[Bioperl-l] Bio::Factory::EMBOSS, CGI and taint

Neil Saunders n.saunders at uq.edu.au
Wed Feb 28 05:25:08 EST 2007


Dear Bioperlers,

I'm trying to understand an error that occurs when Bio::Factory::EMBOSS is used 
in a CGI script.  Using BioPerl 1.5.2 on Ubuntu Dapper, Apache 2.0.55, Perl 5.8.7.

If I load this test CGI script (cgi.pl) in a browser:

BEGIN CODE
----------
#!/usr/bin/perl -Tw
use strict;
use CGI;
use Bio::Factory::EMBOSS;

my $cgi = new CGI;
my $f   = new Bio::Factory::EMBOSS;

print $cgi->header,
       $cgi->start_html,
       $cgi->end_html;
--------
END CODE

I get a 500 server error and the Apache error log reads:
[error] [client 192.168.0.3] Premature end of script headers: cgi.pl

I can fix this in 2 ways:

(1) Move the "my $f = new Bio::Factory::EMBOSS" line to the end of the script, 
which isn't a very useful fix.
(2) Remove the -T switch from the shebang line

There seem to be a few old posts on the list regarding "taint-safe" modules.  It 
seems that the new Bio::Factory::EMBOSS object is interfering with the headers 
in some way, but I'm no CGI.pm guru and wondered if anyone could shed light on this.

thanks,
Neil
-- 
  School of Molecular and Microbial Sciences
  University of Queensland
  Brisbane 4072 Australia

http://nsaunders.wordpress.com


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