From 385530bc6aea4e53a139acac0ef2261f75409753 Mon Sep 17 00:00:00 2001 From: Kori Kuzma Date: Thu, 11 Jul 2024 08:28:21 -0400 Subject: [PATCH] refactor: rename VrsTypes enum to VrsType (#425) --- src/ga4gh/vrs/models.py | 32 ++++++++++++++++---------------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/src/ga4gh/vrs/models.py b/src/ga4gh/vrs/models.py index e0f304da..147fbef6 100644 --- a/src/ga4gh/vrs/models.py +++ b/src/ga4gh/vrs/models.py @@ -125,7 +125,7 @@ def pydantic_class_refatt_map(): class_keys) -class VrsTypes(str, Enum): +class VrsType(str, Enum): """Define VRS Types""" LEN_EXPR = "LengthExpression" @@ -339,8 +339,8 @@ class SequenceString(RootModel): class LengthExpression(_ValueObject): """A sequence expressed only by its length.""" - type: Literal[VrsTypes.LEN_EXPR] = Field( - VrsTypes.LEN_EXPR, description=f'MUST be "{VrsTypes.LEN_EXPR.value}"' + type: Literal[VrsType.LEN_EXPR] = Field( + VrsType.LEN_EXPR, description=f'MUST be "{VrsType.LEN_EXPR.value}"' ) length: Optional[Union[Range, int]] = None @@ -354,8 +354,8 @@ class ga4gh(_ValueObject.ga4gh): class ReferenceLengthExpression(_ValueObject): """An expression of a length of a sequence from a repeating reference.""" - type: Literal[VrsTypes.REF_LEN_EXPR] = Field( - VrsTypes.REF_LEN_EXPR, description=f'MUST be "{VrsTypes.REF_LEN_EXPR.value}"' + type: Literal[VrsType.REF_LEN_EXPR] = Field( + VrsType.REF_LEN_EXPR, description=f'MUST be "{VrsType.REF_LEN_EXPR.value}"' ) length: Union[Range, int] = Field( ..., description='The number of residues of the expressed sequence.' @@ -378,8 +378,8 @@ class ga4gh(_ValueObject.ga4gh): class LiteralSequenceExpression(_ValueObject): """An explicit expression of a Sequence.""" - type: Literal[VrsTypes.LIT_SEQ_EXPR] = Field( - VrsTypes.LIT_SEQ_EXPR, description=f'MUST be "{VrsTypes.LIT_SEQ_EXPR.value}"' + type: Literal[VrsType.LIT_SEQ_EXPR] = Field( + VrsType.LIT_SEQ_EXPR, description=f'MUST be "{VrsType.LIT_SEQ_EXPR.value}"' ) sequence: SequenceString = Field(..., description='the literal sequence') @@ -398,7 +398,7 @@ class ga4gh(_ValueObject.ga4gh): class SequenceReference(_ValueObject): """A sequence of nucleic or amino acid character codes.""" - type: Literal[VrsTypes.SEQ_REF] = Field(VrsTypes.SEQ_REF, description=f'MUST be "{VrsTypes.SEQ_REF.value}"') + type: Literal[VrsType.SEQ_REF] = Field(VrsType.SEQ_REF, 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 ` identifier for the referenced sequence, using the sha512t24u digest.', @@ -416,7 +416,7 @@ class ga4gh(_ValueObject.ga4gh): class SequenceLocation(_Ga4ghIdentifiableObject): """A `Location` defined by an interval on a referenced `Sequence`.""" - type: Literal[VrsTypes.SEQ_LOC] = Field(VrsTypes.SEQ_LOC, description=f'MUST be "{VrsTypes.SEQ_LOC.value}"') + type: Literal[VrsType.SEQ_LOC] = Field(VrsType.SEQ_LOC, 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.' ) @@ -466,7 +466,7 @@ class _VariationBase(_Ga4ghIdentifiableObject): class Allele(_VariationBase): """The state of a molecule at a `Location`.""" - type: Literal[VrsTypes.ALLELE] = Field(VrsTypes.ALLELE, description=f'MUST be "{VrsTypes.ALLELE.value}"') + type: Literal[VrsType.ALLELE] = Field(VrsType.ALLELE, description=f'MUST be "{VrsType.ALLELE.value}"') location: Union[IRI, SequenceLocation] = Field( ..., description='The location of the Allele' ) @@ -486,7 +486,7 @@ class ga4gh(_Ga4ghIdentifiableObject.ga4gh): class CisPhasedBlock(_VariationBase): """An ordered set of co-occurring `Variation` on the same molecule.""" - type: Literal[VrsTypes.CIS_PHASED_BLOCK] = Field(VrsTypes.CIS_PHASED_BLOCK, description=f'MUST be "{VrsTypes.CIS_PHASED_BLOCK.value}"') + type: Literal[VrsType.CIS_PHASED_BLOCK] = Field(VrsType.CIS_PHASED_BLOCK, 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.', @@ -519,7 +519,7 @@ class Adjacency(_VariationBase): potentially with an intervening linker sequence. """ - type: Literal[VrsTypes.ADJACENCY] = Field(VrsTypes.ADJACENCY, description=f'MUST be "{VrsTypes.ADJACENCY.value}"') + type: Literal[VrsType.ADJACENCY] = Field(VrsType.ADJACENCY, 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.", @@ -547,7 +547,7 @@ class SequenceTerminus(_VariationBase): is not allowed and it removes the unnecessary array structure. """ - type: Literal[VrsTypes.SEQ_TERMINUS] = Field(VrsTypes.SEQ_TERMINUS, description=f'MUST be "{VrsTypes.SEQ_TERMINUS.value}"') + type: Literal[VrsType.SEQ_TERMINUS] = Field(VrsType.SEQ_TERMINUS, description=f'MUST be "{VrsType.SEQ_TERMINUS.value}"') location: Union[IRI, SequenceLocation] = Field(..., description="The location of the terminus.") class ga4gh(_Ga4ghIdentifiableObject.ga4gh): @@ -563,7 +563,7 @@ class DerivativeSequence(_VariationBase): sequence composed from multiple sequence adjacencies. """ - type: Literal[VrsTypes.DERIVATIVE_SEQ] = Field(VrsTypes.DERIVATIVE_SEQ, description=f'MUST be "{VrsTypes.DERIVATIVE_SEQ.value}"') + type: Literal[VrsType.DERIVATIVE_SEQ] = Field(VrsType.DERIVATIVE_SEQ, 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.", @@ -597,7 +597,7 @@ class CopyNumberCount(_CopyNumber): (e.g. genome, cell, etc.). """ - type: Literal[VrsTypes.CN_COUNT] = Field(VrsTypes.CN_COUNT, description=f'MUST be "{VrsTypes.CN_COUNT.value}"') + type: Literal[VrsType.CN_COUNT] = Field(VrsType.CN_COUNT, 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' ) @@ -616,7 +616,7 @@ class CopyNumberChange(_CopyNumber): (e.g. genome, cell, etc.) relative to a baseline ploidy. """ - type: Literal[VrsTypes.CN_CHANGE] = Field(VrsTypes.CN_CHANGE, description=f'MUST be "{VrsTypes.CN_CHANGE.value}"') + type: Literal[VrsType.CN_CHANGE] = Field(VrsType.CN_CHANGE, 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).',