monarch-phenotype-profile-ingest

Documentation

monarch kg ingest for phenotypes

Requirements

• Python >= 3.10
• Poetry

Setting Up a New Project

Upon creating a new project from the cookiecutter-monarch-ingest template, you can install and test the project:

cd monarch-phenotype-profile-ingest
make install
make test

There are a few additional steps to complete before the project is ready for use.

GitHub Repository

1. Create a new repository on GitHub.
2. Enable GitHub Actions to read and write to the repository (required to deploy the project to GitHub Pages).
   • in GitHub, go to Settings -> Action -> General -> Workflow permissions and choose read and write permissions

3. Initialize the local repository and push the code to GitHub. For example:

   cd monarch-phenotype-profile-ingest
   git init
   git remote add origin https://github.com/<username>/<repository>.git
   git add -A && git commit -m "Initial commit"
   git push -u origin main
   

Transform Code and Configuration

1. Edit the download.yaml, transform.py, transform.yaml, and metadata.yaml files to suit your needs.
   • For more information, see the Koza documentation and kghub-downloader.
2. Add any additional dependencies to the pyproject.toml file.
3. Adjust the contents of the tests directory to test the functionality of your transform.

Documentation

1. Update this README.md file with any additional information about the project.
2. Add any appropriate documentation to the docs directory.

Note: After the GitHub Actions for deploying documentation runs, the documentation will be automatically deployed to GitHub Pages.
However, you will need to go to the repository settings and set the GitHub Pages source to the gh-pages branch, using the /docs directory.

GitHub Actions

This project is set up with several GitHub Actions workflows.
You should not need to modify these workflows unless you want to change the behavior.
The workflows are located in the .github/workflows directory:

• test.yaml: Run the pytest suite.
• create-release.yaml: Create a new release once a week, or manually.
• deploy-docs.yaml: Deploy the documentation to GitHub Pages (on pushes to main).
• update-docs.yaml: After a release, update the documentation with node/edge reports.

Once you have completed these steps, you can remove the Setting Up a New Project section from this README.md file.

Installation

cd monarch-phenotype-profile-ingest
make install
# or
poetry install

Note that the make install command is just a convenience wrapper around poetry install.

Once installed, you can check that everything is working as expected:

# Run the pytest suite
make test
# Download the data and run the Koza transform
make download
make run

Usage

This project is set up with a Makefile for common tasks.
To see available options:

make help

Download and Transform

Download the data for the monarch_phenotype_profile_ingest transform:

poetry run monarch_phenotype_profile_ingest download

To run the Koza transform for monarch-phenotype-profile-ingest:

poetry run monarch_phenotype_profile_ingest transform

To see available options:

poetry run monarch_phenotype_profile_ingest download --help
# or
poetry run monarch_phenotype_profile_ingest transform --help

Testing

To run the test suite:

make test

---

This project was generated using monarch-initiative/cookiecutter-monarch-ingest.
Keep this project up to date using cruft by occasionally running in the project directory:

cruft update

For more information, see the cruft documentation

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