[Bioperl-l] Bio::Factory::EMBOSS, CGI and taint
n.saunders at uq.edu.au
Wed Feb 28 05:25:08 EST 2007
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:
my $cgi = new CGI;
my $f = new Bio::Factory::EMBOSS;
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.
School of Molecular and Microbial Sciences
University of Queensland
Brisbane 4072 Australia
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