sheet2linkml

A python package for converting the CRDC-H data model, which is currently stored in a Google Sheet. The command line utility built into the package can be used to generate a LinkML representation of the CRDC-H data model.

Installation Requirements and Pre-requisites

• Python 3.9 or higher
• pyenv
  • If you do not have a version of Python greater than 3.9, it is recommended to use pyenv to be able to easily use and switch between multiple Python versions.
  • If you’re experiencing issues with pyenv on macOS, you can consider using miniconda.
• poetry
  • One-time installation commands are available for osx/linux/bash on windows and for windows powershell.

If you are using a Windows machine, typical bash programs will not work on cmd in the same way as they work in the Linux/MacOS terminals. To circumvent this, it is recommended that you use one of the following Bash on Windows strategies

• WSL
• Cygwin
• Git Bash

so you can easily execute the command line utilities that are described later in these docs.

Installing

Create and activate a Python 3.9+ virtual environment within which you can install the package:

python3 -m venv .venv
source .venv/bin/activate
python -m pip install sheet2linkml

Command Line Client Usage

Identify the Google Sheet that you want to convert to LinkML. Note that sheet2linkml is not currently a general-purpose Google Sheet to LinkML converter. It will only work with Google Sheets that have been written in a particular, currently undefined format.

Contact your CCDH colleagues to obtain the correct sheet ID and assert it either in a .env file or in the shell, like this:

export CDM_GOOGLE_SHEET_ID=WbM2Jr869ofmdcSmhX_1E0aLWvnK2-gr47Mo_tzuQKWy

A google_api_credentials.json file is also required in the root of this repo. Documentation is forthcoming.

And the user is responsible for defining

• ~/path/to/crdch_model.yaml
• ~/path/to/logging.ini
  • ./logging.ini may be adaquate for many users

Then perform the conversion:

sheet2linkml --output ~/path/to/crdch_model.yaml --logging-config ~/path/to/logging.ini