Tools and scripts for parsing the GA4GH Genomic Knowledge Standards (GKS) metaschemas. The metaschema processor (MSP) converts JSON Schema Version 2020-12 in YAML to reStructuredText (RST) and JSON files.

Currently used in:

• GKS-Core
• VRS
• VA-Spec
• Cat-VRS

• Python 3.12: We recommend using pyenv.

Fork the repo at https://github.com/ga4gh/gks-metaschema, and initialize a development environment.

git clone [email protected]:YOUR_GITHUB_ID/gks-metaschema.git
cd gks-metaschema
make devready
source venv/3.12/bin/activate

Set up pre-commit hooks:

pre-commit install

To run the tests:

make test

The metaschema processor expects the following hierarchy:

├── docs
│   ├── source
│   |   ├── ...
│   ├── Makefile
├── schema
│   ├──gks_schema
│   |   ├── gks-schema-source.yaml
│   |   ├── Makefile
│   |   ├── prune.mk
│   ├── Makefile

• docs: Sphinx documentation directory. Must be named docs.
  • source: Directory containing documentation written in reStructuredText and Sphinx configuration. Must be named source.
  • Makefile: Commands to create the reStructuredText files. This file should not change across GKS projects.
• schema: Schema directory. Can also contain submodules for other GKS product schemas.
  • gks_schema: Schema directory for GKS product. The directory name should reflect the product, e.g. vrs.
    • gks-schema-source.yaml: Source document for the JSON Schema 2020-12. The file name should reflect the standard, e.g. vrs-source.yaml. The file name must end with -source.yaml.
    • Makefile: Commands to create the reStructuredText and JSON files. This file should not change across GKS projects.
    • prune.mk: Cleanup of files in def and json directories based on source document. This file should not change across GKS projects.
  • Makefile: Commands to create the reStructuredText and JSON files.

To create the corresponding def (reStructuredText) and json files after making changes to the source document, from the schema directory:

    make all

The file structure will now look like:

├── schema
│   ├──gks_schema
|   |   ├── def
│   |   |   ├── ...
|   |   ├── json
│   |   |   ├── ...
│   |   ├── gks-schema-source.yaml
│   |   ├── Makefile
│   |   ├── prune.mk
│   ├── Makefile

GKS specification documentation is written in reStructuredText and located in docs/source.

To build documentation locally, you must install entr:

brew install entr

Then from the docs directory:

make clean watch &

Then, open docs/build/html/index.html. The above make command should build docs when the source changes.

NOTE: Some types of changes require recleaning and building.