cgi-bin/phenome/organism_browser.pl

   1
   2 #!/usr/bin/perl -wT
   3
   4
   5 =head1 SYNOPSIS
   6 A simple script that retrieves common names and their ids, and
   7 writes out id of the selected organism into a file.
   8 It is used to work with the Ajax form for the QTL webform.
   9
  10
  11
  12 =head1 AUTHOR
  13
  14 Isaak Y Tecle iyt2@cornell.edu
  15
  16 =cut
  17
  18
  19
  20 use strict;
  21 use warnings;
  22
  23 use Path::Class;
  24
  25 use CXGN::Scrap::AjaxPage;
  26 use CXGN::DB::Connection;
  27 use CXGN::Login;
  28 use CXGN::Phenome::Qtl;
  29
  30 use CatalystX::GlobalContext qw( $c );
  31
  32 my $doc = CXGN::Scrap::AjaxPage->new();
  33 $doc->send_http_header();
  34
  35
  36 my ($common_name, $common_name_id, $type, $sp_person_id) = $doc->get_encoded_arguments("organism", "organism_id", "type", "sp_person_id");
  37
  38 my $dbh = CXGN::DB::Connection->new();
  39 my ($login_person_id, $login_user_type)=CXGN::Login->new($dbh)->verify_session();
  40
  41 if ($login_user_type eq 'curator' || $login_user_type eq 'submitter' || $login_user_type eq 'sequencer') {
  42
  43     if ($type eq 'browse') {
  44         &browse_organisms($dbh, $type, $common_name);
  45     }
  46     elsif ($type eq 'associate') {
  47         &associate_organism($dbh, $type, $common_name_id, $login_person_id);
  48     }
  49
  50 }
  51
  52 sub browse_organisms {
  53     my ($dbh, $type, $common_name) = @_;
  54     my $organisms;
  55
  56     $common_name =~ s/^\s+|\s+$//g;
  57
  58     if ($type eq 'browse')
  59     {
  60         if ($common_name)
  61         {
  62             my $sth = $dbh->prepare ("SELECT common_name_id, common_name
  63                                               FROM sgn.common_name                                                                                             WHERE common_name ILIKE '$common_name%'"
  64                                     );
  65             $sth->execute();
  66
  67             while (my ($common_name_id, $common_name)   = $sth->fetchrow_array())
  68             {
  69                 $organisms .= "$common_name_id*$common_name_id -- $common_name |";
  70             }
  71             print $organisms;
  72           }
  73     }
  74 }
  75
  76 sub associate_organism {
  77     my ($dbh, $type, $common_name_id, $sp_person_id) = @_;
  78
  79     my $qtl = CXGN::Phenome::Qtl->new($sp_person_id);
  80     my ($temp_qtl_dir, $temp_user_dir) = $qtl->create_user_qtl_dir($c);
  81
  82     my $f = file( $temp_user_dir, 'organism.txt' )->openw
  83         or die "Can't create file: $! \n";
  84     $f->print( "common_name_id\t$common_name_id" );
  85 }
  86