lib/SGN/Controller/Phenotypes.pm

   1 package SGN::Controller::Phenotypes;
   2
   3 =head1 NAME
   4
   5 SGN::Controller::Phenotypes - Catalyst controller for pages dealing with
   6 phenotypes submission and associating them with project, experiments, and stock accessions.
   7
   8 =cut
   9
  10 use Moose;
  11 use namespace::autoclean;
  12 use YAML::Any qw/LoadFile/;
  13
  14 use URI::FromHash 'uri';
  15 use List::Compare;
  16 use File::Temp qw / tempfile /;
  17 use File::Slurp;
  18 use JSON::Any;
  19
  20 use CXGN::Chado::Stock;
  21 use SGN::View::Stock qw/stock_link stock_organisms stock_types/;
  22
  23
  24 BEGIN { extends 'Catalyst::Controller' }
  25 with 'Catalyst::Component::ApplicationAttribute';
  26
  27 has 'schema' => (
  28     is       => 'rw',
  29     isa      => 'DBIx::Class::Schema',
  30     lazy_build => 1,
  31 );
  32 sub _build_schema {
  33     shift->_app->dbic_schema( 'Bio::Chado::Schema', 'sgn_chado' )
  34 }
  35
  36 has 'default_page_size' => (
  37     is      => 'ro',
  38     default => 20,
  39 );
  40
  41 =head1 PUBLIC ACTIONS
  42
  43 =head2 submission_guidelines
  44
  45 Public path: /phenotype/submission_guide
  46
  47 Display the phenotype submission guidelines page
  48
  49 =cut
  50
  51 sub submission_guidelines :Path('/phenotype/submission_guide') Args(0) {
  52     my ($self, $c) = @_;
  53     $c->stash(template => '/phenotypes/submission_guide.mas');
  54
  55 }
  56
  57 sub delete_uploaded_phenotype_files : Path('/breeders/phenotyping/delete/') Args(1) {
  58      my $self  =shift;
  59      my $c = shift;
  60      my $json = new JSON;
  61      my $file_id = shift;
  62      my $decoded;
  63      if ($file_id){
  64                  $decoded = $json->allow_nonref->utf8->decode($file_id);
  65      }
  66         #print STDERR Dumper($file_id);
  67         print "File ID: $file_id\n";
  68      my $dbh = $c->dbc->dbh();
  69      my $h = $dbh->prepare("delete from metadata.md_files where file_id=?;");
  70      $h->execute($decoded);
  71      print STDERR "Layout deleted successfully.\n";
  72         $c->response->redirect('/breeders/phenotyping');
  73 }
  74
  75 #
  76 return 1;
  77 #