GA4GH Variant Annotation (VA) Spec Python

0.4.3 verified Sat May 09 auth: no python

GA4GH Variant Annotation (VA) reference implementation providing Pydantic models for the VA specification. Current version 0.4.3, uses VRS-Python for variant representation and pydantic for validation. Release cadence is irregular, tied to VA spec releases.

pip install ga4gh-va-spec

Common errors

error ImportError: cannot import name 'Statement' from 'ga4gh.va_spec' ↓

cause Trying to import Statement from top-level instead of submodule.

fix

Use: from ga4gh.va_spec.base import Statement

error pydantic_core._pydantic_core.ValidationError: 1 validation error for Statement extra_forbidden ↓

cause Model has additionalProperties=False and extra fields are provided.

fix

Remove any fields not defined in the model, or update model to include them.

Warnings

breaking Version 0.2.0 changed base model namespace; imports from ga4gh.va_spec.base are required, not ga4gh.va_spec directly. ↓

fix Update imports to use submodules (e.g., base, aac_2017).

breaking Version 0.4.0 updated VA spec to 1.0.0, removing deprecated fields and renaming models. ↓

fix Review VA spec 1.0.0 changelog. Use new model names like 'Statement' with standard GA4GH types.

gotcha Models enforce additionalProperties=False by default; extra fields cause validation errors. ↓

fix Ensure all fields match the model schema exactly. Use model_dump() with exclude_unset to inspect.

Imports

Statement

wrong

from ga4gh.va_spec import Statement

correct

from ga4gh.va_spec.base import Statement

Statement is in base submodule, not top-level.

Quickstart

Create a minimal Statement object.

from ga4gh.va_spec.base import Statement
from pydantic import ValidationError

try:
    stmt = Statement(id='test:1', type='Statement', description='Example')
    print(stmt.model_dump(exclude_unset=True))
except ValidationError as e:
    print(e)