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The python library I was referring to is https://streamlit.io/
If you need you can run JavaScript from within Java using Graal.js or Nashorn. To evaluate dynamic user input (Strings) you could also use a ScriptEngine (e.g. JavaScript) or dynamically compile inputs to Java using the JShell API.
I'm not sure what you mean by "pseudo-reactive site". If the generated html is not good enough, I'd probably remove the web frontend and render everything in ChartFX. It already provides plugins for zooming, ranging, visibility toggling, point editing, tooltips etc., so that should already cover most of what you'd need. There are a few other charting libraries too, but I'm less familiar with those.