[Bioperl-l] Permission denied when using Bio::SearchIO in CGI script

[Marcus Claesson]

Thanks for your answers!
 
> This is an error in your directory permissions or something (check the 
> group read/write on teh file that is created with an ls -l). Bioperl 
> does nothing "fancy" about opening files and can't change permissions 
> (obviously) of a file.
 
I noticed that too but the problem is, though I can control
persmissions and locations on my own local files, I cannot do it on a 
remote user's files. The purpose of this cgi script is for web users to
parse their local blast output files and upload the result file onto my
server.

The Bio::Search module behaves differently than the "PerlCGI-way" to open
files. Here's an example:

Both these methods work fine when I run the script on a local file with
the right permissions:

#!/usr/bin/perl -wT
use CGI qw(:standard);
use Bio::SearchIO;
print $q->filefield(-name=>'file',	#A cgi function to browse and
select files to open
                    -size=>20),$q->br;
print $q->submit(-name  =>'upload', 
                 -value =>'Upload file'),$q->br;
if (param('upload')) {
    $fh = $q->upload('file');
    $in = new Bio::SearchIO(-format => 'blast', 
			    -file   => $fh);
    while(<$fh>) {
	print $_; }
    while($result = $in->next_result) {
      etc,etc... }
}
 
But when I try to open C:\Temp\blastfile.out from a remote windows station
I get this error message:

[Mon Jan 27 10:58:38 2003] [error] [client 143.239.131.75] [Mon Jan 27 
10:58:38 2003] bxbrowser1.pl: ------------- EXCEPTION  -------------, 
referer: http://nsfm39.ucc.ie/cgi-bin/bxbrowser1.pl
[Mon Jan 27 10:58:38 2003] [error] [client 143.239.131.75] [Mon Jan 27
10:58:38 2003] bxbrowser1.pl: MSG: Could not open C:\Temp\blastfile.out
for reading: No such file or directory, referer:
http://nsfm39.ucc.ie/cgi-bin/bxbrowser1.pl
[Mon Jan 27 10:58:38 2003] [error] [client 143.239.131.75] [Mon Jan 27
10:58:38 2003] bxbrowser1.pl: STACK Bio::Root::IO::_initialize_io
/usr/lib/perl5/site_perl/5.8.0/Bio/Root/IO.pm:244, referer:
http://nsfm39.ucc.ie/cgi-bin/bxbrowser1.pl
[Mon Jan 27 10:58:38 2003] [error] [client 143.239.131.75] [Mon Jan 27
10:58:38 2003] bxbrowser1.pl: STACK Bio::Root::IO::new
/usr/lib/perl5/site_perl/5.8.0/Bio/Root/IO.pm:192, referer:
http://nsfm39.ucc.ie/cgi-bin/bxbrowser1.pl
[Mon Jan 27 10:58:38 2003] [error] [client 143.239.131.75] [Mon Jan 27
10:58:38 2003] bxbrowser1.pl: STACK Bio::SearchIO::new
/usr/lib/perl5/site_perl/5.8.0/Bio/SearchIO.pm:121, referer:
http://nsfm39.ucc.ie/cgi-bin/bxbrowser1.pl
[Mon Jan 27 10:58:38 2003] [error] [client 143.239.131.75] [Mon Jan 27
10:58:38 2003] bxbrowser1.pl: STACK Bio::SearchIO::blast::new
/usr/lib/perl5/site_perl/5.8.0/Bio/SearchIO/blast.pm:200, referer:
http://nsfm39.ucc.ie/cgi-bin/bxbrowser1.pl
[Mon Jan 27 10:58:38 2003] [error] [client 143.239.131.75] [Mon Jan 27
10:58:38 2003] bxbrowser1.pl: STACK Bio::SearchIO::new
/usr/lib/perl5/site_perl/5.8.0/Bio/SearchIO.pm:134, referer:
http://nsfm39.ucc.ie/cgi-bin/bxbrowser1.pl
[Mon Jan 27 10:58:38 2003] [error] [client 143.239.131.75] [Mon Jan 27
10:58:38 2003] bxbrowser1.pl: STACK toplevel
/var/www/cgi-bin/bxbrowser1.pl:25, referer:
http://nsfm39.ucc.ie/cgi-bin/bxbrowser1.pl
[Mon Jan 27 10:58:38 2003] [error] [client 143.239.131.75] [Mon Jan 27
10:58:38 2003] bxbrowser1.pl: , referer:
http://nsfm39.ucc.ie/cgi-bin/bxbrowser1.pl
[Mon Jan 27 10:58:38 2003] [error] [client 143.239.131.75] [Mon Jan 27
10:58:38 2003] bxbrowser1.pl: --------------------------------------,
referer: http://nsfm39.ucc.ie/cgi-bin/bxbrowser1.pl

Thus, Bio::Search can't even find the file. But to open it and print the 
contents in the 'normal cgi-way' works fine i.e
    while(<$fh>) {
        print $_; 
    }

Howcome do you think?

Regards,
Marcus