cgi-bin/phenome/individual_browser.pl

   1 use strict;
   2 use warnings;
   3
   4 use CXGN::Scrap::AjaxPage;
   5 use CXGN::Login;
   6 #use JSON;
   7
   8 my $doc = CXGN::Scrap::AjaxPage->new();
   9 $doc->send_http_header();
  10 my ($individual_name, $locus_id, $type, $individual_allele_id, $allele_id) = $doc->get_encoded_arguments("individual_name", "locus_id", "type", "individual_allele_id", "allele_id");
  11 print STDERR "my args are: $individual_name, $locus_id, $type, $individual_allele_id, $allele_id \n\n\n";
  12 my $dbh = CXGN::DB::Connection->new();
  13
  14 my($login_person_id, $login_user_type)=CXGN::Login->new($dbh)->verify_session();
  15
  16 if ($login_user_type eq 'curator' || $login_user_type eq 'submitter' || $login_user_type eq 'sequencer') {
  17
  18     if ($type eq 'browse') {
  19         my $individual_query = $dbh->prepare("SELECT individual_id, name, description FROM phenome.individual
  20                                       WHERE individual_id NOT IN (SELECT individual_id FROM phenome.individual JOIN
  21                                       phenome.individual_allele USING(individual_id) JOIN phenome.allele USING(allele_id)
  22                                       WHERE locus_id = ? AND individual_allele.obsolete = 'f')
  23                                      AND  individual.name ilike '%$individual_name%'
  24                                     ");
  25         $individual_query->execute($locus_id);
  26
  27         my ($individual_id, $name, $desc) = $individual_query->fetchrow_array();
  28         my $available_individuals;
  29
  30         while($individual_id){
  31             $available_individuals .= "$individual_id*$name--$desc|";
  32             ($individual_id, $name, $desc) = $individual_query->fetchrow_array();
  33         }
  34
  35         print "$available_individuals";
  36     }
  37     #search from the allele page. Fiter only the existing individuals associated with $allele.
  38     elsif ($type eq 'browse_allele') {
  39                 my $individual_query = $dbh->prepare("SELECT individual_id, name, description FROM phenome.individual
  40                                       WHERE individual_id NOT IN (SELECT individual_id FROM phenome.individual JOIN
  41                                       phenome.individual_allele USING(individual_id)
  42                                       WHERE allele_id = ? AND individual_allele.obsolete = 'f')
  43                                      AND  individual.name ilike '%$individual_name%'
  44                                     ");
  45         $individual_query->execute($allele_id);
  46
  47         my ($individual_id, $name, $desc) = $individual_query->fetchrow_array();
  48         my $available_individuals;
  49
  50         while($individual_id){
  51             $available_individuals .= "$individual_id*$name--$desc|";
  52             ($individual_id, $name, $desc) = $individual_query->fetchrow_array();
  53         }
  54
  55         print "$available_individuals";
  56
  57     }
  58     #obsolete individual-allele association
  59     elsif ($type eq 'obsolete') {
  60         eval {
  61             my $query = "UPDATE phenome.individual_allele SET obsolete='t', modified_date= now() WHERE individual_allele_id = ? ";
  62             my $sth= $dbh->prepare($query);
  63
  64             $sth->execute($individual_allele_id);
  65         };
  66
  67         if ($@) {
  68             warn "individual-allele obsoletion failed! "#$page->message_page("An error occurred during the database operation");
  69         }
  70     }
  71
  72
  73 }