add labels for defects

pyscal · May 28, 2024 · b873e63 · b873e63
1 parent 3e6dc1b
commit b873e63
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Showing 2 changed files with 7 additions and 3 deletions.
diff --git a/atomrdf/network/ontology.py b/atomrdf/network/ontology.py
@@ -84,6 +84,7 @@ def read_ontology():
     #CMSO -> PODO IMPURITY
     combo.add_path(("cmso:Material", "cmso:hasDefect", "podo:SubstitutionalImpurity"))
     combo.add_path(("cmso:Material", "cmso:hasDefect", "podo:InterstitialImpurity"))
+    combo.add_path(("podo:InterstitialImpurity", "rdfs:label", "string"))
     combo.add_path(("cmso:AtomicScaleSample", "podo:hasNumberOfImpurityAtoms", "int"))
     combo.add_path(("cmso:AtomicScaleSample", "podo:hasImpurityConcentration", "float"))
 

diff --git a/atomrdf/structure.py b/atomrdf/structure.py
@@ -1065,11 +1065,14 @@ def add_interstitial_impurities(
             )
             json_io.write_file(outfile, datadict)
 
-            self.add_triples_for_interstitial_impurities(conc_of_impurities, no_of_impurities=no_of_impurities)
+            self.add_triples_for_interstitial_impurities(conc_of_impurities, no_of_impurities=no_of_impurities, label=void_type)
         return sysn
 
-    def add_triples_for_interstitial_impurities(self, conc_of_impurities, no_of_impurities=None):
-        defect = self.graph.create_node(f"{self._name}_InterstitialImpurity", PODO.InterstitialImpurity)
+    def add_triples_for_interstitial_impurities(self, conc_of_impurities, no_of_impurities=None, label=None):
+        if label is not None:
+            defect = self.graph.create_node(f"{self._name}_InterstitialImpurity", PODO.InterstitialImpurity, label=label)
+        else:
+            defect = self.graph.create_node(f"{self._name}_InterstitialImpurity", PODO.InterstitialImpurity)
         self.graph.add((self.material, CMSO.hasDefect, defect))
         self.graph.add((self.sample, PODO.hasImpurityConcentration, Literal(conc_of_impurities, datatype=XSD.float)))
         if no_of_impurities is not None: