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lib/Bio/Graphics/Browser2.pm  view on Meta::CPAN

    my $self = shift;

    my $source = CGI::param('source') || CGI::param('src') || CGI::path_info();
    $source    =~ s!\#$!!;  # get rid of trailing # left by IE
    $source    =~ s!^/+!!;  # get rid of leading & trailing / from path_info()
    $source    =~ s!/+$!!;

    $source;
}

sub update_data_source {
  my $self    = shift;
  my $session    = shift;
  my $new_source = shift;
  my $old_source = $session->source || $self->default_source;

  $new_source ||= $self->get_source_from_cgi();

  my $source;
  if ($self->valid_source($new_source)) {
    $session->source($new_source);

lib/Bio/Graphics/Browser2/Render.pm  view on Meta::CPAN

#
##################################################################3

sub set_default_state {
  my $self = shift;
  my $state = $self->state;
  $self->default_state if !$state->{tracks} # always set in one form or another
                           or param('reset');
}

sub update_state {
  my $self   = shift;
  warn "[$$] update_state()" if DEBUG;
  return if param('gbgff');          # don't let gbgff requests update our coordinates!!!
#  return if url() =~ /gbrowse_img/;  # don't let gbrowse_img requests update our coordinates either!!
  $self->_update_state;
}

sub _update_state {
    my $self = shift;

lib/Bio/Graphics/Browser2/Render/Slave/AWS_Balancer.pm  view on Meta::CPAN

}

sub running_as_instance {
    my $self = shift;
    return -e '/var/lib/cloud/data/previous-instance-id' 
	&& head('http://169.254.169.254');
}


# update conf file with new snapshot images
sub update_data_snapshots {
    my $self = shift;
    my @snapshot_ids = @_;
    my $timestamp     = 'synchronized with local filesystem on '.localtime;
    my $conf_file     = $self->conf_file;
    my ($user,$group) = (stat($conf_file))[4,5];
    open my $in,'<',$conf_file        or die "Couldn't open $conf_file: $!";
    open my $out,'>',"$conf_file.new" or die "Couldn't open $conf_file: $!";
    while (<$in>) {
	chomp;
	s/^(data_snapshots\s*=).*/$1 @snapshot_ids # $timestamp/;

lib/Bio/Graphics/Browser2/UserTracks/Database.pm  view on Meta::CPAN

        $value =~ s/\s+$//; 
        my $result = $uploadsdb->do("UPDATE uploads SET $field = ? WHERE trackid = ?", undef, $value, $file);
        $self->update_modified($file);
        return $result;
    } else {
        return $uploadsdb->selectrow_array("SELECT $field FROM uploads WHERE trackid = ?", undef, $file);
    }
}

# Update Modified (File ID[, User ID]) - Updates the modification date/time of the specified file to right now.
sub update_modified {
    my $self = shift;
    my $uploadsdb = $self->{uploadsdb};
    my $file = shift or return;
    my $now = $self->nowfun;
    # Do not swap out this line for a field() call, since it's used inside field().
    return $uploadsdb->do("UPDATE uploads SET modification_date = $now WHERE trackid = " . $uploadsdb->quote($file));
}

# Created (File ID) - Returns creation date of $file, cannot be set.
sub created {

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