lib/SGN/Controller/AJAX/Transcript.pm

   1
   2 =head1 NAME
   3
   4 SGN::Controller::AJAX::Transcript - a REST controller class to provide the
   5 backend for objects linked with transcripts (AKA unigenes)
   6
   7 =head1 DESCRIPTION
   8
   9 Browse the unigene database for selecting unigenes to be linked with other objects
  10
  11 =head1 AUTHOR
  12
  13 Naama Menda <nm249@cornell.edu>
  14
  15 =cut
  16
  17 package SGN::Controller::AJAX::Transcript;
  18
  19 use Moose;
  20
  21 use List::MoreUtils qw /any /;
  22 use Try::Tiny;
  23 use Scalar::Util qw(looks_like_number);
  24
  25
  26 BEGIN { extends 'Catalyst::Controller::REST' }
  27
  28 __PACKAGE__->config(
  29     default   => 'application/json',
  30     stash_key => 'rest',
  31     map       => { 'application/json' => 'JSON', 'text/html' => 'JSON' },
  32    );
  33
  34
  35 =head2 autocomplete
  36
  37 Public Path: /ajax/transcript/autocomplete
  38
  39 Autocomplete a unigene name.  Takes a single GET param,
  40 C<term>, responds with a JSON array of completions for that term.
  41
  42 =cut
  43
  44 sub autocomplete : Local : ActionClass('REST') { }
  45
  46 sub autocomplete_GET :Args(0) {
  47     my ( $self, $c ) = @_;
  48     my $unigene_name = $c->request->param("term");
  49     my $current      = $c->request->param('current') ; #pass this param for printing only current unigenes
  50     my $organism = $c->request->param('organism');
  51     my ($organism_c, $status_c);
  52    my $dbh = $c->dbc->dbh;
  53     my $query  = "SELECT unigene_id, unigene_build_id, nr_members, build_nr,  database_name, sequence_name, status FROM sgn.unigene LEFT JOIN sgn.unigene_build using(unigene_build_id) WHERE unigene_id = ? ";
  54
  55     my $sth= $dbh->prepare($query);
  56     my @response_list;
  57     $unigene_name =~ s/SGN.?U?//i;
  58     if (looks_like_number($unigene_name) ) {
  59         $sth->execute($unigene_name);
  60         while (my ($unigene_id, $build_id, $nr_members, $build_nr, $db_name, $seq_name, $build_status) = $sth->fetchrow_array() ) {
  61             my $unigene = CXGN::Transcript::Unigene->new($dbh, $unigene_id);
  62             my $unigene_build = $unigene->get_unigene_build;
  63             my $unigene_organism = $unigene_build->get_common_name();
  64             if ($organism && $unigene_organism ne $organism)  { $organism_c = 1; }
  65             if ($current   && $build_status ne "C") { $status_c = 1; }
  66             if (!$organism_c && !$status_c) {
  67                 push @response_list, "SGN-U$unigene_id--build $build_id--$nr_members members";
  68             }
  69         }
  70     }
  71     $c->stash->{rest} = \@response_list;
  72 }
  73
  74 ###
  75 1;#
  76 ###