phenolog-transform

| Documentation |

transform raw phenolog output to kgx format

Requirements

• Python >= 3.10
• Poetry

Starting a new project

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

cd phenolog-transform
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 phenolog-transform
   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.

Once you have completed these steps, you can remove this section from the README.md file.

Installation

cd phenolog-transform
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 phenolog_transform transform:

poetry run phenolog_transform download

To run the Koza transform for phenolog-transform:

poetry run phenolog_transform transform

To see available options:

poetry run phenolog_transform download --help
# or
poetry run phenolog_transform 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