cgi-bin/content/sgn_data.pl

   1 use strict;
   2
   3 use CXGN::Page;
   4
   5 use CXGN::Chado::Organism;
   6 use CXGN::DB::DBICFactory;
   7
   8
   9 # Script to display the major data content of sgn
  10 # Naama Menda, April 2010
  11 #
  12
  13
  14 my $page = CXGN::Page->new("SGN data overview page", "Naama");
  15 #my ($force) = $page->get_encoded_arguments("force");
  16
  17
  18 my $schema = CXGN::DB::DBICFactory
  19     ->open_schema( 'Bio::Chado::Schema',
  20                                   search_path => ['public'],
  21     );
  22
  23
  24
  25 my $type = 'web visible'; # we want only the leaf organisms with 'web visible' organismprop
  26 my $cvterm = $schema->resultset("Cv::Cvterm")->search( { name => $type } )->first();
  27
  28
  29 my $sol=();
  30 my $rub=();
  31 my $planta=();
  32
  33
  34 if ($cvterm) {
  35     my $cvterm_id = $cvterm->get_column('cvterm_id');
  36
  37     my @organisms= $schema->resultset("Organism::Organismprop")->search(
  38         { type_id => $cvterm_id } )->search_related('organism');
  39
  40     foreach my $organism(@organisms) {
  41
  42         my $species = $organism->get_column('species');
  43         my $genus= $organism->get_column('genus');
  44         my $organism_id = $organism->get_column('organism_id');
  45         my $o=CXGN::Chado::Organism->new($schema, $organism_id);
  46         my $root_tax=$o->get_organism_by_tax('family');
  47         if ($root_tax) {
  48             my $family = $root_tax->species();
  49             $sol->{$species}= $organism_id if $family eq 'Solanaceae' ;
  50             $rub->{$species}= $organism_id if $family eq  'Rubiaceae' ;
  51             $planta->{$species}= $organism_id if $family eq  'Plantaginaceae' ;
  52         }
  53     }
  54 }
  55 ##########
  56
  57 $c->forward_to_mason_view("/content/sgn_data.mas" , schema=>$schema, sol=>$sol, rub=>$rub, planta=>$planta );
  58
  59