The below code gets all of the output, whether stdout or stderr.
String line = String.format("paty/to/script.py");
CommandLine cmd = CommandLine.parse(line);
DefaultExecutor executor = new DefaultExecutor();
ByteArrayOutputStream stdout = new ByteArrayOutputStream();
PumpStreamHandler psh = new PumpStreamHandler(stdout);
executor.setStreamHandler(psh);
int exitvalue = executor.execute(cmd);
String output = stdout.toString();
How can I get both streams separately?