fix: robust synthetic property handling for mapped variants

- Refactored MappedVariant view models to ensure robust handling of synthetic and required fields for both ORM and dict contexts.
- Added tests to verify all key attributes and synthetic properties are correctly handled in both construction modes.
- Ensured creation from both dict and ORM contexts, mirroring the approach used for other models.

Author: bencap

src/mavedb/view_models/mapped_variant.py

@@ -55,13 +55,16 @@ class SavedMappedVariant(MappedVariantBase):
     class Config:
         from_attributes = True
 
+    # These 'synthetic' fields are generated from other model properties. Transform data from other properties as needed, setting
+    # the appropriate field on the model itself. Then, proceed with Pydantic ingestion once fields are created. Only perform these
+    # transformations if the relevant attributes are present on the input data (i.e., when creating from an ORM object).
     @model_validator(mode="before")
     def generate_score_set_urn_list(cls, data: Any):
-        if not hasattr(data, "variant_urn") and hasattr(data, "variant"):
+        if hasattr(data, "variant"):
             try:
                 data.__setattr__("variant_urn", None if not data.variant else data.variant.urn)
-            except AttributeError as exc:
-                raise ValidationError(f"Unable to create {cls.__name__} without attribute: {exc}.")  # type: ignore
+            except (AttributeError, KeyError) as exc:
+                raise ValidationError(f"Unable to coerce variant urn for {cls.__name__}: {exc}.")  # type: ignore
         return data
 
 
@@ -97,8 +100,8 @@ def generate_score_set_urn_list(cls, data: Any):
 
 
 # ruff: noqa: E402
-from mavedb.view_models.clinical_control import ClinicalControlBase, ClinicalControl, SavedClinicalControl
-from mavedb.view_models.gnomad_variant import GnomADVariantBase, GnomADVariant, SavedGnomADVariant
+from mavedb.view_models.clinical_control import ClinicalControl, ClinicalControlBase, SavedClinicalControl
+from mavedb.view_models.gnomad_variant import GnomADVariant, GnomADVariantBase, SavedGnomADVariant
 
 MappedVariantUpdate.model_rebuild()
 SavedMappedVariantWithControls.model_rebuild()

tests/view_models/test_mapped_variant.py

@@ -1,10 +1,9 @@
 import pytest
 from pydantic import ValidationError
 
-from mavedb.view_models.mapped_variant import MappedVariantCreate, MappedVariant
-
-from tests.helpers.util.common import dummy_attributed_object_from_dict
+from mavedb.view_models.mapped_variant import MappedVariant, MappedVariantCreate
 from tests.helpers.constants import TEST_MINIMAL_MAPPED_VARIANT, TEST_MINIMAL_MAPPED_VARIANT_CREATE, VALID_VARIANT_URN
+from tests.helpers.util.common import dummy_attributed_object_from_dict
 
 
 def test_minimal_mapped_variant_create():
@@ -72,10 +71,32 @@ def test_cannot_create_mapped_variant_without_variant():
         MappedVariantCreate(**mapped_variant_create)
 
 
+def test_can_create_saved_mapped_variant_with_variant_object():
+    mapped_variant = TEST_MINIMAL_MAPPED_VARIANT.copy()
+    mapped_variant["id"] = 1
+
+    saved_mapped_variant = MappedVariant.model_validate(
+        dummy_attributed_object_from_dict(
+            {**mapped_variant, "variant": dummy_attributed_object_from_dict({"urn": VALID_VARIANT_URN})}
+        )
+    )
+
+    assert all(saved_mapped_variant.__getattribute__(k) == v for k, v in mapped_variant.items())
+    assert saved_mapped_variant.variant_urn == VALID_VARIANT_URN
+
+
 def test_cannot_save_mapped_variant_without_variant():
     mapped_variant = TEST_MINIMAL_MAPPED_VARIANT.copy()
     mapped_variant["id"] = 1
-    mapped_variant["variant"] = dummy_attributed_object_from_dict({"urn": None})
+    mapped_variant["variant"] = None
 
     with pytest.raises(ValidationError):
         MappedVariant.model_validate(dummy_attributed_object_from_dict({**mapped_variant}))
+
+
+def test_can_create_mapped_variant_from_non_orm_context():
+    mapped_variant_create = TEST_MINIMAL_MAPPED_VARIANT_CREATE.copy()
+    mapped_variant_create["variant_urn"] = VALID_VARIANT_URN
+    created_mapped_variant = MappedVariantCreate.model_validate(mapped_variant_create)
+
+    assert all(created_mapped_variant.__getattribute__(k) == v for k, v in mapped_variant_create.items())