#!/usr/bin/perl

# blastall.cgi - a CGI wrapper for running blastall.
# Copyright (C) 2002, Humberto Ortiz Zuazaga.

# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.

# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.

# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.

use Neuroseq;
use CGI qw(:standard);

# Full path to program
$program = '/usr/local/bin/fbcsv';

print Neuroseq::title('blastall - blast a fasta file full of sequences at once.'),
    'Calls blastall to run a fasta file against nr and nt. Please be gentle on our server, It looks like each sequencing run will take an hour and a half to process.',
    p,
    hr;
if (!param()) {
    print start_form,
#    'Enter your email address:',
#    p,
#    textfield('email'),
    p,
    'Enter a fasta formated file of nucleotide sequences',
    p,
    textarea(-name=>'sequence',
                          -default=>'',
                          -rows=>10,
                          -columns=>40),
    p,
    submit,
    reset,
    defaults('Clear'),
    end_form,
    hr;

} else {

    $|=1;			# need this to keep program output in place

    my $sequence = param('sequence');
#    my $email = param('email');

    my $cwd;
    chomp($cwd = `pwd`);
    my $tmpdir = Neuroseq::mktmpdir("./tmp/blastall");

    chdir $tmpdir or die "error changing to $tmpdir: $!";
    #chdir "/usr/local/blast" or die "error changing to blast directory: $!";

    my $filename = "sequence";
    open (SEQ, ">$filename");
    print SEQ $sequence, "\n";
    close SEQ;

#    print p, "You will receive mail at $email notifying you when the results are ready", p, hr;

    print p, "Get your ", a({href=>"$tmpdir/results.csv"}, "results here"), " in an hour or so.";

    open(BATCH, ">batch");
    print BATCH "echo Running ... > results.csv\n";
    print BATCH "$program $filename > csv.txt\n";
    print BATCH "mv -f csv.txt results.csv\n";
    close BATCH;

    system("echo Not yet > results.csv; /usr/bin/batch -f batch -m now");

}

print Neuroseq::footer('2002.02.13');