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wwwblast: blast.REAL process can't read param values from parent process

Frederic Hancy hancy at gene.ucl.ac.be
Mon Apr 26 01:48:52 EST 2004

Hi all,

I have developped a cgi application that allows users to manage their
own blast databases from a web interface, allowing them to upload
their sequence files and create the blast database with formatdb. With
the current wwwblast application, the only way to do that (as far as I
know) is to launch formatdb on your sequence file from your server,
and then to update blast.html form (select database field) and the
blast.rc configuration file.

To do that, I have replaced the blast.html page with a cgi script and
a web template. In addition to the normal blast.html form, the
template contains another form to manage the user's blast db. The
first form sends its query to the normal blast.cgi, the other to my
script which reads for the specified username the list of blast
databases and loads it in the template. In order to avoid conflicts
between users and db files, I've created a subfolder for each user in
the db folder.

That's where I'm stuck: blast.cgi does the following:

#!/bin/csh -f

echo "Content-type: text/html"
echo ""
setenv BLASTDB db

So basically it outputs an HTTP header (Content-type), a blank line
and then it launches a child process blast.REAL which outputs to
STDOUT the blast output in HTML. Parameters are read from the
inherited STDIN from the parent process blast.cgi, which were sent by
the client through an HTTP request.

What I need to do is to replace db with the user's database folder.
Being rather a newbie in bash, I've tried to replace this script with
a perl CGI where I could easily access to the username param, set the
BLASTDB and launch blast.REAL:


use CGI;
use strict;

my $q = new CGI;
my $username = $q->param("username"};

$ENV{BLASTDB} = "db/$username";
print $q->header( "text/html");
exec './blast.REAL' or die "Can't run command blast.REAL: $!";

When I use this script, it returns me a blank page, and a few second
later the old blast.html form.  If I try to redirect blast.REAL output
to a file, no file is created as if the command wasn't executed.  When
using the debug switch ($ENV{DEBUG_COMMAND_LINE} = 'TRUE' on the
original script, a file (__web.in) is created in /tmp. If I use after
the command './blast.REAL < __web.in' in my script, then the blast
output is sent back to my browser.  This file contains all the param
values.  So it seems that the created process doesn't inherit from the
STDIN of the parent process, the < redirection provides the input. A
rather long mail for a rather stupid problem...

Any help is greatly appreciated!


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