Add required variant_urn property to MappedVariant models and update validation tests

Author: bencap

src/mavedb/view_models/mapped_variant.py

@@ -21,6 +21,10 @@ class MappedVariantBase(BaseModel):
     mapping_api_version: str
     current: bool
 
+    # Generated via model validators. On update/create classes, the input should be
+    # a dict. On saved classes, the input should be a model instance.
+    variant_urn: str
+
 
 class MappedVariantUpdate(MappedVariantBase):
     clinical_controls: Sequence["ClinicalControlBase"]
@@ -30,8 +34,8 @@ class MappedVariantUpdate(MappedVariantBase):
     def generate_score_set_urn_list(cls, data: Any):
         if "variant_urn" not in data and "variant" in data:
             try:
-                data.__setattr__("variant_urn", None if not data["variant"] else data["variant"]["urn"])
-            except AttributeError as exc:
+                data["variant_urn"] = None if not data["variant"] else data["variant"]["urn"]
+            except KeyError as exc:
                 raise ValidationError(f"Unable to create {cls.__name__} without attribute: {exc}.")  # type: ignore
         return data
 

tests/view_models/test_mapped_variant.py

@@ -1,19 +1,81 @@
+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 tests.helpers.constants import TEST_MINIMAL_MAPPED_VARIANT, TEST_MINIMAL_MAPPED_VARIANT_CREATE, VALID_VARIANT_URN
 
 
 def test_minimal_mapped_variant_create():
-    mapped_variant_create = MappedVariantCreate(**TEST_MINIMAL_MAPPED_VARIANT_CREATE)
+    mapped_variant_create = TEST_MINIMAL_MAPPED_VARIANT_CREATE.copy()
+    mapped_variant_create["variant_urn"] = VALID_VARIANT_URN
+    created_mapped_variant = MappedVariantCreate(**mapped_variant_create)
+
+    assert all(created_mapped_variant.__getattribute__(k) == v for k, v in mapped_variant_create.items())
+
+
+def test_can_use_variant_object_for_variant_urn_in_mapped_variant_create():
+    mapped_variant_create = TEST_MINIMAL_MAPPED_VARIANT_CREATE.copy()
+    created_mapped_variant = MappedVariantCreate(**{**mapped_variant_create, "variant": {"urn": VALID_VARIANT_URN}})
 
-    assert all(mapped_variant_create.__getattribute__(k) == v for k, v in TEST_MINIMAL_MAPPED_VARIANT_CREATE.items())
+    assert all(created_mapped_variant.__getattribute__(k) == v for k, v in mapped_variant_create.items())
+    assert created_mapped_variant.variant_urn == VALID_VARIANT_URN
 
 
 def test_minimal_mapped_variant():
     mapped_variant = TEST_MINIMAL_MAPPED_VARIANT.copy()
     mapped_variant["id"] = 1
+    mapped_variant["variant_urn"] = VALID_VARIANT_URN
+
+    saved_mapped_variant = MappedVariant.model_validate(dummy_attributed_object_from_dict({**mapped_variant}))
+
+    assert all(saved_mapped_variant.__getattribute__(k) == v for k, v in mapped_variant.items())
+
+
+def test_can_use_variant_object_for_variant_urn_in_mapped_variant():
+    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_urn": VALID_VARIANT_URN}))
+    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_create_mapped_variant_without_variant_urn():
+    mapped_variant_create = TEST_MINIMAL_MAPPED_VARIANT_CREATE.copy()
+    mapped_variant_create["variant_urn"] = None
+
+    with pytest.raises(ValidationError):
+        MappedVariantCreate(**mapped_variant_create)
+
+
+def test_cannot_save_mapped_variant_without_variant_urn():
+    mapped_variant = TEST_MINIMAL_MAPPED_VARIANT.copy()
+    mapped_variant["id"] = 1
+    mapped_variant["variant_urn"] = None
+
+    with pytest.raises(ValidationError):
+        MappedVariant.model_validate(dummy_attributed_object_from_dict({**mapped_variant}))
+
+
+def test_cannot_create_mapped_variant_without_variant():
+    mapped_variant_create = TEST_MINIMAL_MAPPED_VARIANT_CREATE.copy()
+    mapped_variant_create["variant"] = {"urn": None}
+
+    with pytest.raises(ValidationError):
+        MappedVariantCreate(**mapped_variant_create)
+
+
+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})
+
+    with pytest.raises(ValidationError):
+        MappedVariant.model_validate(dummy_attributed_object_from_dict({**mapped_variant}))