cameronraysmith / single-cell-curation

cellxgene curation tools

This repository contains documents and code used by cellxgene's curation team. Issues/suggestions pertaining to datasets and how they interact with cellxgene should be created here.

For information/issues about cellxgene and its portal please refer to:

• single-cell-explorer
• single-cell-data-portal

Installation

The primary curation tool is the cellxgene-schema CLI. It enables curators to perform schema validation for datasets to be hosted on the cellxgene Data Portal.

It requires Python >= 3.8. It is available through pip:

pip install cellxgene-schema

It can also be installed from the source by cloning this repository and running:

make install 

And you can run the tests with:

make unit-test

Usage

The CLI validates an AnnData file (*.h5ad) to ensure that it addresses the schema requirements.

Datasets can be validated using the following command line:

cellxgene-schema validate input.h5ad

If the validation succeeds, the command returns a zero exit code; otherwise, it returns a non-zero exit code and prints validation failure messages.

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The data portal runs the following in the backend:

cellxgene-schema validate --add-labels output.h5ad input.h5ad

This execution validates the dataset as above AND adds the human-readable labels for the ontology and gene IDs as defined in the schema. If the validation is successful, a new AnnData file (output.h5ad) is written to disk with the labels appended.

This option SHOULD NOT be used by data contributors.

Contributing

Please read our contributing guidelines and make sure adhere to the Contributor Covenant code of conduct.

Reporting Security Issues

Please read our security reporting policy