Fix cases where empty list was assumed instead of None

src/gocam/translation/cx2/main.py

@@ -201,6 +201,9 @@ def _add_input_output_nodes(
 
     # Add edges for causal associations between activity nodes
     for activity in gocam.activities:
+        if activity.causal_associations is None:
+            continue
+
         for association in activity.causal_associations:
             if association.downstream_activity in activity_nodes_by_activity_id:
                 relation_style = RELATIONS.get(association.predicate, None)

src/gocam/translation/minerva_wrapper.py

@@ -322,6 +322,8 @@ 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(
@@ -333,6 +335,8 @@ 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(
@@ -366,6 +370,8 @@ def _iter_activities_by_fact_subject(
                     downstream_activity=object_activity.id,
                     evidence=evs,
                 )
+                if subject_activity.causal_associations is None:
+                    subject_activity.causal_associations = []
                 subject_activity.causal_associations.append(rel)
 
         annotations = _annotations(obj)