From ca959547bebd65385497a26176ef47e0d5005754 Mon Sep 17 00:00:00 2001
From: samwaseda <o.waseda@mpie.de>
Date: Thu, 23 Jan 2025 06:15:43 +0000
Subject: [PATCH 1/2] Add test

---
 pyiron_ontology/parser.py |  8 +++++---
 tests/unit/test_parser.py | 12 ++++++++++++
 2 files changed, 17 insertions(+), 3 deletions(-)

diff --git a/pyiron_ontology/parser.py b/pyiron_ontology/parser.py
index b100272..66472bc 100644
--- a/pyiron_ontology/parser.py
+++ b/pyiron_ontology/parser.py
@@ -47,10 +47,12 @@ def get_inputs_and_outputs(node: Node) -> dict:
     for key, value in node.inputs.items():
         if inputs[key] is None:
             inputs[key] = {}
-        inputs[key]["value"] = value.value
+        if value.value is not NOT_DATA:
+            inputs[key]["value"] = value.value
         inputs[key]["connection"] = get_source_output(value)
     for key, value in node.outputs.to_value_dict().items():
-        outputs[key]["value"] = value
+        if value is not NOT_DATA:
+            outputs[key]["value"] = value
     return {
         "inputs": inputs,
         "outputs": outputs,
@@ -129,7 +131,7 @@ def get_triples(
             graph.add((label, RDF.type, PROV.Entity))
             if d.get("uri", None) is not None:
                 graph.add((label, RDF.type, URIRef(d["uri"])))
-            if d.get("value", NOT_DATA) is not NOT_DATA:
+            if "value" in d:
                 graph.add((label, RDF.value, Literal(d["value"])))
             if io_ == "inputs":
                 graph.add((label, PNS.inputOf, URIRef(full_label)))
diff --git a/tests/unit/test_parser.py b/tests/unit/test_parser.py
index 530f381..afc3b4f 100644
--- a/tests/unit/test_parser.py
+++ b/tests/unit/test_parser.py
@@ -178,6 +178,18 @@ def test_namespace(self):
         with self.assertRaises(AttributeError):
             _ = PNS.ahoy
 
+    def test_parsing_without_running(self):
+        wf = Workflow("correct_analysis")
+        wf.addition = add(a=1.0, b=2.0)
+        data = get_inputs_and_outputs(wf.addition)
+        self.assertFalse("value" in data["outputs"])
+        graph = get_triples(data)
+        self.assertEqual(len(list(graph.triples((None, RDF.value, None)))), 2)
+        wf.run()
+        data = get_inputs_and_outputs(wf.addition)
+        graph = get_triples(data)
+        self.assertEqual(len(list(graph.triples((None, RDF.value, None)))), 3)
+
 
 if __name__ == "__main__":
     unittest.main()

From 24554dd8ed0fefe262ee93f183093c63dafca80b Mon Sep 17 00:00:00 2001
From: samwaseda <o.waseda@mpie.de>
Date: Thu, 23 Jan 2025 06:16:39 +0000
Subject: [PATCH 2/2] add error messages

---
 tests/unit/test_parser.py | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/tests/unit/test_parser.py b/tests/unit/test_parser.py
index afc3b4f..d6bb36d 100644
--- a/tests/unit/test_parser.py
+++ b/tests/unit/test_parser.py
@@ -184,11 +184,19 @@ def test_parsing_without_running(self):
         data = get_inputs_and_outputs(wf.addition)
         self.assertFalse("value" in data["outputs"])
         graph = get_triples(data)
-        self.assertEqual(len(list(graph.triples((None, RDF.value, None)))), 2)
+        self.assertEqual(
+            len(list(graph.triples((None, RDF.value, None)))),
+            2,
+            msg="There should be only values for a and b, but not for the output",
+        )
         wf.run()
         data = get_inputs_and_outputs(wf.addition)
         graph = get_triples(data)
-        self.assertEqual(len(list(graph.triples((None, RDF.value, None)))), 3)
+        self.assertEqual(
+            len(list(graph.triples((None, RDF.value, None)))),
+            3,
+            msg="There should be values for a, b and the output",
+        )
 
 
 if __name__ == "__main__":