addresses #338 (comment)

src/ga4gh/core/__init__.py

@@ -13,7 +13,7 @@
     parse_ga4gh_identifier, GA4GHComputeIdentifierWhen, use_ga4gh_compute_identifier_when
 )
 from ._internal.pydantic import (
-    is_pydantic_instance, is_curie_type, is_identifiable, is_literal, pydantic_copy
+    is_pydantic_instance, is_curie_type, is_ga4gh_identifiable, is_literal, pydantic_copy
 )
 from ._internal import models as core_models
 

src/ga4gh/core/_internal/enderef.py

@@ -15,7 +15,7 @@
     is_pydantic_instance,
     is_list,
     is_curie_type,
-    is_identifiable,
+    is_ga4gh_identifiable,
     get_pydantic_root,
     pydantic_copy)
 
@@ -60,7 +60,7 @@ def _enref(o):
 
     if not is_pydantic_instance(o):
         raise ValueError("Called ga4gh_enref() with non-pydantic instance")
-    if not is_identifiable(o):
+    if not is_ga4gh_identifiable(o):
         raise ValueError("Called ga4gh_enref() with non-identifiable object")
 
     # in-place replacement on object copy
@@ -101,7 +101,7 @@ def _deref(o):
 
     if not is_pydantic_instance(o):
         raise ValueError("Called ga4gh_deref() with non-non-pydantic instance")
-    if not is_identifiable(o):
+    if not is_ga4gh_identifiable(o):
         raise ValueError("Called ga4gh_deref() with non-identifiable object")
 
     # in-place replacement on object copy

src/ga4gh/core/_internal/identifiers.py

@@ -28,7 +28,7 @@
 from .pydantic import (
     is_pydantic_instance,
     is_curie_type,
-    is_identifiable,
+    is_ga4gh_identifiable,
     getattr_in,
     get_pydantic_root,
     is_pydantic_custom_type
@@ -143,7 +143,7 @@ def ga4gh_identify(vro):
     'ga4gh:VSL.u5fspwVbQ79QkX6GHLF8tXPCAXFJqRPx'
 
     """
-    if is_identifiable(vro):
+    if is_ga4gh_identifiable(vro):
         when_rule = ga4gh_compute_identifier_when.get(GA4GHComputeIdentifierWhen.ALWAYS)
         do_compute = False
         ir = None
@@ -307,7 +307,7 @@ def identify_all(
             # Assumes any obj with 'digest' should be collapsed.
             collapsed_output_obj = collapse_identifiable_values(output_obj)
             # Add a digest to the output if it is identifiable
-            if is_identifiable(input_obj):
+            if is_ga4gh_identifiable(input_obj):
                 # Compute digest for updated object, not re-running compaction
                 output_obj["digest"] = ga4gh_digest(collapsed_output_obj, do_compact=False)
     else:

src/ga4gh/core/_internal/pydantic.py

@@ -21,15 +21,15 @@ def getattr_in(obj, names) -> Any:
     return v
 
 
-def is_identifiable(o: Any) -> bool:
+def is_ga4gh_identifiable(o: Any) -> bool:
     """
-    Determine if object is identifiable. An object is considered identifiable if
-    contains a `ga4gh_digest` attribute
+    Determine if object is GA4GH identifiable. An object is considered
+    GA4GH identifiable if it contains a `ga4gh_prefix` attribute
 
     :param o: Object
-    :return: `True` if `o` has `ga4gh_digest` attribute. `False` otherwise.
+    :return: `True` if `o` has `ga4gh_prefix` attribute. `False` otherwise.
     """
-    return getattr_in(o, ['ga4gh', 'identifiable'])
+    return bool(getattr_in(o, ['ga4gh', 'prefix']))
 
 
 def is_literal(o: Any) -> bool:

src/ga4gh/vrs/_internal/models.py

@@ -26,7 +26,7 @@
 from pydantic import BaseModel, ConfigDict, Field, RootModel, constr
 
 from ga4gh.core._internal.pydantic import (
-    is_identifiable,
+    is_ga4gh_identifiable,
     getattr_in
 )
 from ga4gh.core._internal.models import IRI, _Entity
@@ -91,7 +91,7 @@ def pydantic_class_refatt_map():
     # Types directly reffable
     reffable_classes = list(filter(
         lambda c: ('id' in c.model_fields
-                   and is_identifiable(c)),
+                   and is_ga4gh_identifiable(c)),
         model_classes
     ))
     # Types reffable because they are a union of reffable types
@@ -172,16 +172,17 @@ class _ValueObject(_Entity):
         description='A sha512t24u digest created using the VRS Computed Identifier algorithm.',
     )
 
+    class ga4gh:
+        keys: List[str]
+
 
 class _Ga4ghIdentifiableObject(_ValueObject):
     """A contextual value object for which a GA4GH computed identifier can be created."""
 
     type: str
 
-    class ga4gh:
-        identifiable = True
+    class ga4gh(_ValueObject.ga4gh):
         prefix: str
-        keys: List[str]
 
 
 class Expression(BaseModel):
@@ -239,7 +240,7 @@ class SequenceReference(_ValueObject):
     )
     residueAlphabet: Optional[ResidueAlphabet] = None
 
-    class ga4gh(_Ga4ghIdentifiableObject.ga4gh):
+    class ga4gh(_ValueObject.ga4gh):
         assigned: bool = Field(
             True,
             description='This special property indicates that the `digest` field follows an alternate convention and is expected to have the value assigned following that convention. For SequenceReference, it is expected the digest will be the refget accession value without the `SQ.` prefix.'
@@ -262,7 +263,7 @@ class ReferenceLengthExpression(_ValueObject):
         None, description='The number of residues in the repeat subunit.'
     )
 
-    class ga4gh(_Ga4ghIdentifiableObject.ga4gh):
+    class ga4gh(_ValueObject.ga4gh):
         keys = [
             'length',
             'repeatSubunitLength',
@@ -278,8 +279,7 @@ class LiteralSequenceExpression(_ValueObject):
     )
     sequence: SequenceString = Field(..., description='the literal sequence')
 
-    class ga4gh(_Ga4ghIdentifiableObject.ga4gh):
-        identifiable = False
+    class ga4gh(_ValueObject.ga4gh):
         keys = [
             'sequence',
             'type'
@@ -421,7 +421,6 @@ class GenotypeMember(_ValueObject):
     )
 
     class ga4gh(_Ga4ghIdentifiableObject.ga4gh):
-        identifiable = False
         keys = [
             'type',
             'count',