revert back to str, Enum

src/ga4gh/core/domain_models.py

@@ -10,14 +10,15 @@
   * `import ga4gh.core`, and refer to models using the fully-qualified
     module name, e.g., `ga4gh.core.domain_models.Gene`
 """
+from enum import Enum
 from typing import Literal, Union, List
 
 from pydantic import Field, RootModel
 
 from ga4gh.core.entity_models import DomainEntity
 
 
-class CommonDomainType:
+class CommonDomainType(str, Enum):
     """Define GKS Common Domain Entity types"""
 
     PHENOTYPE = "Phenotype"
@@ -33,8 +34,8 @@ class Phenotype(DomainEntity):
     """An observable characteristic or trait of an organism."""
 
     type: Literal["Phenotype"] = Field(
-        CommonDomainType.PHENOTYPE,
-        description=f'MUST be "{CommonDomainType.PHENOTYPE}".'
+        CommonDomainType.PHENOTYPE.value,
+        description=f'MUST be "{CommonDomainType.PHENOTYPE.value}".'
     )
 
 
@@ -44,17 +45,17 @@ class Disease(DomainEntity):
     """
 
     type: Literal["Disease"] = Field(
-        CommonDomainType.DISEASE,
-        description=f'MUST be "{CommonDomainType.DISEASE}".'
+        CommonDomainType.DISEASE.value,
+        description=f'MUST be "{CommonDomainType.DISEASE.value}".'
     )
 
 
 class TraitSet(DomainEntity):
     """A set of phenotype and/or disease concepts that together constitute a condition."""
 
     type: Literal["TraitSet"] = Field(
-        CommonDomainType.TRAIT_SET,
-        description=f'MUST be "{CommonDomainType.TRAIT_SET}".'
+        CommonDomainType.TRAIT_SET.value,
+        description=f'MUST be "{CommonDomainType.TRAIT_SET.value}".'
     )
     traits: List[Union[Disease, Phenotype]] = Field(
         ...,
@@ -76,26 +77,26 @@ class TherapeuticAction(DomainEntity):
     """A therapeutic action taken that is intended to alter or stop a pathologic process."""
 
     type: Literal["TherapeuticAction"] = Field(
-        CommonDomainType.TR_ACTION,
-        description=f'MUST be "{CommonDomainType.TR_ACTION}".'
+        CommonDomainType.TR_ACTION.value,
+        description=f'MUST be "{CommonDomainType.TR_ACTION.value}".'
     )
 
 
 class TherapeuticAgent(DomainEntity):
     """An administered therapeutic agent that is intended to alter or stop a pathologic process."""
 
     type: Literal["TherapeuticAgent"] = Field(
-        CommonDomainType.TR_AGENT,
-        description=f'MUST be "{CommonDomainType.TR_AGENT}".'
+        CommonDomainType.TR_AGENT.value,
+        description=f'MUST be "{CommonDomainType.TR_AGENT.value}".'
     )
 
 
 class TherapeuticSubstituteGroup(DomainEntity):
     """A group of therapeutic procedures that may be treated as substitutes for one another."""
 
     type: Literal["TherapeuticSubstituteGroup"] = Field(
-        CommonDomainType.TR_SUB,
-        description=f'MUST be "{CommonDomainType.TR_SUB}".'
+        CommonDomainType.TR_SUB.value,
+        description=f'MUST be "{CommonDomainType.TR_SUB.value}".'
     )
     substitutes: List[Union[TherapeuticAction, TherapeuticAgent]] = Field(
         ...,
@@ -110,8 +111,8 @@ class CombinationTherapy(DomainEntity):
     """
 
     type: Literal["CombinationTherapy"] = Field(
-        CommonDomainType.TR_COMB,
-        description=f'MUST be "{CommonDomainType.TR_COMB}".'
+        CommonDomainType.TR_COMB.value,
+        description=f'MUST be "{CommonDomainType.TR_COMB.value}".'
     )
     components: List[Union[TherapeuticSubstituteGroup, TherapeuticAction, TherapeuticAgent]] = Field(
         ...,
@@ -136,6 +137,6 @@ class Gene(DomainEntity):
     """A basic physical and functional unit of heredity."""
 
     type: Literal["Gene"] = Field(
-        CommonDomainType.GENE,
-        description=f'MUST be "{CommonDomainType.GENE}".'
+        CommonDomainType.GENE.value,
+        description=f'MUST be "{CommonDomainType.GENE.value}".'
     )

src/ga4gh/vrs/models.py

@@ -132,7 +132,7 @@ def pydantic_class_refatt_map():
             class_keys)
 
 
-class VrsType:
+class VrsType(str, Enum):
     """Define  VRS Types"""
 
