lib/SGN/View/Stock.pm

   1 package SGN::View::Stock;
   2 use base 'Exporter';
   3 use strict;
   4 use warnings;
   5
   6 our @EXPORT_OK = qw/
   7     stock_link organism_link cvterm_link
   8     stock_table related_stats
   9     stock_organisms stock_types breeding_programs
  10 /;
  11 our @EXPORT = ();
  12
  13
  14 sub stock_link {
  15     my ($stock) = @_;
  16     my $name = $stock->uniquename;
  17     my $id = $stock->stock_id;
  18     return qq{<a href="/stock/$id/view">$name</a>};
  19 }
  20
  21 sub organism_link {
  22     my ($organism) = @_;
  23     my $id      = $organism->organism_id;
  24     my $species = $organism->species;
  25     return <<LINK;
  26 <span class="species_binomial">
  27 <a href="/chado/organism.pl?organism_id=$id">$species</a>
  28 LINK
  29 }
  30
  31 sub cvterm_link {
  32     my ($cvterm) = @_;
  33     my $name = $cvterm->name;
  34     my $id   = $cvterm->cvterm_id;
  35     return qq{<a href="/cvterm/$id/view">$name</a>};
  36 }
  37
  38 sub stock_table {
  39     my ($stocks) = @_;
  40     my $data = [];
  41     for my $s (@$stocks) {
  42         # Add a row for every stock
  43         push @$data, [
  44             cvterm_link($s->type),
  45             stock_link($s),
  46
  47         ];
  48     }
  49     return $data;
  50 }
  51
  52
  53 sub related_stats {
  54     my ($stocks) = @_;
  55     my $stats = { };
  56     my $total = scalar @$stocks;
  57     for my $s (@$stocks) {
  58             $stats->{cvterm_link($s->type)}++;
  59     }
  60     my $data = [ ];
  61     for my $k (sort keys %$stats) {
  62         push @$data, [ $stats->{$k}, $k ];
  63     }
  64     if( 1 < scalar keys %$stats ) {
  65         push @$data, [ $total, "<b>Total</b>" ];
  66     }
  67     return $data;
  68 }
  69
  70 sub breeding_programs {
  71     my ($schema) = @_;
  72     return [
  73         [ 0, '' ],
  74         map [ $_->project_id, $_->name ],
  75         $schema
  76              ->resultset('Project::Project')->search(
  77             { 'type.name' => 'breeding_program',
  78             },
  79             {
  80                 join      => { 'projectprops' => 'type' },
  81                 select   => [qw[ me.project_id me.name ]],
  82                 distinct => 1,
  83                 order_by => 'me.name',
  84             })
  85         ];
  86 }
  87
  88
  89 sub stock_organisms {
  90     my ($schema) = @_;
  91     return [
  92         [ 0, '' ],
  93         map [ $_->organism_id, $_->species ],
  94         $schema
  95              ->resultset('Stock::Stock')
  96              ->search_related('organism' , {}, {
  97                  select   => [qw[ organism.organism_id species ]],
  98                  distinct => 1,
  99                  order_by => 'species',
 100                })
 101     ];
 102 }
 103
 104 sub stock_types {
 105     my ($schema) = @_;
 106
 107     my $ref = [
 108         map [$_->cvterm_id,$_->name],
 109         $schema
 110     ->resultset('Stock::Stock')
 111     ->search_related(
 112         'type',
 113         {},
 114         { select => [qw[ cvterm_id type.name ]],
 115           group_by => [qw[ cvterm_id type.name ]],
 116           order_by => 'type.name',
 117         },
 118     )
 119     ];
 120     # add an empty option
 121     unshift @$ref , ['0', ''];
 122     return $ref;
 123 }
 124
 125 sub stock_dbxrefprops {
 126     my $stock_dbxref = shift;
 127     my $props = $stock_dbxref->stock_dbxrefprops;
 128     while (my $p = $props->next ) {
 129         my $value = $p->value ;
 130         my $type = $p->type->name;
 131         my $accession = $p->type->dbxref->accession;
 132         my $db_name = $p->type->dbxref->db->name;
 133
 134     }
 135 }
 136
 137 ######
 138 1;
 139 ######