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 $sp_person_id = $c->user() ? $c->user->get_object()->get_sp_person_id() : undef;
  45 my $schema     = $c->dbic_schema( 'CXGN::GEM::Schema', 'sgn_chado', $sp_person_id );
  46 my $sgn_schema = $c->dbic_schema( 'SGN::Schema', undef, $sp_person_id );
  47
  48 my $dbh = CXGN::DB::Connection->new();
  49
  50 ## To do more flexible how the unigene can be called
  51
  52 if (defined $args{'unigene_id'}) {
  53     $args{'id'} = $args{'unigene_id'} ;
  54     $args{'id'} =~ s/^SGN-U//;
  55
  56     # convert CGN-U to SGN-U
  57     if( $args{unigene_id} =~ s/^CGN-?U//i ) {
  58         my ($sgnid) = $dbh->selectrow_array(<<EOS,undef, $args{unigene_id}, 'CGN');
  59 SELECT unigene_id FROM unigene WHERE sequence_name = ? AND database_name=?
  60 EOS
  61         if( $sgnid ) {
  62             $args{'id'} = $sgnid;
  63         }
  64     }
  65 }
  66
  67
  68
  69 ## Random function will get at random unigene from the latest unigene build
  70
  71 if (defined $args{'random'}) {
  72     if ($args{'random'} =~ m/^yes$/i) {
  73         my $last_unigene_build_id = $sgn_schema->resultset('UnigeneBuild')
  74                                                ->search(
  75                                                          undef,
  76                                                          {
  77                                                             order_by => 'unigene_build_id DESC',
  78                                                             limit => 1
  79                                                          }
  80                                                        )
  81                                                ->first()
  82                                                ->get_column('unigene_build_id');
  83
  84         ## Now get all the unigene_id for this unigene_build_id
  85
  86         my $random_unigene_id = $sgn_schema->resultset('Unigene')
  87                                            ->search(
  88                                                       {
  89                                                         unigene_build_id => $last_unigene_build_id
  90                                                       },
  91                                                       {
  92                                                         order_by => 'random()',
  93                                                         limit    => 1
  94                                                       }
  95                                                    )
  96                                            ->first()
  97                                            ->get_column('unigene_id');
  98
  99         ## It will replace $args{'id'}
 100
 101         $args{'id'} = $random_unigene_id;
 102     }
 103 }
 104
 105 ## Now it will take the unigene object based in the unigene_id (it will create an empty object by default)
 106
 107 my $unigene = CXGN::Transcript::Unigene->new($dbh);
 108
 109 if (defined $args{'id'} && $args{'id'} =~ m/^\d+$/) {
 110
 111     $unigene = CXGN::Transcript::Unigene->new($dbh, $args{'id'});
 112 }
 113
 114
 115 ## Now depending if there are enought condition, it will call a mason unigen page ($unigene object has an id)
 116 ## or an error page
 117
 118 if (defined $unigene && defined $unigene->get_unigene_id() ) {
 119
 120     $c->forward_to_mason_view(
 121         '/transcript/unigene_detail.mas',
 122              dbh         => $dbh,
 123              schema      => $schema,
 124              sgn_schema  => $sgn_schema,
 125              unigene     => $unigene,
 126              highlight   => $args{'highlight'},
 127              force_image => $args{'force_image'},
 128              basepath    => $c->config->{basepath},
 129              temp_dir    => $c->tempfiles_subdir('unigene_images'),
 130             );
 131 } else {
 132     $c->forward_to_mason_view(
 133         '/transcript/transcript_page_error.mas',
 134         object      => $unigene );
 135 }