     LEN_EXPR = "LengthExpression"
@@ -370,7 +370,7 @@ class LengthExpression(_ValueObject):
     """A sequence expressed only by its length."""
 
     type: Literal["LengthExpression"] = Field(
-        VrsType.LEN_EXPR, description=f'MUST be "{VrsType.LEN_EXPR}"'
+        VrsType.LEN_EXPR.value, description=f'MUST be "{VrsType.LEN_EXPR.value}"'
     )
     length: Optional[Union[Range, int]] = None
 
@@ -385,7 +385,7 @@ class ReferenceLengthExpression(_ValueObject):
     """An expression of a length of a sequence from a repeating reference."""
 
     type: Literal["ReferenceLengthExpression"] = Field(
-        VrsType.REF_LEN_EXPR, description=f'MUST be "{VrsType.REF_LEN_EXPR}"'
+        VrsType.REF_LEN_EXPR.value, description=f'MUST be "{VrsType.REF_LEN_EXPR.value}"'
     )
     length: Union[Range, int] = Field(
         ..., description='The number of residues of the expressed sequence.'
@@ -409,7 +409,7 @@ class LiteralSequenceExpression(_ValueObject):
     """An explicit expression of a Sequence."""
 
     type: Literal["LiteralSequenceExpression"] = Field(
-        VrsType.LIT_SEQ_EXPR, description=f'MUST be "{VrsType.LIT_SEQ_EXPR}"'
+        VrsType.LIT_SEQ_EXPR.value, description=f'MUST be "{VrsType.LIT_SEQ_EXPR.value}"'
     )
     sequence: SequenceString = Field(..., description='the literal sequence')
 
@@ -430,7 +430,7 @@ class SequenceReference(_ValueObject):
 
     model_config = ConfigDict(use_enum_values=True)
 
-    type: Literal["SequenceReference"] = Field(VrsType.SEQ_REF, description=f'MUST be "{VrsType.SEQ_REF}"')
+    type: Literal["SequenceReference"] = Field(VrsType.SEQ_REF.value, description=f'MUST be "{VrsType.SEQ_REF.value}"')
     refgetAccession: Annotated[str, StringConstraints(pattern=r'^SQ.[0-9A-Za-z_\-]{32}$')] = Field(
         ...,
         description='A `GA4GH RefGet <http://samtools.github.io/hts-specs/refget.html>` identifier for the referenced sequence, using the sha512t24u digest.',
@@ -448,7 +448,7 @@ class ga4gh(_ValueObject.ga4gh):
 class SequenceLocation(_Ga4ghIdentifiableObject):
     """A `Location` defined by an interval on a referenced `Sequence`."""
 
-    type: Literal["SequenceLocation"] = Field(VrsType.SEQ_LOC, description=f'MUST be "{VrsType.SEQ_LOC}"')
+    type: Literal["SequenceLocation"] = Field(VrsType.SEQ_LOC.value, description=f'MUST be "{VrsType.SEQ_LOC.value}"')
     sequenceReference: Optional[Union[IRI, SequenceReference]] = Field(
         None, description='A reference to a `Sequence` on which the location is defined.'
     )
@@ -529,7 +529,7 @@ class _VariationBase(_Ga4ghIdentifiableObject, ABC):
 class Allele(_VariationBase):
     """The state of a molecule at a `Location`."""
 
-    type: Literal["Allele"] = Field(VrsType.ALLELE, description=f'MUST be "{VrsType.ALLELE}"')
+    type: Literal["Allele"] = Field(VrsType.ALLELE.value, description=f'MUST be "{VrsType.ALLELE.value}"')
     location: Union[IRI, SequenceLocation] = Field(
         ..., description='The location of the Allele'
     )
@@ -572,7 +572,7 @@ class ga4gh(_Ga4ghIdentifiableObject.ga4gh):
 class CisPhasedBlock(_VariationBase):
     """An ordered set of co-occurring `Variation` on the same molecule."""
 
-    type: Literal["CisPhasedBlock"] = Field(VrsType.CIS_PHASED_BLOCK, description=f'MUST be "{VrsType.CIS_PHASED_BLOCK}"')
+    type: Literal["CisPhasedBlock"] = Field(VrsType.CIS_PHASED_BLOCK.value, description=f'MUST be "{VrsType.CIS_PHASED_BLOCK.value}"')
     members: List[Union[Allele, IRI]] = Field(
         ...,
         description='A list of `Alleles` that are found in-cis on a shared molecule.',
@@ -605,7 +605,7 @@ class Adjacency(_VariationBase):
     potentially with an intervening linker sequence.
     """
 
