anyvar.storage.mappers

Object mappers for converting between VRS models and database entities.

class anyvar.storage.mappers.AlleleMapper

Maps between Allele entities.

__init__()

Initialize AlleleMapper.

from_db_entity(db_entity)

Convert DB Allele to VRS Allele.

Return type:

Allele

to_db_entity(anyvar_entity)

Convert VRS Allele to DB Allele.

Raises:

AttributeError – if .id field is missing, or uses IRI references in place of full SequenceLocation/SequenceReference

Return type:

Allele

class anyvar.storage.mappers.BaseMapper

Base class for all object mappers.

abstractmethod from_db_entity(db_entity)

Convert DB entity to VRS model.

Return type:

TypeVar(A)

abstractmethod to_db_entity(anyvar_entity)

Convert AnyVar entity to DB entity.

Return type:

TypeVar(D)

class anyvar.storage.mappers.CanonicalAlleleMapper

__init__()

from_db_entity(db_entity)

Convert DB entity to VRS model.

Return type:

CanonicalAllele

to_db_entity(anyvar_entity)

Convert AnyVar entity to DB entity.

Return type:

CanonicalAllele

class anyvar.storage.mappers.ExtensionMapper

Maps between Extension entities.

from_db_entity(db_entity)

Convert DB Extension to AnyVar Extension.

Parameters:

db_entity (Extension) – An ORM Extension instance

Return type:

Extension

Returns:

An Anyvar Extension instance

to_db_entity(anyvar_entity)

Convert AnyVar Extension into DB Extension.

Parameters:

anyvar_entity (Extension) – An Anyvar Extension instance

Return type:

Extension

Returns:

An ORM model Extension instance

class anyvar.storage.mappers.ProteinSequenceConsequenceMapper

__init__()

from_db_entity(db_entity)

Convert DB entity to VRS model.

Return type:

ProteinSequenceConsequence

to_db_entity(anyvar_entity)

Convert AnyVar entity to DB entity.

Return type:

ProteinSequenceConsequence

class anyvar.storage.mappers.SequenceLocationMapper

Maps between SequenceLocation entities.

__init__()

Initialize SequenceLocationMapper.

from_db_entity(db_entity)

Convert DB Location to VRS SequenceLocation.

Return type:

SequenceLocation

to_db_entity(anyvar_entity)

Convert VRS SequenceLocation to DB Location.

Raises:

AttributeError – if .id field is missing

Return type:

Location

class anyvar.storage.mappers.SequenceReferenceMapper

Maps between SequenceReference entities.

from_db_entity(db_entity)

Convert DB SequenceReference to VRS SequenceReference.

Return type:

SequenceReference

to_db_entity(anyvar_entity)

Convert VRS SequenceReference to DB SequenceReference.

Return type:

SequenceReference

class anyvar.storage.mappers.VariationMappingMapper

Maps between VariationMapping entities.

from_db_entity(db_entity)

Convert DB instance into business logic object

Return type:

VariationMapping

to_db_entity(anyvar_entity)

Convert VariationMapping object to DB mapping instance.

Return type:

VariationMapping