replace triples

pyscal · Aug 20, 2024 · 38b9b32 · 38b9b32
1 parent 6208dce
commit 38b9b32
Showing 1 changed file with 11 additions and 9 deletions.
diff --git a/atomrdf/structure.py b/atomrdf/structure.py
@@ -1158,7 +1158,7 @@ def delete(self, ids=None, indices=None, condition=None, selection=False, copy_s
 
             #write mapping for the operation
             if self.sample.toPython() != sys.sample.toPython():
-                activity = self.graph.create_node(f"activity:{uuid.uuid4()}", PROV.Activity, label='DeleteAtom')
+                activity = self.graph.create_node(f"activity:{uuid.uuid4()}", UNSAFEASMO.DeleteAtom)
                 sys.graph.add((sys.sample, PROV.wasDerivedFrom, self.sample))
                 sys.graph.add((sys.sample, PROV.wasGeneratedBy, activity))
 
@@ -1371,7 +1371,7 @@ def substitute_atoms(
 
             #write mapping for the operation
             if self.sample.toPython() != sys.sample.toPython():
-                activity = self.graph.create_node(f"activity:{uuid.uuid4()}", PROV.Activity, label='SubstituteAtom')
+                activity = self.graph.create_node(f"activity:{uuid.uuid4()}", UNSAFEASMO.SubstituteAtom)
                 sys.graph.add((sys.sample, PROV.wasDerivedFrom, self.sample))
                 sys.graph.add((sys.sample, PROV.wasGeneratedBy, activity))
 
@@ -1567,7 +1567,7 @@ def add_interstitial_impurities(
             sys.add_triples_for_interstitial_impurities(conc_of_impurities, no_of_impurities=no_of_impurities, label=void_type)
             #write mapping for the operation
             if self.sample.toPython() != sys.sample.toPython():
-                activity = self.graph.create_node(f"activity:{uuid.uuid4()}", PROV.Activity, label='AddAtom')
+                activity = self.graph.create_node(f"activity:{uuid.uuid4()}", UNSAFEASMO.AddAtom)
                 sys.graph.add((sys.sample, PROV.wasDerivedFrom, self.sample))
                 sys.graph.add((sys.sample, PROV.wasGeneratedBy, activity))
         return sys
@@ -2512,7 +2512,7 @@ def rotate(self, rotation_vectors, graph=None, label=None):
 
     def add_rotation_triples(self, rotation_vectors, child_sample_id):
         activity_id = f"operation:{uuid.uuid4()}"
-        activity = self.graph.create_node(activity_id, UNSAFEASMO.RotationOperation)
+        activity = self.graph.create_node(activity_id, UNSAFEASMO.Rotation)
         self.graph.add((child_sample_id, PROV.wasGeneratedBy, activity))
         self.graph.add((child_sample_id, PROV.wasDerivedFrom, self.sample))
 
@@ -2594,7 +2594,7 @@ def translate(self, translation_vector,
 
     def add_translation_triples(self, translation_vector, plane, distance, ):
         activity_id = f"operation:{uuid.uuid4()}"
-        activity = self.graph.create_node(activity_id, UNSAFEASMO.TranslationOperation)
+        activity = self.graph.create_node(activity_id, UNSAFEASMO.Translation)
         self.graph.add((self.sample, PROV.wasGeneratedBy, activity))
 
         #now add specifics
@@ -2634,7 +2634,7 @@ def shear(self, shear_vector,
 
     def add_shear_triples(self, translation_vector, plane, distance, ):
         activity_id = f"operation:{uuid.uuid4()}"
-        activity = self.graph.create_node(activity_id, UNSAFEASMO.ShearOperation)
+        activity = self.graph.create_node(activity_id, UNSAFEASMO.Shear)
         self.graph.add((self.sample, PROV.wasGeneratedBy, activity))
 
         #now add specifics
@@ -2647,12 +2647,14 @@ def add_shear_triples(self, translation_vector, plane, distance, ):
 
         #if plane is provided, add that as well
         if plane is not None:
-            plane_vector = self.graph.create_node(f"{activity_id}_PlaneVector", CMSO.Vector)
-            self.graph.add((activity, UNSAFECMSO.hasPlane, plane_vector))
+            plane = self.graph.create_node(f"{activity_id}_Plane", CMSO.Plane)
+            plane_vector = self.graph.create_node(f"{activity_id}_PlaneVector", UNSAFECMSO.NormalVector)
+            self.graph.add((activity, UNSAFECMSO.hasPlane, plane))
+            self.graph.add((plane, UNSAFECMSO.hasNormalVector, plane_vector))
             self.graph.add((plane_vector, CMSO.hasComponent_x, Literal(plane[0], datatype=XSD.float),))
             self.graph.add((plane_vector, CMSO.hasComponent_y, Literal(plane[1], datatype=XSD.float),))
             self.graph.add((plane_vector, CMSO.hasComponent_z, Literal(plane[2], datatype=XSD.float),))
-            self.graph.add((activity, UNSAFECMSO.hasDistance, Literal(distance, datatype=XSD.float)))
+            self.graph.add((plane, UNSAFECMSO.hasDistanceFromOrigin, Literal(distance, datatype=XSD.float)))
 
     def copy_defects(self, parent_sample):
         if self.sample is None: