Fix default reference output in OBO flat file format

src/pyobo/struct/reference.py

@@ -185,12 +185,16 @@ def default_reference(prefix: str, identifier: str, name: str | None = None) ->
     return Reference(prefix="obo", identifier=f"{prefix}#{identifier}", name=name)
 
 
-def reference_escape(predicate: Reference | Referenced, *, ontology_prefix: str) -> str:
+def reference_escape(
+    reference: Reference | Referenced, *, ontology_prefix: str, add_name_comment: bool = False
+) -> str:
     """Write a reference with default namespace removed."""
-    if predicate.prefix == "obo" and predicate.identifier.startswith(f"{ontology_prefix}#"):
-        return predicate.identifier.removeprefix(f"{ontology_prefix}#")
-    else:
-        return predicate.preferred_curie
+    if reference.prefix == "obo" and reference.identifier.startswith(f"{ontology_prefix}#"):
+        return reference.identifier.removeprefix(f"{ontology_prefix}#")
+    rv = reference.preferred_curie
+    if add_name_comment and reference.name:
+        rv += f" ! {reference.name}"
+    return rv
 
 
 def comma_separate_references(references: list[Reference]) -> str:

src/pyobo/struct/struct.py

@@ -526,7 +526,7 @@ def iterate_obo_lines(
     ) -> Iterable[str]:
         """Iterate over the lines to write in an OBO file."""
         yield f"\n[{self.type}]"
-        yield f"id: {self.preferred_curie}"
+        yield f"id: {self._reference(self.reference, ontology_prefix)}"
         if self.is_obsolete:
             yield "is_obsolete: true"
         if self.name:
@@ -543,14 +543,14 @@ def iterate_obo_lines(
             yield f"def: {self._definition_fp()}"
 
         for alt in sorted(self.alt_ids):
-            yield f"alt_id: {alt}"  # __str__ bakes in the ! name
+            yield f"alt_id: {self._reference(alt, ontology_prefix, add_name_comment=True)}"
 
         for xref in sorted(xrefs):
-            yield f"xref: {xref}"  # __str__ bakes in the ! name
+            yield f"xref: {self._reference(xref, ontology_prefix, add_name_comment=True)}"
 
         parent_tag = "is_a" if self.type == "Term" else "instance_of"
         for parent in sorted(self.parents):
-            yield f"{parent_tag}: {parent}"  # __str__ bakes in the ! name
+            yield f"{parent_tag}: {self._reference(parent, ontology_prefix, add_name_comment=True)}"
 
         if emit_object_properties:
             yield from self._emit_relations(ontology_prefix, typedefs)
@@ -608,8 +608,12 @@ def _emit_literal_properties(
                 yield f'{predicate_curie} "{value}" {datatype.preferred_curie}'
 
     @staticmethod
-    def _reference(predicate: Reference, ontology_prefix: str) -> str:
-        return reference_escape(predicate, ontology_prefix=ontology_prefix)
+    def _reference(
+        predicate: Reference, ontology_prefix: str, add_name_comment: bool = False
+    ) -> str:
+        return reference_escape(
+            predicate, ontology_prefix=ontology_prefix, add_name_comment=add_name_comment
+        )
 
     @staticmethod
     def _escape(s) -> str:

tests/test_struct.py

@@ -520,3 +520,15 @@ def test_see_also_double(self) -> None:
 
         self.assertIsNone(term.get_relationship(exact_match))
         self.assertIsNone(term.get_species())
+
+    def test_default_term(self) -> None:
+        """Test when a term uses a default reference."""
+        term = Term(reference=default_reference("gard", identifier="genetics", name="Genetics"))
+        self.assert_lines(
+            """\
+            [Term]
+            id: genetics
+            name: Genetics
+            """,
+            term.iterate_obo_lines(ontology_prefix="gard", typedefs={}),
+        )