cgi-bin/search/locus_search.pl

   1 ######################################################################
   2 #
   3 #  Search the phenome database and displays the results.
   4 #
   5 ######################################################################
   6
   7
   8
   9 use strict;
  10
  11 use CXGN::Phenome;
  12 use CXGN::Page;
  13 use CXGN::Page::FormattingHelpers qw/blue_section_html
  14                                      info_section_html
  15                                      page_title_html
  16                                      columnar_table_html
  17                                      /;
  18 use CXGN::Search::CannedForms;
  19 #################################################
  20
  21 # Start a new SGN page.
  22
  23 my $page=CXGN::Page->new("SGN gene search results","Naama");
  24 $page->header();
  25
  26 print page_title_html('Gene search results');
  27
  28
  29 #create the search and query objects
  30 my $search = CXGN::Phenome->new;
  31 my $query = $search->new_query;
  32
  33 $search->page_size(10); #set 10 loci per page
  34
  35
  36
  37 #get the parameters
  38 my %params = $page->get_all_encoded_arguments;
  39 my $any_name = $page->get_encoded_arguments("any_name");
  40
  41
  42 $query->from_request(\%params);
  43
  44
  45
  46 if(%params) {
  47     $query->order_by( locus_symbol=> 'UPPER(&t)');
  48     my $result = $search->do_search($query);  #execute the search
  49
  50     my @results;
  51
  52
  53     while(my $r = $result->next_result) {
  54         #    push @results,$r;
  55         my ($allele_name, $allele_symbol, $phenotype) = ($r->[3], $r->[4], $r->[6]);
  56         my $allele_obsolete = $r->[8];
  57
  58         my $phenotype= substr($r->[6],0,20);
  59         if (defined$r->[6]) {
  60             $phenotype .= '....';
  61         }else {
  62             $phenotype = '--';
  63         }
  64         #if (!$allele_obsolete) { #don't display obsolete alleles! #alleles shouldn't be obsolete now..
  65
  66             push @results, [map {$_} ($r->[14],
  67                                       '<a href="/phenome/locus_display.pl?locus_id='.$r->[0].'">'.$r->[1].'</a>',
  68                                       $r->[2],
  69                                       $allele_name,
  70                                       $allele_symbol,
  71                                       $phenotype,
  72                                       )
  73                             ];
  74         #}
  75     }
  76
  77
  78
  79 #build the HTML to output
  80   my $pagination_html = $search->pagination_buttons_html( $query, $result );
  81
  82
  83    my $results_html = <<EOH;
  84 <div id="searchresults">
  85 EOH
  86
  87 $results_html .= columnar_table_html(headings => ['Organism',
  88                                                   'Locus name',
  89                                                   'Locus symbol',
  90                                                   'Allele name',
  91                                                   'Allele symbol',
  92                                                   'Allele phenotype'],
  93                                      data => \@results,
  94                                      # __alt_freq => 2,
  95                                      # __alt_width => 2,
  96                                      );
  97
  98
  99 $results_html .= <<EOH;
 100 </div>
 101 $pagination_html
 102 EOH
 103
 104
 105 if (@results) {
 106
 107     print blue_section_html('Gene search results', ,sprintf('<span class="paginate_summary">%s matches </span>', $result->total_results,$result->time),$results_html);
 108 }else {
 109     print '<h4><span class="">No matches found</span></h4>';
 110 }
 111
 112   print info_section_html(title    => 'Search again',
 113                           contents =>CXGN::Search::CannedForms::gene_search_form($page,$query)
 114                           );
 115 }
 116
 117
 118
 119 $page->footer();
 120
 121 #############
 122