lib/CXGN/Cview/MapOverviews/ProjectStats.pm

   1
   2
   3 =head1 NAME
   4
   5 CXGN::Cview::Map_overviews::ProjectStats - a class to display the tomato genome sequence project status.
   6
   7 =head1 SYNOPSYS
   8
   9 see L<CXGN::Cview::Map_overviews>.
  10
  11 =head1 DESCRIPTION
  12
  13 This class implements the project status overview graph found on the SGN homepage and the /about/tomato_sequencing.pl page, where each chromosome is represented by a glyph that is filled to the fraction of the estimated number of BACs needed to complete the chromosome sequence.
  14
  15 =head1 AUTHOR(S)
  16
  17 Lukas Mueller (lam87@cornell.edu)
  18
  19 =head1 FUNCTIONS
  20
  21 This class implements the following functions:
  22
  23 =cut
  24
  25 use strict;
  26
  27 package CXGN::Cview::MapOverviews::ProjectStats;
  28
  29 use base "CXGN::Cview::MapOverviews";
  30
  31 use CXGN::Cview::Map::SGN::ProjectStats;
  32 use CXGN::People::BACStatusLog;
  33 use List::Util;
  34
  35 =head2 constructor new()
  36
  37   Synopsis:
  38   Arguments:
  39   Returns:
  40   Side effects:
  41   Description:
  42
  43 =cut
  44
  45 sub new {
  46     my $class = shift;
  47     my $args = shift;
  48
  49     my $map = CXGN::Cview::Map::SGN::ProjectStats->new($args->{dbh});
  50
  51     my $self = $class->SUPER::new($map, $args);
  52     $self->{dbh}= $args->{dbh};
  53     $self->set_horizontal_spacing(50);
  54     $self->set_image_width(586);
  55     $self->set_image_height(160);
  56     $self->set_chr_height(80);
  57     $self->{basepath}=$args->{basepath};
  58     $self->{tempfiles_subdir} = $args->{tempfiles_subdir};
  59 #    print STDERR "Generating new map object...\n";
  60     $self->set_map($map);
  61     return $self;
  62 }
  63
  64 =head2 function generate_image()
  65
  66   Synopsis:
  67   Arguments:
  68   Returns:
  69   Side effects:
  70   Description:
  71
  72 =cut
  73
  74 sub generate_image {
  75     my $self = shift;
  76     $self->render_map();
  77 }
  78
  79 =head2 function send_image()
  80
  81   Synopsis:
  82   Arguments:
  83   Returns:
  84   Side effects:
  85   Description:
  86
  87 =cut
  88
  89 sub send_image {
  90     my $self = shift;
  91     print "Content-Type: image/png\n\n";
  92     return $self->{map_image}->render_png();
  93 }
  94
  95 =head2 function render_map()
  96
  97   Synopsis:
  98   Arguments:
  99   Returns:
 100   Side effects:
 101   Description:
 102
 103 =cut
 104
 105 sub render_map {
 106     my $self = shift;
 107
 108     $self->get_cache()->set_key("project stats overview graph");
 109     $self->get_cache()->set_force(1);
 110     $self->get_cache()->set_expiration_time(40000);  # set expiration time of cache to half a day.
 111     $self->get_cache()->set_map_name("overview_map");
 112
 113     if ($self->get_cache()->is_valid()) {  return; }
 114
 115     my $bac_status_log=CXGN::People::BACStatusLog->new($self->{dbh});
 116
 117 #    print STDERR "WIDTH=".$self->get_image_width()." HEIGHT ".$self->get_image_height()."\n";
 118     $self->{map_image}=CXGN::Cview::MapImage->new("", $self->get_image_width(), $self->get_image_height());
 119     my @c = ();
 120     my @c_len = $bac_status_log->get_chromosome_graph_lengths();
 121     my @bacs_to_complete = $bac_status_log->get_number_bacs_to_complete();
 122     my @c_percent_finished = $bac_status_log->get_chromosomes_percent_finished();
 123
 124     my @bacs_in_progress = $bac_status_log->get_number_bacs_in_progress();
 125     my @bacs_submitted = $bac_status_log->get_number_bacs_uploaded();
 126
 127     my @bacs_phase = $bac_status_log->get_number_bacs_in_phase(3);
 128
 129
 130     for my $i (1..12) {
 131         $c[$i]= CXGN::Cview::Chromosome::Glyph -> new(1, 100, $self->get_horizontal_spacing()*($i-1)+17, 25);
 132         my $m = CXGN::Cview::Marker->new($c[$i],0,0,0,0,0,0,$c_len[$i]);
 133         $m -> hide();
 134         $c[$i]->add_marker($m);
 135         $c[$i]->set_caption($i);
 136         $c[$i]->set_height($self->get_chr_height());
 137         $c[$i]->set_url("/cview/view_chromosome.pl?map_version_id=agp&show_offsets=1&show_ruler=1&chr_nr=$i");
 138
 139         my $percent_in_progress = $bacs_in_progress[$i]/$bacs_to_complete[$i]*100;
 140
 141         my $percent_finished = $c_percent_finished[$i];
 142
 143         my $percent_htgs3 = $bacs_phase[$i]/$bacs_to_complete[$i]*100;
 144
 145         my $percent_available = $bacs_submitted[$i]/$bacs_to_complete[$i]*100;
 146
 147         #$percent_submitted = $percent_submitted - $percent_htgs3;
 148
 149         my $percent_in_progress_base_level = List::Util::max($percent_finished, $percent_htgs3, $percent_available);
 150
 151         $percent_in_progress += $percent_in_progress_base_level;
 152
 153         #print STDERR "Chromosome $i $percent_htgs3, $percent_available, $percent_finished, $percent_in_progress\n";
 154
 155
 156         $c[$i]->set_fill_level(0, $percent_htgs3);
 157         $c[$i]->set_fill_level(1, $percent_available);
 158         $c[$i]->set_fill_level(2, $percent_finished);
 159         $c[$i]->set_fill_level(3, $percent_in_progress);
 160         $c[$i]->set_bac_count(0);
 161         $self->{map_image}->add_chromosome($c[$i]);
 162     }
 163     my $white = $self->{map_image}->get_image()->colorResolve(255,255,255);
 164     $self->{map_image}->get_image()->transparent($white);
 165
 166
 167
 168     $self->get_cache()->set_image_data( $self->{map_image}->render_png_string());
 169     $self->get_cache()->set_image_map_data ($self->{map_image}->get_image_map("overview_map") );
 170
 171 }
 172
 173 =head2 function create_mini_overview()
 174
 175   Synopsis:
 176   Arguments:    none
 177   Returns:      nothing
 178   Side effects: creates the mini overview png image that goes on the
 179                 homepage
 180   Description:
 181
 182 =cut
 183
 184 sub create_mini_overview {
 185     my $self = shift;
 186     $self->set_image_width(400);
 187     $self->set_image_height(100);
 188     $self->set_chr_height(50);
 189     $self->set_horizontal_spacing(30);
 190
 191     my $url = "/documents/tempfiles/frontpage/project_stats_overview.png";
 192     my $path = File::Spec->catfile($self->{basepath}, $url);
 193
 194     $self->render_map();
 195     $self->get_file_png($path);
 196
 197 }
 198
 199 1;