From ad0226dcf31e538d2f8c187ebf70079bda72c75a Mon Sep 17 00:00:00 2001
From: Charles Tapley Hoyt <cthoyt@gmail.com>
Date: Tue, 21 Jan 2025 19:38:13 +0100
Subject: [PATCH] Refactor common code for serializing references/literals

---
 src/pyobo/struct/reference.py | 19 ++++++++++---------
 src/pyobo/struct/struct.py    | 16 +++-------------
 2 files changed, 13 insertions(+), 22 deletions(-)

diff --git a/src/pyobo/struct/reference.py b/src/pyobo/struct/reference.py
index c988a228..4451da5c 100644
--- a/src/pyobo/struct/reference.py
+++ b/src/pyobo/struct/reference.py
@@ -250,15 +250,7 @@ def multi_reference_escape(
 
 def comma_separate_references(elements: Iterable[Reference | OBOLiteral]) -> str:
     """Map a list to strings and make comma separated."""
-    parts = []
-    for element in elements:
-        match element:
-            case Reference():
-                parts.append(get_preferred_curie(element))
-            case OBOLiteral(value, _datatype, _language):
-                # TODO check datatype is URI
-                parts.append(value)
-    return ", ".join(parts)
+    return ", ".join(reference_or_literal_to_str(element) for element in elements)
 
 
 def _ground_relation(relation_str: str) -> Reference | None:
@@ -343,3 +335,12 @@ def _reference_list_tag(
 ) -> Iterable[str]:
     for reference in references:
         yield f"{tag}: {reference_escape(reference, ontology_prefix=ontology_prefix, add_name_comment=True)}"
+
+
+def reference_or_literal_to_str(x: Reference | OBOLiteral) -> str:
+    """Get a string from a reference or literal."""
+    match x:
+        case Reference():
+            return get_preferred_curie(x)
+        case OBOLiteral(value, _, _):
+            return value
diff --git a/src/pyobo/struct/struct.py b/src/pyobo/struct/struct.py
index 628369a0..7998b62e 100644
--- a/src/pyobo/struct/struct.py
+++ b/src/pyobo/struct/struct.py
@@ -36,6 +36,7 @@
     default_reference,
     get_preferred_curie,
     reference_escape,
+    reference_or_literal_to_str,
 )
 from .struct_utils import (
     Annotation,
@@ -341,14 +342,7 @@ def extend_parents(self, references: Collection[Reference]) -> None:
 
     def get_property_literals(self, prop: ReferenceHint) -> list[str]:
         """Get properties from the given key."""
-        rv = []
-        for t in self.properties.get(_ensure_ref(prop), []):
-            match t:
-                case Reference():
-                    rv.append(get_preferred_curie(t))
-                case OBOLiteral(value, _datatype, _language):
-                    rv.append(value)
-        return rv
+        return [reference_or_literal_to_str(t) for t in self.properties.get(_ensure_ref(prop), [])]
 
     def get_property(self, prop: ReferenceHint) -> str | None:
         """Get a single property of the given key."""
@@ -1548,11 +1542,7 @@ def iterate_filtered_properties(
             for t in term.get_property_annotations():
                 if t.predicate != prop:
                     continue
-                match t.value:
-                    case OBOLiteral(value, _datatype):
-                        yield term, value
-                    case Reference():
-                        yield term, get_preferred_curie(t.value)
+                yield term, reference_or_literal_to_str(t.value)
 
     def get_filtered_properties_df(
         self, prop: ReferenceHint, *, use_tqdm: bool = False