lib/SGN/Controller/Feature.pm

   1 package SGN::Controller::Feature;
   2
   3 =head1 NAME
   4
   5 SGN::Controller::Feature - Catalyst controller for pages dealing with
   6 Chado (i.e. Bio::Chado::Schema) features
   7
   8 =cut
   9
  10 use Moose;
  11 use namespace::autoclean;
  12
  13 BEGIN { extends 'Catalyst::Controller' }
  14
  15 =head1 PUBLIC ACTIONS
  16
  17 =cut
  18
  19 # deprecated old paths are now redirects
  20 sub view_by_name :Path('/feature/view/name') Path('/feature/view/id') Args(1) {
  21     my ( $self, $c, $id ) = @_;
  22     $c->res->redirect("/feature/$id/details",301);
  23 }
  24
  25 #######################################
  26
  27 sub feature_details :PathPart('details') :Chained('get_feature') Args(0) {
  28     my ( $self, $c ) = @_;
  29
  30        $c->forward('get_type_specific_data')
  31     && $c->forward('choose_view');
  32 }
  33
  34 sub choose_view :Private {
  35     my ( $self, $c ) = @_;
  36     my $feature   = $c->stash->{feature};
  37     my $type_name = lc $feature->type->name;
  38     my $template  = "/feature/types/default.mas";
  39
  40     $c->stash->{feature}     = $feature;
  41     $c->stash->{featurelocs} = $feature->featureloc_features;
  42
  43     # look up site xrefs for this feature
  44     my @xrefs = map $c->feature_xrefs( $_, { exclude => 'featurepages' } ),
  45                 ( $feature->name, $feature->synonyms->get_column('name')->all );
  46     unless( @xrefs ) {
  47         @xrefs = map {
  48             $c->feature_xrefs( $_->srcfeature->name.':'.($_->fmin+1).'..'.$_->fmax, { exclude => 'featurepages' } )
  49         }
  50         #$c->stash->{featurelocs}->all
  51         $c->stash->{featurelocs}->search({locgroup => 0,},)->all
  52     }
  53     $c->stash->{xrefs} = \@xrefs;
  54
  55     if ($c->view('Mason')->component_exists("/feature/types/$type_name.mas")) {
  56         $template         = "/feature/types/$type_name.mas";
  57         $c->stash->{type} = $type_name;
  58     }
  59     $c->stash->{template} = $template;
  60
  61     return 1;
  62 }
  63
  64 sub get_feature : Chained('/') CaptureArgs(1) PathPart('feature') {
  65     my ($self, $c, $id ) = @_;
  66
  67     $c->stash->{blast_url} = '/tools/blast';
  68
  69     my $identifier_type = $c->stash->{identifier_type}
  70         || $id =~ /[^-\d]/ ? 'name' : 'feature_id';
  71
  72     if( $identifier_type eq 'feature_id' ) {
  73         $id > 0
  74             or $c->throw_client_error( public_message => 'Feature ID must be a positive integer.' );
  75     }
  76
  77     #debug mode
  78     #$c->dbic_schema('Bio::Chado::Schema','sgn_chado')->storage->debug(1);
  79
  80     my $matching_features =
  81         $c->dbic_schema('Bio::Chado::Schema','sgn_chado')
  82           ->resultset('Sequence::Feature')
  83           ->search(
  84               #{ 'me.'.$identifier_type => $id },
  85             { 'me.'.$identifier_type => $id, 'featureloc_features.locgroup' => 0 },
  86               { prefetch => [ 'organism', 'type', 'featureloc_features'  ] },
  87             );
  88
  89     if( $matching_features->count > 1 ) {
  90         $c->throw_client_error( public_message => 'Multiple matching features' );
  91     }
  92
  93     my ( $feature ) = $matching_features->all;
  94     $c->stash->{feature} = $feature
  95         or $c->throw_404( "Feature not found" );
  96
  97     return 1;
  98 }
  99
 100 sub get_type_specific_data :Private {
 101     my ( $self, $c ) = @_;
 102
 103     my $type_name = $c->stash->{feature}->type->name;
 104
 105     # look for an action with private path /feature/types/<type>/get_specific_data
 106     my $action = $c->get_action( 'get_specific_data', $self->action_namespace."/types/$type_name" );
 107     if( $action ) {
 108         $c->forward( $action ) or return;
 109     }
 110
 111     return 1;
 112 }
 113
 114 1;