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
Authorization
sheet2linkml uses the pygsheets
library in order to access sheets in
Google Drive. To authorize it to access your Google Sheets, you will need to create and download Google Drive client credentials. First,
enable the Google Drive API. After the API is enabled,
create and download the client credentials
from the Google API Console. Save the file as google_api_credentials.json
in
the root directory of this project. Detailed instructions and screenshots
are also available from the pygsheets
documentation.
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=1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4
A google_api_credentials.json
file is also required in the root of this repo as detailed in the Authorization section above.
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
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