mason/transcript/unigene_build/basic_unigene_build_info.mas

   1 <%doc>
   2
   3 =head1 NAME
   4
   5  basic_unigene_build_info.mas
   6  Mason code to show basic data for  unigene_build web_page.
   7
   8 =cut
   9
  10 =head1 VERSION
  11
  12 0.1
  13
  14 =cut
  15
  16 =head1 SYNOPSIS
  17
  18 <& '/transcript/unigene_build/basic_unigene_build_info.mas', schema => $schema, unigene_build => $unigene_build &>
  19
  20 where: $bcs, a DBIx::Class::Schema object with the classes of Bio::Chado::Schema
  21        $schema, a DBIx::Class::Schema object with the classes of SGN::Schema
  22        $unigene_build, an CXGN::Transcript::UnigeneBuild object
  23
  24 =cut
  25
  26 =head1 DESCRIPTION
  27
  28  This mason script coordinate different mason component to create the unigene build page.
  29
  30  Its controller is: unigene_build.pl
  31
  32 =cut
  33
  34 =head 1 AUTHOR
  35
  36  Aureliano Bombarely (ab782@cornell.edu)
  37
  38 =cut
  39
  40 </%doc>
  41
  42
  43 <%args>
  44 $bcs
  45 $schema
  46 $unigene_build
  47 </%args>
  48
  49
  50 <%perl>
  51
  52 use strict;
  53 use warnings;
  54
  55 use CXGN::Transcript::UnigeneBuild;
  56 use CXGN::Chado::Dbxref;
  57 use CXGN::Page::FormattingHelpers  qw/ info_section_html info_table_html columnar_table_html page_title_html html_break_string /;
  58
  59 my $basic_info_content;
  60 my $unigene_build_name;
  61
  62 ## If there aren't any unigene_build that comes from unigene_build_detail.mas, it will return a error message.
  63
  64 if (defined $ARGS{'unigene_build'}->get_unigene_build_id) {
  65
  66    ## Get the object
  67    my $id =  $unigene_build->get_unigene_build_id();
  68
  69    my $build_name = $unigene_build->get_organism_group_name();
  70    my $build_nr = $unigene_build->get_build_nr();
  71    $unigene_build_name = $build_name." ".$build_nr;
  72    my $build_date = $unigene_build->get_build_date();
  73    my $status = $unigene_build->get_status();
  74    my $status_html;
  75    if ($status eq 'C') {
  76        $status_html = '<font color="green"><b>CURRENT</b></font>';
  77    } elsif ($status eq 'P') {
  78        $status_html = '<font color="orange"><i>Previous to current</i></font>';
  79    } elsif ($status eq 'D') {
  80        $status_html = '<font color="red"><i>Deprecated</i></font>';
  81    }
  82
  83    my @organism_html_list;
  84    my $organism_group_id = $unigene_build->get_organism_group_id();
  85    my $group_linkage_rs = $schema->resultset('GroupLinkage')
  86                                  ->search({ group_id => $organism_group_id });
  87
  88    my @organism_ids = $group_linkage_rs->get_column('member_id')->all();
  89
  90    foreach my $organism_id (@organism_ids) {
  91
  92        if ($organism_id =~ m/^\d+$/) {
  93            my @organism_rows = $bcs->resultset('Organism::Organism')
  94                                    ->search({ sgn_organism_id => $organism_id });
  95
  96            foreach my $organism_row (@organism_rows) {
  97
  98                my $org_id = $organism_row->get_column('organism_id');
  99                my $organism_name = $organism_row->get_column('species');
 100                my $organism_link = '/chado/organism.pl?organism_id='.$organism_id;
 101                my $organism_html = "<a href=$organism_link>$organism_name</a>";
 102                if (defined $org_id) {
 103                    push @organism_html_list, $organism_html;
 104                }
 105            }
 106        }
 107    }
 108    my $organism_html_list = join('<br>', @organism_html_list);
 109
 110    ## Get the number of unigene, contig and singlets using DBIx::Class (this should be replaced by the right object)
 111
 112    my $unigene_nr = $schema->resultset('Unigene')
 113                            ->search({ unigene_build_id => $id})
 114                            ->count();
 115
 116    my $contig_nr = $schema->resultset('Unigene')
 117                           ->search({ unigene_build_id => $id, nr_members => {'>', 1} })
 118                           ->count();
 119
 120    my $singlet_nr = $schema->resultset('Unigene')
 121                            ->search({ unigene_build_id => $id, nr_members => {'=', 1} })
 122                            ->count();
 123
 124    my $member_nr = $schema->resultset('Unigene')
 125                           ->search({ unigene_build_id => $id }, {join => 'unigene_members'})
 126                           ->count();
 127
 128    ## Create the HTML table
 129
 130    $basic_info_content = <<HTML;
 131
 132     <table width="75%">
 133            <tr> <td> <b>Unigene Build ID: </b>           </td> <td> $id </td></tr>
 134            <tr> <td> <b>Unigene Build Name: </b>         </td> <td> $unigene_build_name </td></tr>
 135            <tr> <td> <b>Date: </b>                       </td> <td> $build_date </td></tr>
 136            <tr> <td> <b>Status: </b>                     </td> <td> $status_html </td></tr>
 137            <tr> <td> <b>Organism: </b>                   </td> <td> $organism_html_list </td></tr>
 138            <tr> <td> <b>Number of Unigenes: </b>         </td> <td> $unigene_nr </td></tr>
 139            <tr> <td> <b>Number of Contigs: </b>          </td> <td> $contig_nr </td></tr>
 140            <tr> <td> <b>Number of Singlets: </b>         </td> <td> $singlet_nr </td></tr>
 141            <tr> <td> <b>Members Assembled:</b> </td> <td> $member_nr </td></tr>
 142    </table>
 143
 144    <br>
 145
 146 HTML
 147
 148 }
 149 else {
 150    $basic_info_content = "<big>There aren't any unigene build data for the specified parameters.</big>";
 151 }
 152
 153 my $basic_info_html;
 154 if (defined $unigene_build_name) {
 155    $basic_info_html = "<center><big><b>Unigene Build: $unigene_build_name</b></big></center><br>";
 156 }
 157 $basic_info_html .= info_section_html( title => "Unigene Build Basic Information", contents => $basic_info_content );
 158
 159 </%perl>
 160
 161 <% $basic_info_html %>
 162