fix: robust synthetic property handling for variants

- Refactored Variant 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/variant.py

@@ -4,9 +4,9 @@
 from pydantic import model_validator
 
 from mavedb.lib.validation.exceptions import ValidationError
-from mavedb.view_models.mapped_variant import MappedVariant, SavedMappedVariant
 from mavedb.view_models import record_type_validator, set_record_type
 from mavedb.view_models.base.base import BaseModel
+from mavedb.view_models.mapped_variant import MappedVariant, SavedMappedVariant
 
 
 class VariantEffectMeasurementBase(BaseModel):
@@ -51,18 +51,19 @@ class SavedVariantEffectMeasurementWithMappedVariant(SavedVariantEffectMeasureme
 
     mapped_variant: Optional[SavedMappedVariant] = None
 
+    # 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, "mapped_variant"):
+    def generate_associated_mapped_variant(cls, data: Any):
+        if hasattr(data, "mapped_variants"):
             try:
-                mapped_variant = None
-                if data.mapped_variants:
-                    mapped_variant = next(
-                        mapped_variant for mapped_variant in data.mapped_variants if mapped_variant.current
-                    )
+                mapped_variant = next(
+                    (mapped_variant for mapped_variant in data.mapped_variants if mapped_variant.current), None
+                )
                 data.__setattr__("mapped_variant", mapped_variant)
-            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 mapped variant for {cls.__name__}: {exc}.")  # type: ignore
         return data
 
 

tests/view_models/test_variant.py

@@ -1,7 +1,15 @@
-from mavedb.view_models.variant import VariantEffectMeasurementCreate, VariantEffectMeasurement
-
+from mavedb.view_models.variant import (
+    SavedVariantEffectMeasurementWithMappedVariant,
+    VariantEffectMeasurement,
+    VariantEffectMeasurementCreate,
+)
+from tests.helpers.constants import (
+    TEST_MINIMAL_MAPPED_VARIANT,
+    TEST_MINIMAL_VARIANT,
+    TEST_POPULATED_VARIANT,
+    TEST_SAVED_VARIANT,
+)
 from tests.helpers.util.common import dummy_attributed_object_from_dict
-from tests.helpers.constants import TEST_MINIMAL_VARIANT, TEST_POPULATED_VARIANT, TEST_SAVED_VARIANT
 
 
 def test_minimal_variant_create():
@@ -19,3 +27,51 @@ def test_saved_variant():
         dummy_attributed_object_from_dict({**TEST_SAVED_VARIANT, "score_set_id": 1})
     )
     assert all(variant.__getattribute__(k) == v for k, v in TEST_SAVED_VARIANT.items())
+
+
+def test_can_create_saved_variant_with_mapping_with_all_attributed_properties():
+    variant = TEST_SAVED_VARIANT.copy()
+    variant["score_set_id"] = 1
+    variant["mapped_variants"] = [
+        dummy_attributed_object_from_dict(
+            {
+                **TEST_MINIMAL_MAPPED_VARIANT,
+                "id": 1,
+                "variant": dummy_attributed_object_from_dict({"urn": "urn:mavedb:variant-xxx"}),
+            }
+        )
+    ]
+    variant_attributed_object = dummy_attributed_object_from_dict(variant)
+    saved_variant = SavedVariantEffectMeasurementWithMappedVariant.model_validate(variant_attributed_object)
+    assert saved_variant.mapped_variant is not None
+    assert saved_variant.mapped_variant.variant_urn == "urn:mavedb:variant-xxx"
+    for k, v in TEST_SAVED_VARIANT.items():
+        assert saved_variant.__getattribute__(k) == v
+
+
+# Missing attributed properties here are unproblematic, as they are optional on the view model.
+def test_can_create_saved_variant_with_mapping_with_missing_attributed_properties():
+    variant = TEST_SAVED_VARIANT.copy()
+    variant.pop("mapped_variants", None)
+    variant["score_set_id"] = 1
+
+    variant_attributed_object = dummy_attributed_object_from_dict(variant)
+    saved_variant = SavedVariantEffectMeasurementWithMappedVariant.model_validate(variant_attributed_object)
+    for k, v in TEST_SAVED_VARIANT.items():
+        assert saved_variant.__getattribute__(k) == v
+
+
+def test_can_create_saved_variant_with_mapping_from_non_orm_context():
+    variant = TEST_SAVED_VARIANT.copy()
+    variant["score_set_id"] = 1
+    variant["mapped_variant"] = {
+        **TEST_MINIMAL_MAPPED_VARIANT,
+        "id": 1,
+        "variant_urn": "urn:mavedb:variant-xxx",
+    }
+
+    saved_variant = SavedVariantEffectMeasurementWithMappedVariant.model_validate(variant)
+    assert saved_variant.mapped_variant is not None
+    assert saved_variant.mapped_variant.variant_urn == "urn:mavedb:variant-xxx"
+    for k, v in TEST_SAVED_VARIANT.items():
+        assert saved_variant.__getattribute__(k) == v