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refactor: rename VrsTypes enum to VrsType #425

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Jul 11, 2024
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refactor: rename VrsTypes enum to VrsType #425

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32 changes: 16 additions & 16 deletions src/ga4gh/vrs/models.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
Expand Down Expand Up @@ -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

Expand All @@ -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.'
Expand All @@ -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')

Expand All @@ -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 <http://samtools.github.io/hts-specs/refget.html>` identifier for the referenced sequence, using the sha512t24u digest.',
Expand All @@ -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.'
)
Expand Down Expand Up @@ -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'
)
Expand All @@ -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.',
Expand Down Expand Up @@ -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.",
Expand Down Expand Up @@ -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):
Expand All @@ -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.",
Expand Down Expand Up @@ -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'
)
Expand All @@ -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).',
Expand Down
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