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Ok I've found the problem. The conversion script works on the command line, but not through a web browser.
The reason for this is the temporary ODT file it creates (like /tmp/tempOdt_54f81bba0e6ed.odt) has very low permissions on it: -rw------- 1 www-data www-data
So the conversion java command always fails because it cannot read the input file. And because all script output is sent to dev/null you never get this error appear on the web page.
I've fixed this by adding passthru('chmod 444 '.$tempDoc); just after line 112 after the initial passthru() command.
While this works, is there a better way to do this?
Thanks,
Seb