my $self = shift if (defined(caller(1)));

  my $file = shift;
  my $source_id = shift;
  my $species_id = shift;
  my $verbose = shift;

  my ($type, $my_args) = split(/:/,$file);

  my $user  ="ensro";
  my $host;
  my $port;
  my $dbname;
  my $pass;

  if($my_args =~ /host[=][>](\S+?)[,]/){
    $host = $1;
  }
  if($my_args =~ /port[=][>](\S+?)[,]/){
    $port =  $1;
  }
  if($my_args =~ /dbname[=][>](\S+?)[,]/){
    $dbname = $1;
  }
  if($my_args =~ /pass[=][>](\S+?)[,]/){
    $pass = $1;
  }
  if($my_args =~ /user[=][>](\S+?)[,]/){
    $user = $1;
  }

  my %source;
  $source{"RFAM"}     = $self->get_source_id_for_source_name('RFAM')    || die "Could not get source_id for RFAM";
  $source{"miRBase"}  = $self->get_source_id_for_source_name('miRBase') || die "Could not get source_id for miRBase";


  my $dbi2 = $self->dbi2($host, $port, $user, $dbname, $pass);
  if(!defined($dbi2)){
    return 1;
  }

  my $sql=(<<SQL);
  SELECT transcript_stable_id, transcript_dbid, source, xref_name, xref_primary_id, xref_description
    FROM ncRNA_Xref
      WHERE taxonomy_id = $species_id
SQL

  my ($stable_id, $dbid, $source_name, $label, $acc, $desc);
  my $sth = $dbi2->prepare($sql);
  $sth->execute() or croak( $dbi2->errstr() );
  $sth->bind_columns(\$stable_id,\$ dbid,\$ source_name,\$ label,\$ acc,\$ desc);
  my $added = 0;
  while ( $sth->fetch() ) {
    my ($description,$junk) = split("[[]Source:",$desc);

    if(!defined($source{$source_name})){
      print STDERR "Could not find source_id for source $source_name for xref $acc\n";
      next;
    }
    my $xref_id = $self->get_xref($acc,$source{$source_name}, $species_id);
    if(!defined($xref_id)){
      $xref_id = $self->add_xref($acc,"",$label,$description,$source{$source_name}, $species_id,"DIRECT");
      $added++;
    }
    my $transcript_id = $dbid;
    if(defined($stable_id) and $stable_id ne ""){
      $transcript_id = $stable_id;
    }
    $self->add_direct_xref($xref_id, $transcript_id, "Transcript", "") if (defined($transcript_id));    

  }
  $sth->finish;

  print "Added $added Xrefs for ncRNAs\n" if($verbose);
  return 0;
}

1;