update props

Author: srmnitc

atomrdf/datamodels/structure.py

@@ -500,7 +500,7 @@ def from_graph(cls, graph, sample):
         ]
 
         datadict = {
-            "volume": {"value": volume},
+            "volume": {"value": volume,},
             "number_of_atoms": {"value": int(number_of_atoms)},
             "repetitions": {"value": repetitions},
             "length": {"value": length},
@@ -600,10 +600,13 @@ def from_graph(cls, graph, sample):
             data = json.load(fin)
             positions = data[position_identifier]["value"]
             species = data[species_identifier]["value"]
-
+        
+        position=DataProperty(value=positions)
+        species=DataProperty(value=species)
+        
         return cls(
-            position=DataProperty(value=positions),
-            species=DataProperty(value=species),
+            position=position,
+            species=species,
         )
 
 
@@ -690,7 +693,7 @@ def from_graph(cls, graph, sample_id):
         if sample_type is None:
             raise ValueError(f"Sample {sample_id} not found in graph.")
 
-        
+
         # material, simulation_cell, atom_attribute handled separately (if needed)
         kwargs["material"] = Material.from_graph(graph, sample)
         kwargs["simulation_cell"] = SimulationCell.from_graph(graph, sample)

atomrdf/datamodels/workflow/property.py

@@ -4,7 +4,8 @@
 import yaml
 import uuid
 import json
-from pydantic import Field, field_validator
+from pydantic import Field, field_validator, PrivateAttr
+
 from atomrdf.datamodels.basemodels import (
     TemplateMixin,
     DataProperty,
@@ -23,9 +24,16 @@
     ASMO,
     MDO,
 )
+from atomrdf.graph import KnowledgeGraph
 
 
 class Property(DataProperty):
+    graph: Optional[KnowledgeGraph] = Field(default=None)  # Private attribute for graph
+    
+    model_config = {
+        "arbitrary_types_allowed": True
+    }
+
     def _add_value(self, graph, property):
         if self.value is not None:
             graph.add(

atomrdf/graph.py

@@ -47,7 +47,7 @@
 from atomrdf.workflow.workflow import Workflow
 from atomrdf.sample import Sample
 import atomrdf.mp as amp
-from atomrdf.io.write import write
+
 
 from atomrdf.namespace import (
     Namespace,