cgi-bin/search/unigene.pl

   1 #!/usr/bin/perl
   2
   3 =head1 NAME
   4
   5   unigene_mason.pl
   6   Controller to show the web_page for unigene using MASON.
   7
   8 =cut
   9
  10 =head1 SYNOPSIS
  11
  12
  13 =head1 DESCRIPTION
  14
  15   This is the script to show the web_page using MASON
  16
  17 =cut
  18
  19 =head1 AUTHORS
  20
  21  Aureliano Bombarely Gomez
  22  (ab782@cornell.edu)
  23
  24 =cut
  25
  26
  27 use strict;
  28 use warnings;
  29
  30 use CGI ();
  31
  32 use CXGN::DB::Connection;
  33
  34 use CXGN::Transcript::Unigene;
  35
  36 use CatalystX::GlobalContext '$c';
  37
  38 ## Use of CXGN::Page to take the arguments from the URL
  39
  40 my $q = CGI->new;
  41
  42 my %args = $q->Vars;
  43
  44 my $schema     = $c->dbic_schema( 'CXGN::GEM::Schema', 'sgn_chado' );
  45 my $sgn_schema = $c->dbic_schema( 'SGN::Schema' );
  46
  47 my $dbh = CXGN::DB::Connection->new();
  48
  49 ## To do more flexible how the unigene can be called
  50
  51 if (defined $args{'unigene_id'}) {
  52     $args{'id'} = $args{'unigene_id'} ;
  53     $args{'id'} =~ s/^SGN-U//;
  54
  55     # convert CGN-U to SGN-U
  56     if( $args{unigene_id} =~ s/^CGN-?U//i ) {
  57         my ($sgnid) = $dbh->selectrow_array(<<EOS,undef, $args{unigene_id}, 'CGN');
  58 SELECT unigene_id FROM unigene WHERE sequence_name = ? AND database_name=?
  59 EOS
  60         if( $sgnid ) {
  61             $args{'id'} = $sgnid;
  62         }
  63     }
  64 }
  65
  66
  67
  68 ## Random function will get at random unigene from the latest unigene build
  69
  70 if (defined $args{'random'}) {
  71     if ($args{'random'} =~ m/^yes$/i) {
  72         my $last_unigene_build_id = $sgn_schema->resultset('UnigeneBuild')
  73                                                ->search(
  74                                                          undef,
  75                                                          {
  76                                                             order_by => 'unigene_build_id DESC',
  77                                                             limit => 1
  78                                                          }
  79                                                        )
  80                                                ->first()
  81                                                ->get_column('unigene_build_id');
  82
  83         ## Now get all the unigene_id for this unigene_build_id
  84
  85         my $random_unigene_id = $sgn_schema->resultset('Unigene')
  86                                            ->search(
  87                                                       {
  88                                                         unigene_build_id => $last_unigene_build_id
  89                                                       },
  90                                                       {
  91                                                         order_by => 'random()',
  92                                                         limit    => 1
  93                                                       }
  94                                                    )
  95                                            ->first()
  96                                            ->get_column('unigene_id');
  97
  98         ## It will replace $args{'id'}
  99
 100         $args{'id'} = $random_unigene_id;
 101     }
 102 }
 103
 104 ## Now it will take the unigene object based in the unigene_id (it will create an empty object by default)
 105
 106 my $unigene = CXGN::Transcript::Unigene->new($dbh);
 107
 108 if (defined $args{'id'} && $args{'id'} =~ m/^\d+$/) {
 109
 110     $unigene = CXGN::Transcript::Unigene->new($dbh, $args{'id'});
 111 }
 112
 113
 114 ## Now depending if there are enought condition, it will call a mason unigen page ($unigene object has an id)
 115 ## or an error page
 116
 117 if (defined $unigene && defined $unigene->get_unigene_id() ) {
 118
 119     $c->forward_to_mason_view(
 120         '/transcript/unigene_detail.mas',
 121              dbh         => $dbh,
 122              schema      => $schema,
 123              sgn_schema  => $sgn_schema,
 124              unigene     => $unigene,
 125              highlight   => $args{'highlight'},
 126              force_image => $args{'force_image'},
 127              basepath    => $c->config->{basepath},
 128              temp_dir    => $c->tempfiles_subdir('unigene_images'),
 129             );
 130 } else {
 131     $c->forward_to_mason_view(
 132         '/transcript/transcript_page_error.mas',
 133         object      => $unigene );
 134 }