You can do it from separate domains since those are each run in their own JVM, but then each would have to have at least its own port, or you could give each instance its own IP so they could all be port 80.
If you go this method, you can use SMF and it can start each instance of glassfish with actual user who own each script, yet you can still run on port 80, SMF can grant you the appropriate privilege.
Otherwise your webapps would just sudo appropriately to run the scripts, though you may have to run something like 'expect' for that.
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