Add intermediate named reference class (#155)

biopragmatics · Feb 5, 2025 · 4a42b1a · 4a42b1a
1 parent c4fb747
commit 4a42b1a
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Showing 3 changed files with 47 additions and 1 deletion.
diff --git a/src/curies/__init__.py b/src/curies/__init__.py
@@ -5,6 +5,7 @@
     DuplicatePrefixes,
     DuplicateURIPrefixes,
     DuplicateValueError,
+    NamableReference,
     NamedReference,
     Prefix,
     PrefixMap,
@@ -39,6 +40,7 @@
     "DuplicatePrefixes",
     "DuplicateURIPrefixes",
     "DuplicateValueError",
+    "NamableReference",
     "NamedReference",
     "Prefix",
     "PrefixMap",

diff --git a/src/curies/api.py b/src/curies/api.py
@@ -45,6 +45,7 @@
     "DuplicatePrefixes",
     "DuplicateURIPrefixes",
     "DuplicateValueError",
+    "NamableReference",
     "NamedReference",
     "Prefix",
     "PrefixMap",
@@ -458,7 +459,46 @@ def from_curie(
         return cls.model_validate({"prefix": prefix, "identifier": identifier}, context=converter)
 
 
-class NamedReference(Reference):
+class NamableReference(Reference):
+    """A reference, maybe with a name."""
+
+    name: str | None = Field(
+        None,
+        description="The name of the entity referenced by this object's prefix and identifier, if exists.",
+    )
+
+    model_config = ConfigDict(frozen=True)
+
+    @classmethod
+    def from_curie(  # type:ignore
+        cls,
+        curie: str,
+        name: str | None = None,
+        *,
+        sep: str = ":",
+        converter: Converter | None = None,
+    ) -> NamableReference:
+        """Parse a CURIE string and populate a reference.
+
+        :param curie: A string representation of a compact URI (CURIE)
+        :param name: The optional name of the reference
+        :param sep: The separator
+        :param converter: The converter to use as context when parsing
+        :return: A reference object
+
+        >>> NamableReference.from_curie("chebi:1234")
+        NamableReference(prefix='chebi', identifier='1234', name=None)
+
+        >>> NamableReference.from_curie("chebi:1234", "6-methoxy-2-octaprenyl-1,4-benzoquinone")
+        NamableReference(prefix='chebi', identifier='1234', name='6-methoxy-2-octaprenyl-1,4-benzoquinone')
+        """
+        prefix, identifier = _split(curie, sep=sep)
+        return cls.model_validate(
+            {"prefix": prefix, "identifier": identifier, "name": name}, context=converter
+        )
+
+
+class NamedReference(NamableReference):
     """A reference with a name."""
 
     name: str = Field(

diff --git a/tests/test_api.py b/tests/test_api.py
@@ -17,6 +17,7 @@
     DuplicatePrefixes,
     DuplicateURIPrefixes,
     ExpansionError,
+    NamableReference,
     NamedReference,
     NoCURIEDelimiterError,
     PrefixStandardizationError,
@@ -108,7 +109,9 @@ def test_named_set_membership(self) -> None:
             NamedReference.from_curie("a:2", "name2"),
         }
         self.assertIn(Reference.from_curie("a:1"), references)
+        self.assertIn(NamableReference.from_curie("a:1"), references)
         self.assertIn(NamedReference.from_curie("a:1", "name1"), references)
+        self.assertIn(NamableReference.from_curie("a:1", "name1"), references)
         # the following is a weird case, but shows how this works
         self.assertIn(NamedReference.from_curie("a:1", "name2"), references)
 
@@ -117,6 +120,7 @@ def test_named_set_membership(self) -> None:
             Reference.from_curie("a:2"),
         }
         self.assertIn(Reference.from_curie("a:1"), references_2)
+        self.assertIn(NamableReference.from_curie("a:1", "name1"), references_2)
         self.assertIn(NamedReference.from_curie("a:1", "name1"), references_2)