Question

Can I replace an executable (accessed via a system call from ruby) with an executable that expects certain input and supplies the expected output in a consistent amount of time? I’m mainly operating on Mac OSX 10.6 (Snow Leopard), but I also have access to Linux and Windows. I’m using MRI ruby 1.8.7.

Background: I’m looking at doing several DNA sequence alignments, one in each thread. When I try using BioRuby for this, either BioRuby or ruby’s standard library’s tempfile sometimes raise exceptions (which is better than failing silently!).

I set up a test that reproduces the problem, but only some of the time. I assume the main sources of variability between tests are the threading, the tempfile system, and the executable used for alignment (ClustalW). Since ClustalW probably isn’t malfunctioning, but can be a source of variability, I’m thinking that eliminating it may aid reproducibility.

For those thinking select isn’t broken – that’s what I’m wondering too. However, according to the changelog, there was concern about tempfile’s thread safety in August 2009. Also, I’ve checked on the BioRuby mailing list whether I’m calling the BioRuby code correctly, and that seems to be the case.

Answer 1

I really don’t understand what the problem is or what exactly are you after, can’t you just write something like

#!/bin/sh
#Test for input (syntax might be wrong, but you get the idea)
if [ $* ne "expected input" ]; then
    echo "expected output for failure"
    exit -1
fi
#have it work in a consistent amount of time 
$CONSISTENT_AMOUNT_OF_TIME = 20
sleep $CONSISTENT_AMOUNT_OF_TIME
echo "expected output"