This will require more elaborate code for saving. First extract the save/load logic to their own functions.
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load_graph_from_disk = function()
local f = App.open_for_reading(Filename)
Nodes = json.decode(f:read('*a'))
f:close()
end
save_graph_to_disk = function()
local f = App.open_for_writing(Filename)
f:write(json.encode(Nodes))
f:close()
end