GA4GH Genomic Knowledge Standards Meta-schema

0.3.2 verified Sat May 09 auth: no python

Tools for working with the GA4GH Genomic Knowledge Standards (GKS) meta-schema, including schema parsing, validation, and code generation. Current version: 0.3.2, requires Python >=3.12. Release cadence: irregular, with minor fixes and CI improvements.

pip install ga4gh-gks-metaschema

Common errors

error ModuleNotFoundError: No module named 'ga4gh_gks_metaschema' ↓

cause Using the PyPI package name (with hyphens) as the import path.

fix

Use 'import gks_metaschema' or 'from gks_metaschema import ...'.

error AttributeError: module 'gks_metaschema' has no attribute 'SchemaParser' ↓

cause The class or function name might be outdated or not imported correctly.

fix

Check the documentation for the correct class name; common entry points are SchemaParser, MetaSchema, etc.

error pydantic.errors.PydanticUserError: A custom validator may not have type-checking... ↓

cause Using an older version of pydantic that is incompatible with the metaschema parser.

fix

Update pydantic to >=2.0.0 or follow the library's pinned dependency.

Warnings

gotcha The import path uses underscores (gks_metaschema), not hyphens (ga4gh-gks-metaschema). A common mistake is using the PyPI name directly in imports. ↓

fix Use 'from gks_metaschema import ...'.

breaking Version 0.3.0 dropped Python 3.11 support; requires Python >=3.12. ↓

fix Ensure your environment uses Python 3.12 or later.

deprecated The 'build_inheritance_dicts' function had a length check removed in version 0.3.2. Code relying on that check may behave differently. ↓

fix Update to 0.3.2 and adjust any code that assumed the length check.

Imports

SchemaParser
wrong
```
from ga4gh_gks_metaschema import SchemaParser
```
correct
```
from gks_metaschema import SchemaParser
```
The correct package name on PyPI uses hyphens, but the import uses underscores.

Quickstart

Basic usage: parse a GKS meta-schema YAML file into Python objects.

from gks_metaschema import SchemaParser

# Load a metaschema YAML file
parser = SchemaParser()
schema = parser.parse('path/to/schema.yaml')
print(schema)