Merge pull request #122 from pyiron/property

Append properties not defined in the graph
pyiron · Feb 8, 2025 · b89e516 · b89e516
2 parents 19af8df + 355d08e
commit b89e516
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Showing 2 changed files with 24 additions and 11 deletions.
diff --git a/pyiron_ontology/parser.py b/pyiron_ontology/parser.py
@@ -373,6 +373,7 @@ def parse_workflow(
     graph: Graph | None = None,
     inherit_properties: bool = True,
     ontology=PNS,
+    append_missing_items: bool = True,
 ) -> Graph:
     """
     Generate RDF graph from a pyiron workflow object
@@ -405,4 +406,22 @@ def parse_workflow(
         )
     if inherit_properties:
         _inherit_properties(graph, ontology=ontology)
+    if append_missing_items:
+        graph = _append_missing_items(graph)
+    return graph
+
+
+def _append_missing_items(graph: Graph) -> Graph:
+    """
+    This function makes sure that all properties defined in the descriptions
+    become valid.
+    """
+    for p, o in zip(
+        [OWL.onProperty, OWL.someValuesFrom, OWL.allValuesFrom],
+        [RDF.Property, OWL.Class, OWL.Class],
+    ):
+        for obj in graph.objects(None, p):
+            triple = (obj, RDF.type, o)
+            if not triple in graph:
+                graph.add(triple)
     return graph
diff --git a/tests/unit/test_parser.py b/tests/unit/test_parser.py
@@ -136,13 +136,7 @@ def test_triples(self):
 
     def test_correct_analysis(self):
         def get_graph(wf):
-            graph = Graph()
-            graph.add((EX.HasOperation, RDF.type, RDF.Property))
-            graph.add((EX.Addition, RDF.type, OWL.Class))
-            graph.add((EX.Multiplication, RDF.type, OWL.Class))
-            for value in wf.children.values():
-                data = get_inputs_and_outputs(value)
-                graph += get_triples(data=data)
+            graph = parse_workflow(wf)
             _inherit_properties(graph)
             DeductiveClosure(OWLRL_Semantics).expand(graph)
             return graph
@@ -173,12 +167,12 @@ def test_parse_workflow(self):
         graph = parse_workflow(wf)
         tag = "correct_analysis.addition.inputs.a"
         self.assertEqual(
-            len(list(graph.triples((URIRef(tag), RDFS.label, Literal(tag))))), 1,
+            len(list(graph.triples((URIRef(tag), RDFS.label, Literal(tag))))),
+            1,
         )
         self.assertTrue(
-            EX.Addition in list(
-                graph.objects(URIRef("correct_analysis.addition"), RDF.type)
-            )
+            EX.Addition
+            in list(graph.objects(URIRef("correct_analysis.addition"), RDF.type))
         )
 
     def test_macro(self):