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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.pm  view on Meta::CPAN

  warn '[',Bio::Graphics::Browser2::Session->time,'] ',"[$$] remove_track_from_state($label)" if DEBUG;
  delete $self->state->{features}{$label};
}

sub track_visible {
    my $self  = shift;
    my $label = shift;
    return $self->state->{features}{$label}{visible};
}

sub update_state_from_cgi {
  my $self  = shift;
  my $state = $self->state;
  warn "state = $state" if DEBUG;
  $self->update_options($state);
  $self->update_coordinates($state);
  $self->update_region($state);

  if (param('revert')) {
      $self->default_tracks($state);
  }

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

    my $self = shift;
    my ($semconf,$length) = @_;
    my @ranges = keys %$semconf;
    for my $r (@ranges) {
	my ($low,$hi) = split ':',$r;
	return $r if $length >= $low && (!defined $hi || $length < $hi);
    }
    return;
}

sub update_options {
  my $self  = shift;
  my $state = shift || $self->state;
  my $data_source = shift || $self->data_source;

  #  return unless param('width'); # not submitted
  $state->{width} ||= $self->setting('default width');  # working around a bug during development

  $state->{grid} = 1 unless exists $state->{grid};  # to upgrade from older settings
  $state->{flip} = 0;  # obnoxious for this to persist

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

  }

  else  {
    $state->{name} ||= '';
    $state->{name} =~ s/^\s+//; # strip leading
    $state->{name} =~ s/\s+$//; # and trailing whitespace
  }
  $self->session->modified;
}

sub update_tracks {
  my $self  = shift;
  my $state = shift;

  if (my @add = multi_param('add')) {
      my @style = multi_param('style');
      $self->handle_quickie(\@add,\@style);
  }

  # selected tracks can be set by the 'l', 'label' or 't' parameter
  # the preferred parameter is 'l', because it implements correct

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

# 2. If param('ref'),param('start') and param('stop') are defined, or if param('q') is defined, then we
#    reset {ref,start,stop}
# 3. Otherwise, if {ref,start,stop} are defined, then
#    2a. interrogate param('span'). If span != (stop-start+1) then user has changed the zoom popup menu and we do a zoom.
#    2b. interrogate /left|right|zoom|nav|regionview|overview/, which define the various zoom and scroll buttons.
#        If any of them exist, then we do the appropriate coordinate adjustment
# 3. If we did NOT change the coordinates, then we look for param('name') and use that to set the coordinates
#    using a database search.
# 4. set {name} to "ref:start..stop"

sub update_coordinates {
  my $self  = shift;
  my $state = shift || $self->state;

  delete $self->{region}; # clear cached region
  my $position_updated;

  if (param('ref')) {
    $state->{ref}   = param('ref');
    $state->{view_start} = param('start') if defined param('start') && param('start') =~ /^[\d-]+/;
    $state->{view_stop}  = param('stop')  if defined param('stop')  && param('stop')  =~ /^[\d-]+/;

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

		}
	    }
	}

	# update our "name" state and the CGI parameter
	$state->{name} = $self->region_string;
    }
    $position_updated;
}

sub update_state_from_details_mult {
    my $self = shift;
    my $state = $self->state;

    my $view_start = $state->{view_start} || 0;
    my $view_stop  = $state->{view_stop}  || 0;

    my $details_mult = $self->details_mult;

    my $length         = $view_stop - $view_start;
    my $length_to_load = int($length * $details_mult);

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

  my $click_position = $state->{region_size}  * ($position_data-$padl)/$regionview_width;
  my $span           = $state->{stop} - $state->{start} + 1;

  my ($regionview_start, $regionview_end) = $self->regionview_bounds();

