Merge pull request #109 from pyiron/bugfix

Move the location of units and change node names
pyiron · Jan 27, 2025 · 06f0e94 · 06f0e94
2 parents d6e38aa + 99c4a56
commit 06f0e94
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Showing 2 changed files with 55 additions and 26 deletions.
diff --git a/pyiron_ontology/parser.py b/pyiron_ontology/parser.py
@@ -62,9 +62,19 @@ def get_inputs_and_outputs(node: Node) -> dict:
     }
 
 
-def _translate_has_value(graph: Graph, label: URIRef, tag: str, value: Any):
+def _translate_has_value(
+    graph: Graph,
+    label: URIRef,
+    tag: str,
+    value: Any = None,
+    units: URIRef | None = None,
+) -> Graph:
     graph.add((label, PNS.hasValue, URIRef(tag)))
-    graph.add((URIRef(tag), RDF.value, Literal(value)))
+    if value is not None:
+        graph.add((URIRef(tag), RDF.value, Literal(value)))
+    if units is not None:
+        graph.add((URIRef(tag), PNS.hasUnits, URIRef(units)))
+        graph.add((URIRef(units), RDF.value, Literal(units)))
     return graph
 
 
@@ -142,30 +152,22 @@ def get_triples(
                 graph.add((label, PNS.inputOf, URIRef(full_label)))
             elif io_ == "outputs":
                 graph.add((label, PNS.outputOf, URIRef(full_label)))
-            if d.get("units", None) is not None:
-                graph.add((label, PNS.hasUnits, URIRef(d["units"])))
-            if "value" in d:
-                if io_ == "inputs" and d.get("connection", None) is not None:
-                    graph = _translate_has_value(
-                        graph,
-                        label,
-                        workflow_namespace + d["connection"] + ".value",
-                        d["value"],
-                    )
-                elif io_ == "inputs":
-                    graph = _translate_has_value(
-                        graph,
-                        label,
-                        str(d["value"]),
-                        d["value"],
-                    )
-                else:
-                    graph = _translate_has_value(
-                        graph,
-                        label,
-                        label + ".value",
-                        d["value"],
-                    )
+            if io_ == "inputs" and d.get("connection", None) is not None:
+                graph = _translate_has_value(
+                    graph,
+                    label,
+                    workflow_namespace + d["connection"] + ".value",
+                    d.get("value", None),
+                    units=d.get("units", None),
+                )
+            else:
+                graph = _translate_has_value(
+                    graph,
+                    label,
+                    label + ".value",
+                    d.get("value", None),
+                    units=d.get("units", None),
+                )
             if d.get("connection", None) is not None and io_ == "inputs":
                 graph.add(
                     (
@@ -283,6 +285,7 @@ def _inherit_properties(graph: Graph, n: int | None = None):
         "    FILTER(?p != ns:inheritsPropertiesFrom)",
         "    FILTER(?p != rdfs:label)",
         "    FILTER(?p != rdf:value)",
+        "    FILTER(?p != ns:hasValue)",
         "    FILTER(?p != rdf:type)",
         "}",
     )

diff --git a/tests/unit/test_parser.py b/tests/unit/test_parser.py
@@ -88,6 +88,32 @@ def test_parser(self):
         for label in ["inputs", "outputs", "function", "label"]:
             self.assertIn(label, output_dict)
 
+    def test_units_with_sparql(self):
+        wf = Workflow("speed")
+        wf.speed = calculate_speed()
+        wf.run()
+        graph = parse_workflow(wf)
+        query_txt = [
+            "PREFIX ex: <http://example.org/>",
+            "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>",
+            f"PREFIX pns: <{PNS.BASE}>",
+            "SELECT DISTINCT ?speed ?units",
+            "WHERE {",
+            "    ?output pns:hasValue ?output_tag .",
+            "    ?output_tag rdf:value ?speed .",
+            "    ?output_tag pns:hasUnits ?units_arg .",
+            "    ?units_arg rdf:value ?units .",
+            "}",
+        ]
+        query = "\n".join(query_txt)
+        results = graph.query(query)
+        self.assertEqual(len(results), 3)
+        result_list = [[value.value for value in row] for row in graph.query(query)]
+        self.assertEqual(
+            sorted(result_list),
+            [[2.0, "second"], [5.0, "meter/second"], [10.0, "meter"]],
+        )
+
     def test_triples(self):
         speed = calculate_speed()
         data = get_inputs_and_outputs(speed)