#! /usr/bin/perl

# Time-stamp: <2005-05-04 12:50:03 kasper>

use warnings;
use strict;
use SQLWriter;
use Getopt::Long;
use Bio::SearchIO;
use DBI;
use constant USAGE =><<END;

SYNOPSIS:

 blast2sql.pl [OPTIONS] <database_name> <inputfile> <inputfile> ...

DESCRIPTION:

This script creates database from blast report.

OPTIONS:

       --help
             Prints this help.
       --quiet
             Makes the script run without progress messages.
       --prefix <string>
             Prefix to names of tables.
       --noempty
             Skips blast reports with no hits.
       --overwrite
             Forces overwrite of old database of same name.
       --password
             Promts for database password.
       --host <host>
             Name of machine hosting the database.
       --user <user>
             Name of the user. Defualts to the environmental variable
             USER.
       --port <port>
             Port number.

EXAMPLES:

 blast2sql.pl --prefix myblast_ --noempty mydatabase blast.report

 # .my.cnf may look like this:

 [client]
 host=appserver
 user=kurt
 password=kurt

DEPENDENCIES:

A MySQL database. The class: SQLWriter. It is not on CPAN but send me
an email (kasper at binf.ku.dk) and I will be more than happy to send it.

AUTHOR:

Kasper Munch

COPYRIGHT:

This program is free software. You may copy and redistribute it under
the same terms as Perl itself.

END

my $help = 0;
my $prefix = '';
my $noempty = 0;
my $overwrite = 0;
my $quiet = 0;
my $adding = 0;
my $password = '';
my $user = $ENV{USER};
my $host = 'db';
my $port = 3306;

GetOptions(
           "help" => \$help,
           "prefix=s" => \$prefix,
           "quiet" => \$quiet,
           "overwrite" => \$overwrite,
           "noempty" => \$noempty,
           "password" => \$password,
           "host=s" => \$host,
           "user=s" => \$user,
           "port=i" => \$port
          ) or die USAGE;

$help and die USAGE;

my $database = shift @ARGV or die $!;
my @files = @ARGV or die "You have to specify at least one blast report file.\n";
my $files = scalar @files;

# Ask for password if option specified without option value:
if ($password) {
  #turn off echoing but don't interfere with STDIN
  open (TTY, "/dev/tty") or die "Cannot open terminal\n";
  system ("stty -echo < /dev/tty");
  print STDERR "Enter password: ";
  chomp ($password = <TTY>);
  system ("stty echo < /dev/tty");
  close (TTY);
  print STDERR "\n";
}

# Defualt password:
$password ||= 'kasper';

my $result = "${prefix}result";
my $hit = "${prefix}hit";
my $hsp = "${prefix}hsp";

# Connect to the database:
my $dsn = "DBI:mysql:$database:$host;port=$port";
my %attr = ( RaiseError => 1, AutoCommit => 0 );
my $dbh = DBI->connect ($dsn, $user, $password, \%attr);

if ($overwrite) {
  eval {
    $dbh->do("DROP TABLE $result") if exist($dbh, $result);
    $dbh->do("DROP TABLE $hit") if exist($dbh, $hit);
    $dbh->do("DROP TABLE $hsp") if exist($dbh, $hsp);
    $dbh->commit;
  };
  if ($@) {
    $dbh->rollback;
    die "Failed dropping existing tables.";
  }
}

# Create a SQLWriter obj.:
my $writer = SQLWriter->new(dbh => $dbh,
                            result => $result,
                            hit => $hit,
                            hsp => $hsp,
                            noempty => $noempty # this is new.
                           );

print STDERR "\nDumping blastreport file to database: $database" if !$quiet and $files == 1;
print STDERR ".\n\n" unless $quiet;

foreach my $file (@files) {
  my $searchio = new Bio::SearchIO(-format => 'blast',
                                   -file   => $file);
#  $writer->dumpsql($searchio, $noempty);
  $writer->dumpsql($searchio); # This is new.
}

$dbh->disconnect() or warn $dbh->errstr();

sub exist {
  my $table = shift;
  my $exist = 0;
  my $check = $dbh->prepare(qq{show tables});
  $check->execute();
  my $tables = $check->fetchall_arrayref();
  for my $t (@$tables) {
    $exist = 1 if $$t[0] eq "$table";
  }
  return $exist;
}

=head1 SYNOPSIS:

 blast2sql.pl [OPTIONS] <database_name> <inputfile> <inputfile> ...

=head1 DESCRIPTION:

This script creates database from blast report.

=head1 OPTIONS:

=over 4

=item --help

Prints this help.

=item --quiet

Makes the script run without progress messages.

=item --prefix <string>

Prefix to names of tables.

=item --noempty

Skips blast reports with no hits.

=item --overwrite

Forces overwrite of old database of same name.

=item --password

Promts for database password.

=item --host <host>

Name of machine hosting the database.

=item --user <user>

Name of the user. Defualts to the environmental variable
USER.

=item --port <port>

Port number.

=back

=head1 EXAMPLES:

 blast2sql.pl --prefix myblast_ --noempty mydatabase blast.report

 # .my.cnf may look like this:

 [client]
 host=appserver
 user=kurt
 password=kurt

=head1 DEPENDENCIES:

A MySQL database. The class: SQLWriter. It is not on CPAN but send me
an email (kasper at binf.ku.dk) and I will be more than happy to send it.

=head1 AUTHOR:

Kasper Munch

=head1 COPYRIGHT:

This program is free software. You may copy and redistribute it under
the same terms as Perl itself.


=cut