-    type: Literal["Adjacency"] = Field(VrsType.ADJACENCY, description=f'MUST be "{VrsType.ADJACENCY}"')
+    type: Literal["Adjacency"] = Field(VrsType.ADJACENCY.value, description=f'MUST be "{VrsType.ADJACENCY.value}"')
     adjoinedSequences: List[Union[IRI, SequenceLocation]] = Field(
         ...,
         description="The terminal sequence or pair of adjoined sequences that defines in the adjacency.",
@@ -633,7 +633,7 @@ class SequenceTerminus(_VariationBase):
     is not allowed and it removes the unnecessary array structure.
     """
 
-    type: Literal["SequenceTerminus"] = Field(VrsType.SEQ_TERMINUS, description=f'MUST be "{VrsType.SEQ_TERMINUS}"')
+    type: Literal["SequenceTerminus"] = Field(VrsType.SEQ_TERMINUS.value, description=f'MUST be "{VrsType.SEQ_TERMINUS.value}"')
     location: Union[IRI, SequenceLocation] = Field(..., description="The location of the terminus.")
 
     class ga4gh(_Ga4ghIdentifiableObject.ga4gh):
@@ -649,7 +649,7 @@ class DerivativeSequence(_VariationBase):
     sequence composed from multiple sequence adjacencies.
     """
 
-    type: Literal["DerivativeSequence"] = Field(VrsType.DERIVATIVE_SEQ, description=f'MUST be "{VrsType.DERIVATIVE_SEQ}"')
+    type: Literal["DerivativeSequence"] = Field(VrsType.DERIVATIVE_SEQ.value, description=f'MUST be "{VrsType.DERIVATIVE_SEQ.value}"')
     components: List[Union[IRI, Adjacency, Allele, SequenceTerminus, CisPhasedBlock]] = Field(
         ...,
         description="The sequence components that make up the derivative sequence.",
@@ -683,7 +683,7 @@ class CopyNumberCount(_CopyNumber):
     (e.g. genome, cell, etc.).
     """
 
-    type: Literal["CopyNumberCount"] = Field(VrsType.CN_COUNT, description=f'MUST be "{VrsType.CN_COUNT}"')
+    type: Literal["CopyNumberCount"] = Field(VrsType.CN_COUNT.value, description=f'MUST be "{VrsType.CN_COUNT.value}"')
     copies: Union[Range, int] = Field(
         ..., description='The integral number of copies of the subject in a system'
     )
@@ -704,7 +704,7 @@ class CopyNumberChange(_CopyNumber):
 
     model_config = ConfigDict(use_enum_values=True)
 
-    type: Literal["CopyNumberChange"] = Field(VrsType.CN_CHANGE, description=f'MUST be "{VrsType.CN_CHANGE}"')
+    type: Literal["CopyNumberChange"] = Field(VrsType.CN_CHANGE.value, description=f'MUST be "{VrsType.CN_CHANGE.value}"')
     copyChange: CopyChange = Field(
         ...,
         description='MUST be one of "efo:0030069" (complete genomic loss), "efo:0020073" (high-level loss), "efo:0030068" (low-level loss), "efo:0030067" (loss), "efo:0030064" (regional base ploidy), "efo:0030070" (gain), "efo:0030071" (low-level gain), "efo:0030072" (high-level gain).',

tests/validation/test_models.py

@@ -101,18 +101,18 @@ def test_prev_vrs_version():
 
 def test_valid_types():
     """Ensure that type enums values correct. Values should correspond to class"""
-    for gks_models, gks_type in [(models, VrsType), (domain_models, CommonDomainType)]:
-        for attr, value in gks_type.__dict__.items():
-            if not attr.startswith("__"):
-                if hasattr(gks_models, value):
-                    gks_class = getattr(gks_models, value)
-                    try:
-                        assert gks_class(type=value)
-                    except ValidationError as e:
-                        found_type_mismatch = False
-                        for error in e.errors():
-                            if error["loc"] == ("type",):
-                                found_type_mismatch = True
-                        assert not found_type_mismatch, f"Found mismatch in type literal: {value} vs {error['ctx']['expected']}"
-                else:
-                    assert False, f"{str(gks_models)} class not found: {value}"
+    for gks_models, gks_enum in [(models, VrsType), (domain_models, CommonDomainType)]:
+        for enum_val in gks_enum.__members__.values():
+            enum_val = enum_val.value
+            if hasattr(gks_models, enum_val):
+                gks_class = getattr(gks_models, enum_val)
+                try:
+                    assert gks_class(type=enum_val)
+                except ValidationError as e:
+                    found_type_mismatch = False
+                    for error in e.errors():
+                        if error["loc"] == ("type",):
+                            found_type_mismatch = True
+                    assert not found_type_mismatch, f"Found mismatch in type literal: {enum_val} vs {error['ctx']['expected']}"
+            else:
+                assert False, f"{str(gks_models)} class not found: {enum_val}"