Direct Integration of PathVisio with WikiPathways GitHub

This project aims to develop a Direct GitHub Integration Plugin for PathVisio to transform the pathway curation workflow from outdated systems to the WikiPathways GitHub repository. This proposal delivers a Java-based plugin which uses GitHub REST APIs to carry forward Git Operations. The PathVisio-GitHub Integration plugin will provide a clean and user friendly UI for biologists unfamiliar with Git Operations. The main goal of this proposal is to build an automation of Git Operations directly from PathVisio to WikiPathways GitHub repository for WikiPathways contributors.

The plugin features authorization of users via GitHub using OAuth Device Authorization Grant and provides automatic forking of repositories and branching in the background using GitHub REST APIs. An encoding of GPML pathway files into Base64 format takes place before the plugin stages commits and opens Pull Requests directly from the PathVisio dashboard without freezing the main application thread. This is ensured by Java SwingWorker running in the background. Furthermore, the project integrates GitHub Actions to automatically validate file formats and metadata completeness upon final submission.

Ultimately, this plugin helps to simplify complex Git operations of contributing to biological pathways, enabling the global biological research community to effortlessly work on PathVisio.