test: fix 'test_types'

src/anyvlm/utils/types.py

@@ -6,7 +6,7 @@
 
 from anyvar.utils.liftover_utils import ReferenceAssembly
 from ga4gh.va_spec.base import CohortAlleleFrequencyStudyResult
-from pydantic import BaseModel, BeforeValidator, StringConstraints
+from pydantic import AfterValidator, BaseModel, BeforeValidator, StringConstraints
 
 
 class AncillaryResults(BaseModel):
@@ -93,12 +93,12 @@ def _normalize_chromosome_name(chromosome_name: str) -> str:
         return chromosome_name
 
     raise ValueError(
-        "Invalid chromosome. Must be either a number between 1-22, or "
-        "'one of the values 'X', 'Y', or 'MT'; optionally prefixed with 'chr'."
+        "Invalid chromosome name. Must be a string consisting of either a number between 1-22, "
+        "or one of the values 'X', 'Y', or 'MT'; optionally prefixed with 'chr'."
     )
 
 
-ChromosomeName = Annotated[str, BeforeValidator(_normalize_chromosome_name)]
+ChromosomeName = Annotated[str, AfterValidator(_normalize_chromosome_name)]
 
 
 class Zygosity(StrEnum):

tests/unit/test_types → tests/unit/test_types.py

@@ -1,12 +1,14 @@
 """Tests for types and validator functions found in src/anyvlm/utils/types.py"""
 
-from pydantic import TypeAdapter, ValidationError
 import pytest
+from pydantic import TypeAdapter, ValidationError
+
 from anyvlm.utils.types import ChromosomeName, _normalize_chromosome_name
 
 
 @pytest.fixture
-def valid_chromosomes():
+def valid_chromosomes() -> list[tuple[str, str]]:
+    """List of tuples of unnormalized chromosome names & expected normalized values"""
     return [
         ("1", "1"),
         ("22", "22"),
@@ -19,23 +21,14 @@ def valid_chromosomes():
         ("chrMT", "MT"),
     ]
 
+
 @pytest.fixture
-def invalid_chromosomes():
-    return [
-        "0",
-        "23",
-        "chr23",
-        "M",
-        "chrM",
-        "XY",
-        "",
-        "chr",
-        "1a",
-        None
-    ]
+def invalid_chromosomes() -> list[str | None]:
+    return ["0", "23", "chr23", "M", "chrM", "XY", "", "chr", "1a", None]
+
 
 @pytest.fixture
-def chromosome_adapter():
+def chromosome_adapter() -> TypeAdapter[ChromosomeName]:
     return TypeAdapter(ChromosomeName)
 
 
@@ -47,8 +40,18 @@ def test_normalize_chromosome_name_valid(valid_chromosomes):
 
 def test_normalize_chromosome_name_invalid(invalid_chromosomes):
     for chromosome_name in invalid_chromosomes:
-        with pytest.raises(ValueError):
-            _normalize_chromosome_name(chromosome_name)
+        if chromosome_name is not None:
+            with pytest.raises(
+                ValueError,
+                match=(
+                    "Invalid chromosome name. Must be a string consisting of either a number between 1-22, "
+                    "or one of the values 'X', 'Y', or 'MT'; optionally prefixed with 'chr'."
+                ),
+            ):
+                _normalize_chromosome_name(chromosome_name)
+        else:
+            with pytest.raises(AttributeError):
+                _normalize_chromosome_name(chromosome_name)
 
 
 ### Test ChromosomeName annotated type ###