Merge pull request #24 from geneontology/dependabot/pip/all-dependenc…

…ies-59ef4215ff

Bump the all-dependencies group with 58 updates

Makefile

@@ -193,7 +193,7 @@ $(PYMODEL):
 	mkdir -p $@
 
 $(PYDANTIC): $(SOURCE_SCHEMA_PATH)
-	$(RUN) gen-pydantic --pydantic-version 2 $< > $@.tmp && mv $@.tmp $@
+	$(RUN) linkml generate pydantic $< > $@.tmp && mv $@.tmp $@
 
 $(DOCDIR):
 	mkdir -p $@

src/gocam/schema/gocam.yaml

@@ -238,42 +238,46 @@ classes:
   BiologicalProcessAssociation:
     description: An association between an activity and a biological process term
     is_a: TermAssociation
-    slot_usage:
-      term:
-        range: BiologicalProcessTermObject
+    attributes:
       happens_during:
         description: Optional extension describing where the BP takes place
         range: PhaseTermObject
       part_of:
         description: Optional extension allowing hierarchical nesting of BPs
         range: BiologicalProcessTermObject
+    slot_usage:
+      term:
+        range: BiologicalProcessTermObject
 
   CellularAnatomicalEntityAssociation:
     description: An association between an activity and a cellular anatomical entity term
     is_a: TermAssociation
+    attributes:
+      part_of:
+        range: CellTypeAssociation
     slot_usage:
       term:
         range: CellularAnatomicalEntityTermObject
-      part_of:
-        range: CellTypeAssociation
 
   CellTypeAssociation:
     description: An association between an activity and a cell type term
     is_a: TermAssociation
+    attributes:
+      part_of:
+        range: GrossAnatomyAssociation
     slot_usage:
       term:
         range: CellTypeTermObject
-      part_of:
-        range: GrossAnatomyAssociation
 
   GrossAnatomyAssociation:
     description: An association between an activity and a gross anatomical structure term
     is_a: TermAssociation
+    attributes:
+      part_of:
+        range: GrossAnatomyAssociation
     slot_usage:
       term:
         range: GrossAnatomicalStructureTermObject
-      part_of:
-        range: GrossAnatomyAssociation
 
   MoleculeAssociation:
     description: An association between an activity and a molecule term

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)