Skip to content

Commit

Permalink
addresses #427
Browse files Browse the repository at this point in the history
  • Loading branch information
ahwagner committed Jul 15, 2024
1 parent 96893c9 commit 06bc1b5
Showing 1 changed file with 17 additions and 2 deletions.
19 changes: 17 additions & 2 deletions src/ga4gh/vrs/models.py
Original file line number Diff line number Diff line change
Expand Up @@ -232,7 +232,9 @@ def has_valid_digest(self):

def compute_digest(self, store=True, as_version=None) -> str:
"""A sha512t24u digest created using the VRS Computed Identifier algorithm.
Stores the digest in the object if store is True.
Stores the digest in the object if store is True. If 'as_version' is set to
a version string, other parameters are ignored and a digest returned
following the conventions of the VRS version indicated by 'as_version'.
"""
if as_version is None:
digest = sha512t24u(self.model_dump_json().encode("utf-8"))
Expand All @@ -259,6 +261,10 @@ def get_or_create_ga4gh_identifier(self, in_place='default', recompute=False, as
even when empty
Digests will be recalculated even if present if recompute is True.
If 'as_version' is set to a version string, other parameters are
ignored and an identifier returned following the conventions of
the VRS version indicated by 'as_version'.
"""
if as_version is not None:
return self.compute_ga4gh_identifier(as_version=as_version)
Expand All @@ -279,7 +285,12 @@ def get_or_create_ga4gh_identifier(self, in_place='default', recompute=False, as
return self.compute_ga4gh_identifier(recompute)

def compute_ga4gh_identifier(self, recompute=False, as_version=None):
"""Returns a GA4GH Computed Identifier"""
"""Returns a GA4GH Computed Identifier.
If 'as_version' is set to a version string, other parameters are
ignored and a computed identifier returned following the conventions
of the VRS version indicated by 'as_version'.
"""
if as_version is None:
self.get_or_create_digest(recompute)
return f'{CURIE_NAMESPACE}{CURIE_SEP}{self.ga4gh.prefix}{GA4GH_PREFIX_SEP}{self.digest}'
Expand Down Expand Up @@ -446,6 +457,8 @@ class SequenceLocation(_Ga4ghIdentifiableObject):
sequence: Optional[SequenceString] = Field(None, description="The literal sequence encoded by the `sequenceReference` at these coordinates.")

def ga4gh_serialize_as_version(self, as_version):
"""This method will return a serialized string following the conventions for
SequenceLocation serialization as defined in the VRS version specified by 'as_version`."""
if as_version == '1.3':
out = list()
for value in [self.start,self.end]:
Expand Down Expand Up @@ -511,6 +524,8 @@ class Allele(_VariationBase):
)

def ga4gh_serialize_as_version(self, as_version):
"""This method will return a serialized string following the conventions for
Allele serialization as defined in the VRS version specified by 'as_version`."""
location_digest = self.location.compute_digest(as_version=as_version)
sequence = get_pydantic_root(self.state.sequence)
if sequence is None:
Expand Down

0 comments on commit 06bc1b5

Please sign in to comment.