Google Sheets to LinkML generator for the CRDC-H model
Project description
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 3.7 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.
- If you do not have a version of Python greater than 3.9, it is recommended to use
- 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:
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
Project details
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