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ga4gh-va-spec

library0.4.3pypypi✓ verified 86d ago

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.

serialization data ai-ml

pip install ga4gh-va-spec

github ↗package ↗homepage ↗docs ↗changelog ↗

INSTALL

IMPORT

SIG · GA4GH-VA-SPEC

ga4gh-va-spec

serializationpythonv0.4.3

harness data pending

Install & Compatibility

Where this runs

No compatibility data collected yet for this library.

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

Statement

✓ from ga4gh.va_spec.base import Statement

✗ from ga4gh.va_spec import Statement

Statement is in base submodule, not top-level.

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)

Debug

Known issues

breakingVersion 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).

affects: >=0.2.0

breakingVersion 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.

affects: <0.4.0

gotchaModels 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.

affects: >=0.4.0

Errors

Common errors & fixes

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

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

fix

Use: from ga4gh.va_spec.base import Statement

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

Model has additionalProperties=False and extra fields are provided.

fix

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

Upgrade

Version history

0.4.3latest on PyPI · released Dec 23, 2025

Audit

Dependencies

vrs-pythonrequiredCore dependency for variant representation models (VRS/GA4GH)

pydanticrequiredData validation and serialization

Agent activity

12 hits · last 30 days

node

OpenAI (training)

Resources

githubhttps://github.com/ga4gh/va-spec-python ↗

packagehttps://pypi.org/project/ga4gh-va-spec/ ↗

homepagehttps://ga4gh-va-spec.readthedocs.io ↗

docshttps://github.com/ga4gh/va-spec-python ↗

changeloghttps://github.com/ga4gh/va-spec-python/releases ↗