state variables glyphs are not loaded properly from SBGN-ML when their state sub-element is prefixed

iVis-at-Bilkent / newt

A web application to visualize and edit pathway models

http://newteditor.org

GNU Lesser General Public License v3.0

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state variables glyphs are not loaded properly from SBGN-ML when their state sub-element is prefixed #706

Closed adrienrougny closed 4 months ago

adrienrougny commented 7 months ago

State variables are not loaded properly from SBGN-ML when the element inside the state variable element is prefixed (e.g., ). The state variable is represented but it has no text inside (the value and variable inside the element are not taken into account). Here is a minimal SBGN-ML file to reproduce the issue:

<?xml version="1.0" encoding="UTF-8"?>

umut-er commented 4 months ago

I tracked this down. It is because of a typo in libsbgn.js. See this. It is currently sate instead of state. I have opened a PR that resolves this issue.

ugurdogrusoz commented 4 months ago

@hasanbalci can we make sure this is used by Newt deployments

hasanbalci commented 4 months ago

I merged the PR by @umut-er. The fix is currently available in the dev version: http://newt.cs.bilkent.edu.tr/.