lib/SGN/Controller/Variant.pm

   1 =head1 NAME
   2
   3 SGN::Controller::Variant
   4
   5 =head1 DESCRIPTION
   6
   7 Controller for pages related to genotype markers (those stored in nd_protocolprop
   8 and summarized in the marker materialized view).
   9
  10 =cut
  11
  12 package SGN::Controller::Variant;
  13
  14 use strict;
  15 use Moose;
  16 use CXGN::Marker::SearchMatView;
  17
  18 BEGIN { extends 'Catalyst::Controller' }
  19
  20
  21 #
  22 # VARIANT DETAIL PAGE
  23 #
  24 # PATH: /variant/{variant_name}/details
  25 #   - Get variant details
  26 #   - Stash the variant's marker information
  27 #   - Display variant detail page
  28 #
  29 sub get_variant_details: Chained('get_variant') PathPart('details') :Args(0) {
  30     my ( $self, $c ) = @_;
  31     my $schema = $c->dbic_schema("Bio::Chado::Schema");
  32     my $variant_name = $c->stash->{variant_name};
  33
  34     # Get variant details
  35     my $msearch = CXGN::Marker::SearchMatView->new(bcs_schema => $schema);
  36     my $variant_details = $msearch->query({ variant => $variant_name });
  37     my $markers = $variant_details->{'variants'}->{$variant_name};
  38
  39     # No markers found
  40     if ( !$markers ) {
  41         $c->stash->{template} = "generic_message.mas";
  42             $c->stash->{message} = "<strong>No Markers Found</strong> for variant $variant_name<br />You can view and search for markers from the <a href='/search/variants'>Marker Search Page</a>";
  43         $c->detach();
  44     }
  45
  46     $c->stash->{markers} = $markers;
  47     $c->stash->{template} = '/markers/genotyped/variant_details.mas';
  48 }
  49
  50
  51 #
  52 # PATH: /variant/{variant_name}
  53 #   - Stash variant_name
  54 #
  55 sub get_variant: Chained('/') PathPart('variant') :CaptureArgs(1) {
  56     my ( $self, $c, $variant ) = @_;
  57     $c->stash->{variant_name} = $variant;
  58 }
  59
  60
  61
  62
  63 1;