Ensure multivalued slots appear in YAML serialization

src/gocam/cli.py

@@ -69,7 +69,7 @@ def fetch(model_ids, format):
 
     for model_id in model_ids:
         model = wrapper.fetch_model(model_id)
-        model_dict = model.model_dump(exclude_none=True, exclude_unset=True)
+        model_dict = model.model_dump(exclude_none=True, exclude_defaults=True)
 
         if format == "json":
             click.echo(json.dumps(model_dict, indent=2))

src/gocam/translation/minerva_wrapper.py

@@ -68,7 +68,9 @@ def _annotations_multivalued(obj: Dict) -> Dict[str, List[str]]:
 
 def _setattr_with_warning(obj, attr, value):
     if getattr(obj, attr, None) is not None:
-        logger.warning(f"Overwriting {attr} for {obj.id if hasattr(obj, 'id') else obj}")
+        logger.warning(
+            f"Overwriting {attr} for {obj.id if hasattr(obj, 'id') else obj}"
+        )
     setattr(obj, attr, value)
 
 
@@ -320,8 +322,6 @@ def _iter_activities_by_fact_subject(
         for activity, term, evs in _iter_activities_by_fact_subject(
             fact_property=HAS_INPUT
         ):
-            if activity.has_input is None:
-                activity.has_input = []
             activity.has_input.append(MoleculeAssociation(term=term, evidence=evs))
 
         for activity, term, evs in _iter_activities_by_fact_subject(
@@ -333,8 +333,6 @@ def _iter_activities_by_fact_subject(
         for activity, term, evs in _iter_activities_by_fact_subject(
             fact_property=HAS_OUTPUT
         ):
-            if activity.has_output is None:
-                activity.has_output = []
             activity.has_output.append(MoleculeAssociation(term=term, evidence=evs))
 
         for activity, term, evs in _iter_activities_by_fact_subject(
@@ -368,8 +366,6 @@ def _iter_activities_by_fact_subject(
                     downstream_activity=object_activity.id,
                     evidence=evs,
                 )
-                if not subject_activity.causal_associations:
-                    subject_activity.causal_associations = []
                 subject_activity.causal_associations.append(rel)
 
         annotations = _annotations(obj)

tests/test_translation/test_minerva_wrapper.py

@@ -96,6 +96,8 @@ def test_multivalued_input_and_output():
         minerva_object = json.load(f)
     model = mw.minerva_object_to_model(minerva_object)
 
-    cs_activity = next(a for a in model.activities if a.molecular_function.term == "GO:0004108")
+    cs_activity = next(
+        a for a in model.activities if a.molecular_function.term == "GO:0004108"
+    )
     assert len(cs_activity.has_input) == 3
     assert len(cs_activity.has_output) == 2