fix: revert Pydantic custom serializer (#435)

* The Pydantic custom serializer resulted in `model_dump` to only
include minimal fields for ga4gh serialization. This caused issues in
downstream apps that leverage FastAPI

pyproject.toml

@@ -38,6 +38,7 @@ dependencies = [
     "pydantic~=2.1",
     "bioutils",
     "requests",
+    "canonicaljson",
 ]
 
 [project.optional-dependencies]

src/ga4gh/core/entity_models.py

@@ -14,7 +14,7 @@
 from typing import Any, Dict, Annotated, Optional, Union, List
 from enum import Enum
 
-from pydantic import BaseModel, Field, RootModel, StringConstraints, model_serializer, ConfigDict
+from pydantic import BaseModel, Field, RootModel, StringConstraints, ConfigDict
 
 from ga4gh.core import GA4GH_IR_REGEXP
 
@@ -78,7 +78,6 @@ class IRI(RootModel):
     def __hash__(self):
         return self.root.__hash__()
 
-    @model_serializer(when_used='json')
     def ga4gh_serialize(self):
         m = GA4GH_IR_REGEXP.match(self.root)
         if m is not None:

src/ga4gh/core/identifiers.py

@@ -14,7 +14,7 @@
 For that reason, they are implemented here in one file.
 
 """
-
+from canonicaljson import encode_canonical_json
 import contextvars
 import re
 from contextlib import ContextDecorator
@@ -194,6 +194,6 @@ def ga4gh_serialize(obj: BaseModel, as_version: PrevVrsVersion | None = None) ->
     PrevVrsVersion.validate(as_version)
 
     if as_version is None:
-        return obj.model_dump_json().encode("utf-8")
+        return encode_canonical_json(obj.ga4gh_serialize())
     else:
         return obj.ga4gh_serialize_as_version(as_version)

src/ga4gh/vrs/models.py

@@ -26,7 +26,8 @@
 )
 from ga4gh.core.pydantic import get_pydantic_root
 
-from pydantic import BaseModel, Field, RootModel, StringConstraints, model_serializer, ConfigDict
+from canonicaljson import encode_canonical_json
+from pydantic import BaseModel, Field, RootModel, StringConstraints, ConfigDict
 
 from ga4gh.core.pydantic import (
     getattr_in
@@ -178,7 +179,7 @@ def _recurse_ga4gh_serialize(obj):
     elif isinstance(obj, _ValueObject):
         return obj.ga4gh_serialize()
     elif isinstance(obj, RootModel):
-        return _recurse_ga4gh_serialize(obj.model_dump(mode='json'))
+        return _recurse_ga4gh_serialize(obj.model_dump())
     elif isinstance(obj, str):
         return obj
     elif isinstance(obj, list):
@@ -193,9 +194,8 @@ class _ValueObject(DomainEntity, ABC):
     """
 
     def __hash__(self):
-        return self.model_dump_json().__hash__()
+        return encode_canonical_json(self.ga4gh_serialize()).decode("utf-8").__hash__()
 
-    @model_serializer(when_used='json')
     def ga4gh_serialize(self) -> Dict:
         out = OrderedDict()
         for k in self.ga4gh.keys:
@@ -242,7 +242,7 @@ def compute_digest(self, store=True, as_version: PrevVrsVersion | None = None) -
         returned following the conventions of the VRS version indicated by ``as_version_``.
         """
         if as_version is None:
-            digest = sha512t24u(self.model_dump_json().encode("utf-8"))
+            digest = sha512t24u(encode_canonical_json(self.ga4gh_serialize()))
             if store:
                 self.digest = digest
         else:
@@ -580,7 +580,6 @@ class CisPhasedBlock(_VariationBase):
     )
     sequenceReference: Optional[SequenceReference] = Field(None, description="An optional Sequence Reference on which all of the in-cis Alleles are found. When defined, this may be used to implicitly define the `sequenceReference` attribute for each of the CisPhasedBlock member Alleles.")
 
-    @model_serializer(when_used="json")
     def ga4gh_serialize(self) -> Dict:
         out = _ValueObject.ga4gh_serialize(self)
         out["members"] = sorted(out["members"])

tests/validation/test_models.py

@@ -24,7 +24,7 @@ def ga4gh_1_3_serialize(*args, **kwargs):
     return ga4gh_serialize(*args, **kwargs)
 
 fxs = {
-    "ga4gh_serialize": lambda o: ga4gh_serialize(o).decode() if ga4gh_serialize(o) else None,
+    "ga4gh_serialize": ga4gh_serialize,
     "ga4gh_digest": ga4gh_digest,
     "ga4gh_identify": ga4gh_identify,
     "ga4gh_1_3_digest": ga4gh_1_3_digest,
@@ -60,6 +60,8 @@ def flatten_tests(vts):
 def test_validation(cls, data, fn, exp):
     o = getattr(models, cls)(**data)
     fx = fxs[fn]
+    if fn == "ga4gh_serialize":
+        exp = exp.encode("utf-8")
     assert fx(o) == exp