Gen3 Validator¶

Gen3 Validator is a Python toolkit designed to make working with Gen3 metadata schemas and data validation straightforward for developers.

With this tool, you can:

Resolve and flatten Gen3 JSON schemas so you can work with them programmatically.
Validate JSON metadata files against Gen3 schemas, catching schema violations early in your pipeline.
Check linkage integrity between data nodes (e.g., ensuring all sample-to-subject references are valid).
Parse Excel-based metadata templates and convert them to JSON for Gen3 ingestion.
Get detailed validation results and summary stats as Python data structures or pandas DataFrames, making it easy to integrate with your own scripts or reporting tools.

Getting Started:¶

Installation:

pip install gen3_validator

For more details, see the README.

Usage:

Clone this repo and walk through the examples in the usage page.
The usage examples load data from the tests/data directory so you can see how the data is structured.

Modules

gen3_validator package — Main package: dictionary handling, linkage, schema resolution, and validation.
gen3_validator.parsers package — Parsers for data and Excel files.

See the license page for more information.