MATRIX validator

A validation tool for KG edges and nodes in KGX format.

Users

Install the validator:

pip install matrix-validator

Run the validator:

matrix-validator python \
		--report-dir tmp/ \
		--edges abc_edges.tsv \
		--nodes abc_nodes.tsv

Currently available options for validator are "pandera", "python" and "polars".

Getting started for Developers

1. Make sure you have poetry installed
2. Run make install to install the poetry environment
3. Run make run_small_tests to see if it worked

The tool is currently divided in the following files (basic layout):

• src/matrix_validator/cli.py contains all CLI methods (click-based) and should not contain any code other than CLI boilerplate (in particular no IO)
• src/matrix_validator/validator.py contains the abstract validation class.
• src/matrix_validator/datamodels.py contains the edge and nodes schemas.
• src/matrix_validator/util.py contains any utility methods that we might need.
• We currently experiment with a number of different implementations:
  • src/matrix_validator/validator_polars.py: A very efficient pure polars implementation.
  • src/matrix_validator/validator_purepython.py: A pure python implementation
  • src/matrix_validator/validator_schema.py: A schema-based validation approach based on LinkML generated pandera schemas.

Acknowledgements

This cookiecutter project was developed from the monarch-project-template template and will be kept up-to-date using cruft.