Solves ClassCreation duplication & formats Mappings md table properly

src/oaklib/implementations/simpleobo/simple_obo_implementation.py

@@ -822,16 +822,22 @@ def _id():
             return generate_change_id()
 
         node_is_deleted = False
+        node_is_created = False
         if stanza1 is None and stanza2 is None:
             raise ValueError("Both stanzas are None")
         if stanza1 is None:
             stanza1 = Stanza(id=stanza2.id, type=stanza2.type)
             if stanza2.type == "Term":
-                yield kgcl.ClassCreation(id=_id(), about_node=stanza2.id)
+                yield kgcl.ClassCreation(
+                    id=_id(), about_node=stanza2.id, name=stanza2.singular_value(TAG_NAME)
+                )
             elif stanza2.type == "Typedef":
-                yield kgcl.NodeCreation(id=_id(), about_node=stanza2.id)
+                yield kgcl.NodeCreation(
+                    id=_id(), about_node=stanza2.id, name=stanza2.singular_value(TAG_NAME)
+                )
             else:
                 raise ValueError(f"Unknown stanza type: {stanza2.type}")
+            node_is_created = True
         if stanza2 is None:
             stanza2 = Stanza(id=stanza1.id, type=stanza1.type)
             if stanza1.type == "Term":
@@ -867,16 +873,23 @@ def _tv_dict(stanza: Stanza) -> Dict[str, List[str]]:
                 continue
             logging.info(f"Difference in {tag}: {vals1} vs {vals2}")
             if tag == TAG_NAME:
-                if node_is_deleted:
+                if node_is_deleted or node_is_created:
                     continue
                 if vals1 and vals2:
                     yield kgcl.NodeRename(
                         id=_id(), about_node=t1id, new_value=vals2list[0], old_value=vals1list[0]
                     )
-                elif vals1:
-                    yield kgcl.NodeDeletion(id=_id(), about_node=t1id)
+                elif vals2:
+                    # Existing node goes from having no name to having a name
+                    # In future KGCL may have a NodeNewName. For now we use NodeRename.
+                    yield kgcl.NodeRename(
+                        id=_id(), about_node=t1id, new_value=vals2list[0], old_value=None
+                    )
                 else:
-                    yield kgcl.ClassCreation(id=_id(), about_node=t2id, name=vals2list[0])
+                    #! KGCL may have NameDeletion in the future.
+                    yield kgcl.NodeRename(
+                        id=_id(), about_node=t2id, old_value=vals2list[0], new_value=None
+                    )
             elif tag == TAG_DEFINITION:
                 if node_is_deleted:
                     continue

src/oaklib/utilities/writers/change_handler.py

@@ -307,11 +307,13 @@ def handle_add_node_to_subset(self, value):
     def handle_mapping_creation(self, value):
         rows = list(
             {
-                f"""| {self._format_entity_labels(change.subject)}
-                | {change.predicate} | {self._format_entity_labels(change.object)} |"""
+                f"""| {self._format_entity_labels(change.subject)} | """
+                f"""{change.predicate} | """
+                f"""{self._format_entity_labels(change.object)} |"""
                 for change in value
             }
         )
+
         header = "| Subject | Predicate | Object |"
         self.write_markdown_table(f"Mappings added: {len(rows)}", header, rows)
 
@@ -336,11 +338,13 @@ def handle_mapping_predicate_change(self, value):
     def handle_remove_mapping(self, value):
         rows = list(
             {
-                f"""| {self._format_entity_labels(change.about_node)}
-                | {change.predicate} | {self._format_entity_labels(change.object)} |"""
+                f"""| {self._format_entity_labels(change.about_node)} | """
+                f"""{change.predicate} | """
+                f"""{self._format_entity_labels(change.object)} |"""
                 for change in value
             }
         )
+
         header = "| Subject | Predicate | Object |"
         self.write_markdown_table(f"Mappings removed: {len(rows)}", header, rows)
 

tests/test_implementations/__init__.py

@@ -1081,7 +1081,6 @@ def test_diff(self, oi: DifferInterface, oi_modified: DifferInterface):
                 old_value="enzyme activity",
                 new_value="catalytic activity",
             ),
-            kgcl.ClassCreation(id=FIXED_ID, about_node="GO:0033673"),
             kgcl.MappingCreation(
                 id=FIXED_ID,
                 subject=CELLULAR_COMPONENT,