Update System data model in plugin

src/nomad_material_processing/general.py

@@ -17,13 +17,20 @@
     SectionProperties,
 )
 from nomad.datamodel.metainfo.basesections import (
-    CompositeSystem,
-    CompositeSystemReference,
     ElementalComposition,
     Process,
     ProcessStep,
     SynthesisMethod,
-    SystemComponent,
+)
+from nomad.datamodel.metainfo.basesections2 import (
+    System,
+    SystemReference,
+    Process,
+    ProcessStep,
+    SynthesisMethod,
+    NestedSubSystem,
+    ReferencedSubSystem,
+    GeometricalSpace,
 )
 from nomad.datamodel.metainfo.workflow import (
     Link,
@@ -47,7 +54,7 @@
 configuration = config.get_plugin_entry_point('nomad_material_processing:schema')
 
 
-class Geometry(ArchiveSection):
+class Geometry(GeometricalSpace):
     """
     Geometrical shape attributes of a system.
     Sections derived from `Geometry` represent concrete geometrical shapes.
@@ -797,7 +804,7 @@ class ElectronicProperties(ArchiveSection):
     )
 
 
-class Substrate(CompositeSystem):
+class Substrate(System):
     """
     A thin free standing sheet of material. Not to be confused with the substrate role
     during a deposition, which can be a `Substrate` with `ThinFilm`(s) on it.
@@ -874,7 +881,7 @@ class CrystallineSubstrate(Substrate):
     )
 
 
-class ThinFilm(CompositeSystem):
+class ThinFilm(System):
     """
     A thin film of material which exists as part of a stack.
     """
@@ -887,7 +894,7 @@ class ThinFilm(CompositeSystem):
     )
 
 
-class ThinFilmReference(CompositeSystemReference):
+class ThinFilmReference(SystemReference):
     """
     Class autogenerated from yaml schema.
     """
@@ -908,7 +915,7 @@ class ThinFilmReference(CompositeSystemReference):
     )
 
 
-class SubstrateReference(CompositeSystemReference):
+class SubstrateReference(SystemReference):
     """
     A section for describing a system component and its role in a composite system.
     """
@@ -929,7 +936,7 @@ class SubstrateReference(CompositeSystemReference):
     )
 
 
-class ThinFilmStack(CompositeSystem):
+class ThinFilmStack(System):
     """
     A stack of `ThinFilm`(s). Typically deposited on a `Substrate`.
     """
@@ -968,17 +975,19 @@ def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
         """
         self.components = []
         if self.layers:
-            self.components = [
-                SystemComponent(system=layer.reference)
+            self.sub_systems = [
+                SubSystem(referenced_system=layer.reference)
                 for layer in self.layers
                 if layer.reference
             ]
         if self.substrate.reference:
-            self.components.append(SystemComponent(system=self.substrate.reference))
+            self.sub_systems.append(
+                SubSystem(referenced_system=self.substrate.reference)
+            )
         super().normalize(archive, logger)
 
 
-class ThinFilmStackReference(CompositeSystemReference):
+class ThinFilmStackReference(SystemReference):
     """
     Class autogenerated from yaml schema.
     """
@@ -1168,7 +1177,7 @@ class EtchingStep(ProcessStep):
             component=ELNComponentEnum.EnumEditQuantity,
         ),
     )
-    etching_reagents = SubSection(section_def=CompositeSystem, repeats=True)
+    etching_reagents = SubSection(section_def=System, repeats=True)
 
 
 class Etching(Process, EntryData):
@@ -1367,7 +1376,7 @@ class CleaningStep(ProcessStep):
         ),
     )
     cleaning_reagents = SubSection(
-        section_def=CompositeSystemReference,
+        section_def=SystemReference,
     )