXDL enumeration and returns options."""
-    if elem is not None:
-        has_enums, enums = nexus.get_enums(elem)
-        if has_enums and (
-            isinstance(value, list) or value not in enums[0:-1] or value == ""
        ):
-            return False, enums
+    for elem in elist:
+        enums = nexus.get_enums(elem)
+        if enums is not None:
+            return value in enums, enums
     return True, []
 
 
@@ -465,7 +463,7 @@ def check_optionality_based_on_parent_group(path, nxdl_path, nxdl_root, data, te
         if is_nxdl_path_a_child(
             nxdl_path, optional_parent_nxdl
         ) and not all_required_children_are_set(optional_parent, data, nxdl_root):
-            raise LookupError(
+            logger.warning(
                 f"The data entry, {path}, has an optional parent, "
                 f"{optional_parent}, with required children set. Either"
                 f" provide no children for {optional_parent} or provide"
@@ -617,9 +615,12 @@ def validate_data_dict(template, data, nxdl_root: ET.Element):
                     else "NXDL_TYPE_UNAVAILABLE"
                 )
                 data[path] = is_valid_data_field(data[path], nxdl_type, path)
-                is_valid_enum, enums = is_value_valid_element_of_enum(data[path], elem)
+                elist = nexus.get_inherited_nodes(
+                    nxdl_path, path.rsplit("/", 1)[-1], nxdl_root
+                )[2]
+                is_valid_enum, enums = is_value_valid_element_of_enum(data[path], elist)
                 if not is_valid_enum:
-                    raise ValueError(
+                    logger.warning(
                         f"The value at {path} should be on of the "
                         f"following strings: {enums}"
                     )

diff --git a/pynxtools/definitions b/pynxtools/definitions
diff --git a/pynxtools/nexus-version.txt b/pynxtools/nexus-version.txt
@@ -1 +1 @@
-v2020.10-1637-g2ac33b2cf
+v2020.10-1652-g88ff21539
diff --git a/tests/dataconverter/test_helpers.py b/tests/dataconverter/test_helpers.py
@@ -335,7 +335,7 @@ def fixture_filled_test_data(template, tmp_path):
             ),
             (
                 "The value at /ENTRY[my_entry]/NXODD_name[nxodd_name]/type should be on of the following"
-                " strings: [1st type,2nd type,3rd type,4th type]"
+                " strings: ['1st type', '2nd type', '3rd type', '4th type']"
             ),
             id="wrong-enum-choice",
         ),
@@ -430,6 +430,14 @@ def test_validate_data_dict(
         captured_logs = caplog.records
         helpers.validate_data_dict(template, data_dict, nxdl_root)
         assert any(error_message in rec.message for rec in captured_logs)
+    elif request.node.callspec.id in (
+        "wrong-enum-choice",
+        "atleast-one-required-child-not-provided-optional-parent",
+    ):
+        with caplog.at_level(logging.WARNING):
+            helpers.validate_data_dict(template, data_dict, nxdl_root)
+
+        assert error_message in caplog.text
     else:
         with pytest.raises(Exception) as execinfo:
             helpers.validate_data_dict(template, data_dict, nxdl_root)
+10 −10		contributed_definitions/NXapm.nxdl.xml
+2 −2		contributed_definitions/NXapm_charge_state_analysis.nxdl.xml
+152 −0		contributed_definitions/NXapm_compositionspace_config.nxdl.xml
+375 −0		contributed_definitions/NXapm_compositionspace_results.nxdl.xml
+1 −1		contributed_definitions/NXapm_paraprobe_intersector_config.nxdl.xml
+77 −47		contributed_definitions/NXapm_paraprobe_nanochem_config.nxdl.xml
+66 −49		contributed_definitions/NXapm_paraprobe_nanochem_results.nxdl.xml
+1 −1		contributed_definitions/NXcg_primitive_set.nxdl.xml
+2 −2		contributed_definitions/NXcrystal_structure.nxdl.xml
+3 −3		contributed_definitions/NXdelocalization.nxdl.xml
+1 −6		contributed_definitions/NXebeam_column.nxdl.xml
+1 −1		contributed_definitions/NXevent_data_apm.nxdl.xml
+1 −1		contributed_definitions/NXgraph_edge_set.nxdl.xml
+1 −1		contributed_definitions/NXgraph_node_set.nxdl.xml
+1 −1		contributed_definitions/NXion.nxdl.xml
+6 −6		contributed_definitions/NXlens_em.nxdl.xml
+1 −1		contributed_definitions/NXms.nxdl.xml
+1 −1		contributed_definitions/NXms_feature_set.nxdl.xml
+3 −3		contributed_definitions/NXms_recon.nxdl.xml
+1 −1		contributed_definitions/NXms_score_results.nxdl.xml
+6 −6		contributed_definitions/NXms_snapshot_set.nxdl.xml
+1 −1		contributed_definitions/NXoptical_system_em.nxdl.xml
+9 −9		contributed_definitions/NXunit_cell.nxdl.xml
+11 −11		contributed_definitions/nyaml/NXapm.yaml
+2 −2		contributed_definitions/nyaml/NXapm_charge_state_analysis.yaml
+0 −879		contributed_definitions/nyaml/NXapm_composition_space_results.yaml
+94 −0		contributed_definitions/nyaml/NXapm_compositionspace_config.yaml
+275 −0		contributed_definitions/nyaml/NXapm_compositionspace_results.yaml
+1 −1		contributed_definitions/nyaml/NXapm_paraprobe_intersector_config.yaml
+63 −33		contributed_definitions/nyaml/NXapm_paraprobe_nanochem_config.yaml
+53 −40		contributed_definitions/nyaml/NXapm_paraprobe_nanochem_results.yaml
+1 −1		contributed_definitions/nyaml/NXcg_primitive_set.yaml
+2 −2		contributed_definitions/nyaml/NXcrystal_structure.yaml
+3 −3		contributed_definitions/nyaml/NXdelocalization.yaml
+1 −1		contributed_definitions/nyaml/NXebeam_column.yaml
+1 −1		contributed_definitions/nyaml/NXevent_data_apm.yaml
+1 −1		contributed_definitions/nyaml/NXgraph_edge_set.yaml
+1 −1		contributed_definitions/nyaml/NXgraph_node_set.yaml
+1 −1		contributed_definitions/nyaml/NXion.yaml
+6 −6		contributed_definitions/nyaml/NXlens_em.yaml
+1 −1		contributed_definitions/nyaml/NXms.yaml
+2 −2		contributed_definitions/nyaml/NXms_feature_set.yaml
+3 −3		contributed_definitions/nyaml/NXms_recon.yaml
+1 −1		contributed_definitions/nyaml/NXms_score_results.yaml
+2 −2		contributed_definitions/nyaml/NXms_snapshot_set.yaml
+1 −1		contributed_definitions/nyaml/NXoptical_system_em.yaml
+4 −4		contributed_definitions/nyaml/NXunit_cell.yaml
+59 −3		dev_tools/tests/test_nxdl_utils.py
+70 −34		dev_tools/utils/nxdl_utils.py
+17 −0		manual/source/classes/contributed_definitions/apm-structure.rst