cgi-bin/phenome/trait.pl

   1 ######################################################################
   2 #
   3 #  Displays a static user submitted trait detail page.
   4 #
   5 ######################################################################
   6
   7 my $trait_detail_page=CXGN::Phenome::TraitDetailPage->new();
   8
   9 package CXGN::Phenome::TraitDetailPage;
  10
  11 use base qw/CXGN::Page::Form::SimpleFormPage/;
  12
  13 use strict;
  14
  15 use CXGN::Page;
  16 use CXGN::Page::FormattingHelpers qw/info_section_html
  17                                      page_title_html
  18                                      columnar_table_html
  19                                      info_table_html
  20                                      html_optional_show
  21                                     /;
  22
  23 use CXGN::Phenome::UserTrait;
  24 use CXGN::People::PageComment;
  25
  26
  27 sub new {
  28     my $class=shift;
  29     my $schema='phenome';
  30     my $self= $class->SUPER::new(@_);
  31     return $self;
  32 }
  33
  34 sub define_object {
  35     my $self=shift;
  36     $self->set_dbh(CXGN::DB::Connection->new('phenome'));
  37     my %args= $self->get_args();
  38
  39     my $user_trait_id="";
  40     if (exists($args{trait}) && defined($args{trait}))  {
  41         my $ut = CXGN::Phenome::UserTrait::->new_with_name($self->get_dbh(), $args{trait});
  42         $user_trait_id = $ut->get_user_trait_id();
  43     }
  44     else {
  45         $user_trait_id= $args{trait_id};
  46     }
  47     unless (!$user_trait_id || $user_trait_id =~m /^\d+$/) { $self->get_page->message_page("No term exists for identifier $user_trait_id"); }
  48     $self->set_object_id($user_trait_id);
  49     $self->set_object(CXGN::Phenome::UserTrait->new($self->get_dbh, $self->get_object_id));
  50
  51     $self->set_primary_key("user_trait_id");
  52
  53 }
  54
  55
  56
  57 sub display_page {
  58     my $self=shift;
  59     my %args = $self->get_args();
  60
  61
  62     my $ut=$self->get_object();
  63     my $ut_id=$self->get_object_id();
  64     my $ut_name=$ut->get_name();
  65
  66     my $definition = $ut->get_definition() ;
  67     my $page="/phenome/trait.pl?trait_id=$ut_id";
  68     my $action= $args{action} || "";
  69     if (!$ut_id) {  $self->get_page->message_page("No term exists for this identifier")  } ;
  70
  71     $self->get_page->header("SGN: $ut_name " );
  72     print page_title_html("$ut_name\n");
  73
  74     my $trait_html= "<br />" .$self->get_form()->as_table_string()."<br />";
  75
  76
  77
  78     print info_section_html(title    => 'Trait details',
  79                             contents => $trait_html,
  80                             );
  81
  82     my @pops = $ut->get_all_populations_trait();
  83     my $pop_list;
  84
  85     foreach my $pop (@pops) {
  86         my $pop_id = $pop->get_population_id();
  87         my $pop_name = $pop->get_name();
  88
  89         $pop_list .= qq |<a href="../phenome/population_indls.pl?population_id=$pop_id&amp;cvterm_id=$ut_id">$pop_name</a> <br />|;
  90     }
  91
  92     my $pop_count = scalar(@pops);
  93     if ($pop_count > 0) {
  94         $pop_count .= " " . 'populations';
  95     }
  96
  97    print info_section_html(title    => "Phenotype data/QTLs ($pop_count)",
  98                             contents => $pop_list,
  99                             collapsible=>1,
 100                             collapsed=>0,
 101                             );
 102
 103
 104     ####add page comments
 105     if ($ut_name) {
 106         my $page_comment_obj = CXGN::People::PageComment->new($self->get_dbh(), "trait", $ut_id, $self->get_page()->{request}->uri()."?".$self->get_page()->{request}->args());
 107         print $page_comment_obj->get_html();
 108     }
 109
 110
 111     $self->get_page()->footer();
 112 }
 113
 114
 115 sub generate_form {
 116     my $self=shift;
 117     $self->init_form();
 118     my $ut=$self->get_object();
 119
 120     my %args=$self->get_args();
 121
 122     my $ut_name=$ut->get_name();
 123
 124     my $definition = $ut->get_definition() ;
 125
 126     $self->get_form()->add_label(
 127                                  display_name =>"Term name",
 128                                  field_name   =>"term_name",
 129                                  contents     => $ut_name,
 130                                  );
 131     $self->get_form()->add_label(
 132                                  display_name =>"Definition",
 133                                  field_name   =>"definition",
 134                                  contents     => $definition,
 135                                  );
 136
 137
 138     if ($self->get_action=~ /view/) {
 139
 140         $self->get_form->from_database();
 141     }
 142
 143 }
 144
 145 #########################################################
 146