Refix reference (#604)

* fix the Reference.

* ruff.

Author: RubelMozumder

src/pynxtools/nomad/schema.py

@@ -176,45 +176,55 @@ def get_entry_reference(archive, f_name):
 
 
 class NexusIdentifiers(ArchiveSection):
-    NeXus_identifiers = SubSection(
+    Nexus_identifiers = SubSection(
         section_def=AnchoredReference,
         repeats=True,
         description="These are the NOMAD references correspond to NeXus identifierNAME fields.",
     )
 
     def normalize(self, archive, logger):
         # Consider multiple identifiers exists in the same group/section
-        def generate_anchored_reference_and_normalize(value, idname):
+        def generate_anchored_reference_and_normalize(
+            attr_obj, id_value, idname, is_full_storage=False
+        ):
             """Generate anchored reference, connect to m quantities, and normalize."""
             field_n = idname.split("__field")[0]
-            logger.info(f"Lab id {value} to be created")
-            nx_id = AnchoredReference(lab_id=value, name=field_n)
-            nx_id.m_set_section_attribute(
-                "m_nx_data_path",
-                self.m_get_quantity_attribute(idname, "m_nx_data_path"),
-            )
-            nx_id.m_set_section_attribute(
-                "m_nx_data_file",
-                self.m_get_quantity_attribute(idname, "m_nx_data_file"),
-            )
+            logger.info(f"Lab id {id_value} to be created")
+            nx_id = AnchoredReference(lab_id=id_value, name=field_n)
+            if not is_full_storage:
+                nx_data_path = attr_obj.m_get_quantity_attribute(
+                    idname, "m_nx_data_path"
+                )
+                nx_data_file = attr_obj.m_get_quantity_attribute(
+                    idname, "m_nx_data_file"
+                )
+            else:
+                nx_data_path = attr_obj.attributes.get("m_nx_data_path")
+                nx_data_file = attr_obj.attributes.get("m_nx_data_file")
+
+            nx_id.m_set_section_attribute("m_nx_data_path", nx_data_path)
+            nx_id.m_set_section_attribute("m_nx_data_file", nx_data_file)
+
+            self.Nexus_identifiers.append(nx_id)
             nx_id.normalize(archive, logger)
-            self.NeXus_identifiers.append(nx_id)
 
         identifiers = [
             key
             for key in self.__dict__.keys()
             if key.startswith("identifier") and key.endswith("__field")
         ]
         if identifiers:
-            self.NeXus_identifiers = []
+            self.Nexus_identifiers = []
             for identifier in identifiers:
                 if not (val := getattr(self, identifier)):
                     continue
                 if isinstance(val, dict):
                     for idname, idobj in val.items():
-                        generate_anchored_reference_and_normalize(idobj.value, idname)
+                        generate_anchored_reference_and_normalize(
+                            idobj, idobj.value, idname, True
+                        )
                 else:
-                    generate_anchored_reference_and_normalize(val, identifier)
+                    generate_anchored_reference_and_normalize(self, val, identifier)
         super().normalize(archive, logger)