GA4GH Genomic Knowledge Standards meta-schema tools
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gks-metaschema
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:
Installing for development
Prerequisites
- Python 3.12: We recommend using pyenv.
Installation Steps
Fork the repo at https://github.com/ga4gh/gks-metaschema, and initialize a development environment.
git clone git@github.com:YOUR_GITHUB_ID/gks-metaschema.git
cd gks-metaschema
make devready
source venv/3.12/bin/activate
Set up the pre-commit hook
cp ./scripts/pre-commit ./.git/hooks/
Testing
To run the tests:
make test
Usage
File Hierarchy
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 nameddocs.source: Directory containing documentation written in reStructuredText and Sphinx configuration. Must be namedsource.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 indefandjsondirectories based on source document. This file should not change across GKS projects.
Makefile: Commands to create the reStructuredText and JSON files.
Contributing to the schema
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
Contributing to the docs
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.
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