Make score range classification options literal strings

Author: bencap

src/mavedb/lib/validation/constants/score_set.py

@@ -2,16 +2,14 @@
 from __future__ import annotations
 
 from datetime import date
-from typing import Any, Collection, Dict, Optional, Sequence
+from typing import Any, Collection, Dict, Optional, Sequence, Literal
 
 from humps import camelize
 from pydantic import root_validator
 
 from mavedb.lib.validation import urn_re
-from mavedb.lib.validation.constants.score_set import default_ranges
 from mavedb.lib.validation.exceptions import ValidationError
 from mavedb.lib.validation.utilities import inf_or_float, is_null
-from mavedb.lib.utils import sanitize_string
 from mavedb.models.enums.mapping_state import MappingState
 from mavedb.models.enums.processing_state import ProcessingState
 from mavedb.view_models import PublicationIdentifiersGetter, record_type_validator, set_record_type
@@ -56,23 +54,13 @@ class Config:
 class ScoreRange(BaseModel):
     label: str
     description: Optional[str]
-    classification: str
+    classification: Literal["normal", "abnormal", "not_specified"]
     # Purposefully vague type hint because of some odd JSON Schema generation behavior.
     # Typing this as tuple[Union[float, None], Union[float, None]] will generate an invalid
     # jsonschema, and fail all tests that access the schema. This may be fixed in pydantic v2,
     # but it's unclear. Even just typing it as Tuple[Any, Any] will generate an invalid schema!
     range: list[Any]  # really: tuple[Union[float, None], Union[float, None]]
 
-    @validator("classification")
-    def range_classification_value_is_accepted(cls, field_value: str):
-        classification = sanitize_string(field_value)
-        if classification not in default_ranges:
-            raise ValidationError(
-                f"Unexpected classification value(s): {classification}. Permitted values: {default_ranges}"
-            )
-
-        return classification
-
     @validator("range")
     def ranges_are_not_backwards(cls, field_value: tuple[Any]):
         if len(field_value) != 2:

src/mavedb/view_models/score_set.py

@@ -1,7 +1,6 @@
 import pytest
 from fastapi.encoders import jsonable_encoder
 
-from mavedb.lib.validation.constants.score_set import default_ranges
 from mavedb.view_models.publication_identifier import PublicationIdentifierCreate
 from mavedb.view_models.score_set import ScoreSetCreate, ScoreSetModify
 from mavedb.view_models.target_gene import TargetGeneCreate
@@ -483,13 +482,10 @@ def test_cannot_create_score_set_without_default_ranges():
     with pytest.raises(ValueError) as exc_info:
         ScoreSetModify(**jsonable_encoder(score_set_test))
 
-    assert (
-        "Unexpected classification value(s): other. Permitted values: ['normal', 'abnormal', 'not_specified']"
-        in str(exc_info.value)
-    )
+    assert "unexpected value; permitted: 'normal', 'abnormal', 'not_specified'" in str(exc_info.value)
 
 
-@pytest.mark.parametrize("classification", default_ranges)
+@pytest.mark.parametrize("classification", ["normal", "abnormal", "not_specified"])
 def test_can_create_score_set_with_any_range_classification(classification):
     wt_score = -0.5 if classification == "normal" else None
     score_set_test = TEST_MINIMAL_SEQ_SCORESET.copy()