#!/usr/bin/perl
use strict;
use warnings;
use Adrian::Goodies ':dirs';
use File::Temp;
use File::Spec::Functions;
use Env::Path 'PATH';

PATH->Append(BLAST_BIN_DIR) if BLAST_BIN_DIR;

#my %VALID_PROGS = (blastn => 'allnucl', tblastn => 'allnucl', tblastx => 'allnucl',
#                   blastp => 'allprot', blastx => 'allprot');
#my %VALID_DBS = (allnucl => 'allnucl', nucl => 'allnucl', allflanks => 'allnucl',
#                 flanks => 'allnucl', allprot => 'allprot', prot => 'allprot');

my $cgi = CGI->new();

my ($title, $prog, $db, $seq) = ($cgi->param('title') || "notitle" . time(),
                                 $cgi->param('prog'),
                                 $cgi->param('db'),
                                 $cgi->param('sequence'));



$title =~ s/\s/ /g;
$title = "notitle" . time() if $title eq '';
$seq =~ s/[^A-Za-z]//g;
if ($cgi->request_method() eq 'POST' #and exists $VALID_PROGS{$prog} and
    #exists $VALID_DBS{$db} 
	and $seq) {
    my $seqfile = File::Temp->new();
    open (my $fh, '>', $seqfile);
    print $fh ">$title\n";
    print $fh $seq, "\n";
    close $fh;
    my $execstring;
    # currently is secure
    if ($prog eq "blastp" and $db eq "allnucl"){
        $execstring = "/home/groupii/ncbi-blast/bin/$prog -db \"" . catfile(BLAST_DB_DIR, "allprot") . "\" -max_target_seqs 10 -word_size 5 -evalue 100 -query \"$seqfile\"";
    } elsif ($prog eq "blastx" and $db eq "allnucl"){
        $execstring = "/home/groupii/ncbi-blast/bin/$prog -db \"" . catfile(BLAST_DB_DIR, "allprot") . "\" -max_target_seqs 10 -word_size 5 -evalue 100 -query \"$seqfile\"";
    } elsif ($prog eq "blastn") {
        $execstring = "/home/groupii/ncbi-blast/bin/$prog -db \"" . catfile(BLAST_DB_DIR, $db) . "\" -max_target_seqs 10 -word_size 5  -penalty -3 -reward 2 -task blastn -evalue 100 -query \"$seqfile\"";
    } else {
        $execstring = "/home/groupii/ncbi-blast/bin/$prog -db \"" . catfile(BLAST_DB_DIR, $db) . "\" -max_target_seqs 10 -word_size 5 -evalue 100 -query \"$seqfile\"";
    }
    print $cgi->header('text/plain');
    print qx{$execstring};
}
else {
    print $cgi->redirect('../blast.html');
}
exit;