  $state->{start} = int($click_position - $span/2 + $regionview_start);
  $state->{stop}  = $state->{start} + $span - 1;
}

sub update_region {
  my $self  = shift;
  my $state = shift || $self->state;

  if ($self->setting('region segment')) {
    $state->{region_size} = param('region_size') 
	if defined param('region_size');
    $state->{region_size} = $self->setting('region segment') 
	unless defined $state->{region_size};
  }
  else {
    delete $state->{region_size};
  }
}

sub update_section_visibility {
  my $self = shift;
  my $state = shift;

  for my $div (grep {/^div_visible_/} CGI::cookie()) {
    my ($section)   = $div =~ /^div_visible_(\w+)/ or next;
    my $visibility  = CGI::cookie($div);
    $state->{section_visible}{$section} = $visibility;
  }
}

sub update_galaxy_url {
    my $self  = shift;
    my $state = shift;
    if (my $url = param('GALAXY_URL')) {
	warn "[$$] setting galaxy" if DEBUG;
	$state->{GALAXY_URL} = $url;
    } elsif (param('clear_galaxy')) {
	warn "clearing galaxy" if DEBUG;
	delete $state->{GALAXY_URL};
    }
}

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/Render/Slave/AWS_Balancer.pm  view on Meta::CPAN

		$self->remove_slave($c);
		$reconfigure++;
	    }
	}
	# we reconfigure master immediately to avoid calling instance that were terminated
	$self->reconfigure_master() if $reconfigure;
    }
}

# this is called to act on state changes in spot requests and instances
sub update_requests {
    my $self = shift;
    my @requests = $self->pending_spot_requests;
    for my $sr (@requests) {
	my $state    = $sr->current_status;
	$self->log_debug("Status of $sr is $state");
	my $instance = $sr->instance;
	if ($state eq 'fulfilled' && $instance && $instance->instanceState eq 'running') {
	    $instance->add_tag(Name => 'GBrowse Slave');
	    $self->log_debug("New instance $instance; testing readiness");
	    next unless $self->ping_slave($instance);   # not ready - try again on next poll

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

sub get_file_id { warn "get_file_id() has been called, without properly inheriting subclass Database.pm"; }
sub filename { warn "filename() has been called, without properly inheriting a subclass (like Filesystem.pm or Database.pm)"; }
sub nowfun { warn "nowfun() has been called, without properly inheriting subclass Database.pm"; }
sub get_uploaded_files { warn "get_uploaded_files() has been called, without properly inheriting a subclass (like Filesystem.pm or Database.pm)"; }
sub get_public_files { warn "get_public_files() has been called, without properly inheriting subclass Database.pm"; }
sub get_imported_files { warn "get_imported_files() has been called, without properly inheriting a subclass (like Filesystem.pm or Database.pm)"; }
sub get_shared_files { warn "get_shared_files() has been called, without properly inheriting subclass Database.pm"; }
sub share { warn "share() has been called, without properly inheriting subclass Database.pm"; }
sub unshare { warn "unshare() has been called, without properly inheriting subclass Database.pm"; }
sub field { warn "field() has been called, without properly inheriting subclass Database.pm"; }
sub update_modified { warn "update_modified() has been called, without properly inheriting subclass Database.pm"; }
sub created { warn "created() has been called, without properly inheriting a subclass (like Filesystem.pm or Database.pm)"; }
sub modified { warn "modified() has been called, without properly inheriting a subclass (like Filesystem.pm or Database.pm)"; }
sub description { warn "description() has been called, without properly inheriting a subclass (like Filesystem.pm or Database.pm)"; }
sub add_file { warn "add_file() has been called, without properly inheriting a subclass (like Filesystem.pm or Database.pm)"; }
sub delete_file { warn "delete_file() has been called, without properly inheriting a subclass (like Filesystem.pm or Database.pm)"; }
sub is_imported { warn "is_imported() has been called, without properly inheriting a subclass (like Filesystem.pm or Database.pm)"; }
sub permissions { warn "permissions() has been called, without properly inheriting subclass Database.pm"; }
sub is_mine { warn "is_mine() has been called, without properly inheriting a subclass (like Filesystem.pm or Database.pm)"; }
sub owner { warn "owner() has been called, without properly inheriting a subclass (like Filesystem.pm or Database.pm)"; }
sub is_shared_with_me { warn "is_shared_with_me() has been called, without properly inheriting subclass Database.pm"; }

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 {