mason/gem/platform/basic_platform_info.mas

   1 <%doc>
   2
   3 =head1 NAME
   4
   5  basic_platform_info.mas
   6  Mason component to show the basic information for platform web page.
   7
   8 =cut
   9
  10 =head1 VERSION
  11
  12 0.1
  13
  14 =cut
  15
  16 =head1 DESCRIPTION
  17
  18  Mason component to show the basic information for platform web page.
  19
  20  - Mason root page = platform_detail.mas
  21  - Perl controller = platform.pl
  22
  23  This component use out schema dbi connection to get data about CXGN::People::Person
  24
  25 =cut
  26
  27 =head 1 AUTHOR
  28
  29  Aureliano Bombarely (ab782@cornell.edu)
  30
  31 =cut
  32
  33 </%doc>
  34
  35
  36 <%args>
  37 $dbh
  38 $platform
  39 </%args>
  40
  41 <%init>
  42 use strict;
  43 use warnings;
  44
  45 use CXGN::GEM::Schema;
  46 use CXGN::Biosource::Sample;
  47 use CXGN::Page::FormattingHelpers  qw/ info_section_html info_table_html columnar_table_html page_title_html html_break_string /;
  48 </%init>
  49
  50 <%perl>
  51
  52 my $basic_info_content;
  53 my $platform_accession;
  54
  55 my $default_message = '<i><font color="gray">data not available</font></i>';
  56
  57 ## If there aren't any experiment_row that comes from experimental_design_detail.mas, it will return a message.
  58
  59 if (defined $platform->get_platform_id()) {
  60
  61    ## Get the schema object
  62    my $schema = $platform->get_schema();
  63
  64    my $platform_name = $platform->get_platform_name();
  65    my $description = $platform->get_description();
  66    $platform_accession = $platform_name;
  67
  68    my $template_count = $platform->count_templates();
  69    my $probe_count = $platform->count_probes();
  70
  71    my $techtype = $platform->get_technology_type();
  72    my $techtype_name = $techtype->get_technology_name();
  73
  74    ## Get the platform design links
  75
  76    my @design_links;
  77    my @sample_id_list = $platform->get_design_list();
  78    foreach my $sample_id (@sample_id_list) {
  79        my $sample = CXGN::Biosource::Sample->new($schema, $sample_id);
  80        my $sample_name = $sample->get_sample_name();
  81        my $sample_link = '/biosource/sample.pl?id=' . $sample_id;
  82        my $sample_html = "<a href=$sample_link>$sample_name</a>";
  83
  84        push @design_links, $sample_html;
  85    }
  86    my $design_links = join('<br>', @design_links) || $default_message;
  87
  88    ## Get the external links
  89
  90    my @dbxref_list_id = $platform->get_dbxref_list();
  91    my @dbxref_html_list = ();
  92
  93    foreach my $dbxref_id (@dbxref_list_id) {
  94        my ($dbxref_row) = $schema->resultset('General::Dbxref')
  95                                  ->search({ dbxref_id => $dbxref_id });
  96
  97        if (defined $dbxref_row) {
  98            my ($db_row) = $schema->resultset('General::Db')
  99                                  ->search({ db_id => $dbxref_row->get_column('db_id') });
 100
 101            my $dbxref_link = $db_row->get_column('urlprefix') .
 102                              $db_row->get_column('url') .
 103                              $dbxref_row->get_column('accession');
 104
 105            my $dbxref_html = $db_row->get_column('name') .
 106                              ": <a href=$dbxref_link>" .
 107                              $dbxref_row->get_column('accession')."</a>";
 108
 109            push @dbxref_html_list, $dbxref_html;
 110        }
 111    }
 112
 113    my $dbxref_html_list = join('<br>', @dbxref_html_list) || $default_message;
 114
 115    ## Get information of the contact
 116
 117    my $person_id = $platform->get_contact_id();
 118    my ($complete_name, $contact_email);
 119    if (defined $person_id) {
 120
 121        my $person = CXGN::People::Person->new($dbh, $person_id);
 122
 123        my $salutation = $person->get_salutation() || 'Dr.';
 124        my $first_name = $person->get_first_name();
 125        my $last_name = $person->get_last_name();
 126        $contact_email = $person->get_contact_email || $default_message;
 127        if (defined $salutation && defined $first_name && defined $last_name) {
 128            $complete_name = "$salutation $first_name $last_name";
 129        } else {
 130            $complete_name = $default_message;
 131        }
 132
 133    } else {
 134       $complete_name = $default_message;
 135       $contact_email = $default_message;
 136    }
 137
 138
 139
 140    ## Create the HTML table
 141
 142    $basic_info_content = <<HTML;
 143
 144    <table width="100%">
 145            <tr> <td width="25%"> <b>Platform name:</b>            </td> <td> $platform_name </td></tr>
 146            <tr> <td width="25%"> <b>Technology type:</b>          </td> <td> $techtype_name </td></tr>
 147            <tr> <td width="25%"> <b>Description:</b>              </td> <td> $description </td></tr>
 148            <tr> <td width="25%"> <b>Template number:</b>          </td> <td> $template_count </td></tr>
 149            <tr> <td width="25%"> <b>Probe number:</b>             </td> <td> $probe_count </td></tr>
 150            <tr> <td width="25%"> <b>Design datasets:</b>          </td> <td> $design_links </td></tr>
 151            <tr> <td width="25%"> <b>Platform external links:</b>  </td> <td> $dbxref_html_list </td></tr>
 152            <tr> <td width="25%"> <b>Contact info:</b>             </td> <td> <b>Name:</b> $complete_name </td></tr>
 153            <tr> <td width="">                                     </td> <td> <b>E-mail:</b> $contact_email </td></tr>
 154
 155    </table>
 156
 157 HTML
 158
 159 } else {
 160    $basic_info_content = "<big>There aren't any platform data for the specified parameters.</big>";
 161 }
 162
 163 my $basic_info_html;
 164 if (defined $platform_accession) {
 165    $basic_info_html = "<center><big><b>Expression Platform: $platform_accession</b></big></center><br>";
 166 }
 167
 168 $basic_info_html .= info_section_html( title => "Platform Basic Information", contents => $basic_info_content );
 169
 170 </%perl>
 171
 172 <% $basic_info_html %>
 173
 174 <&
 175    /util/import_javascript.mas,
 176    classes => 'CXGN.Effects'
 177 &>