lib/SGN/Controller/Cvterm.pm

   1
   2 package SGN::Controller::Cvterm;
   3
   4 #use CXGN::Chado::Cvterm; #DEPRECATE this !!
   5 use CXGN::Cvterm;
   6
   7 use Moose;
   8
   9 BEGIN { extends 'Catalyst::Controller' };
  10 with 'Catalyst::Component::ApplicationAttribute';
  11
  12 has 'schema' => (
  13     is       => 'rw',
  14     isa      => 'DBIx::Class::Schema',
  15     lazy_build => 1,
  16 );
  17 sub _build_schema {
  18     shift->_app->dbic_schema( 'Bio::Chado::Schema', 'sgn_chado' )
  19 }
  20
  21
  22 =head2 view_cvterm
  23
  24 Public path: /cvterm/<cvterm_id>/view
  25
  26 View a cvterm detail page.
  27
  28 Chained off of L</get_cvterm> below.
  29
  30 =cut
  31
  32 sub view_cvterm : Chained('get_cvterm') PathPart('view') Args(0) {
  33     my ( $self, $c, $action) = @_;
  34     my $cvterm = $c->stash->{cvterm};
  35     my $cvterm_id = $cvterm ? $cvterm->cvterm_id : undef ;
  36
  37     my $bcs_cvterm = $cvterm->cvterm;
  38
  39     my ($person_id, $user_role, $curator, $submitter, $sequencer);
  40     my $logged_user = $c->user;
  41     $person_id = $logged_user->get_object->get_sp_person_id if $logged_user;
  42     $user_role = 1 if $logged_user;
  43     $curator   = $logged_user->check_roles('curator') if $logged_user;
  44     $submitter = $logged_user->check_roles('submitter') if $logged_user;
  45     $sequencer = $logged_user->check_roles('sequencer') if $logged_user;
  46     my $props = $self->_cvtermprops($cvterm);
  47     my $editable_cvterm_props = "trait_format,trait_default_value,trait_minimum,trait_maximum,trait_details,trait_categories";
  48
  49
  50     $c->stash(
  51         template => '/chado/cvterm.mas',
  52         cvterm   => $cvterm, #deprecate this maybe?
  53         cvtermref => {
  54             cvterm    => $bcs_cvterm,
  55             curator   => $curator,
  56             submitter => $submitter,
  57             sequencer => $sequencer,
  58             person_id => $person_id,
  59             props     => $props,
  60             editable_cvterm_props => $editable_cvterm_props,
  61         }
  62         );
  63
  64 }
  65
  66
  67 =head2 get_cvterm
  68
  69 Chain root for fetching a cvterm object to operate on.
  70
  71 Path part: /cvterm/<cvterm_id>
  72
  73 =cut
  74
  75 sub get_cvterm : Chained('/')  PathPart('cvterm')  CaptureArgs(1) {
  76     my ($self, $c, $cvterm_id) = @_;
  77
  78     my $identifier_type = $c->stash->{identifier_type}
  79         || $cvterm_id =~ /[^-\d]/ ? 'accession' : 'cvterm_id';
  80
  81     my $cvterm;
  82     if( $identifier_type eq 'cvterm_id' ) {
  83         $cvterm = CXGN::Cvterm->new({ schema=>$self->schema, cvterm_id => $cvterm_id } );
  84     } elsif ( $identifier_type eq 'accession' )  {
  85         $cvterm = CXGN::Cvterm->new({ schema=>$self->schema, accession=>$cvterm_id } ) ;
  86     }
  87     my $found_cvterm = $cvterm->cvterm
  88         or $c->throw_404( "Cvterm $cvterm_id not found" );
  89
  90     $c->stash->{cvterm}     = $cvterm;
  91
  92     return 1;
  93 }
  94
  95
  96
  97 sub _cvtermprops {
  98     my ($self,$cvterm) = @_;
  99
 100     my $properties ;
 101     if ($cvterm) {
 102         my $bcs_cvterm = $cvterm->cvterm;
 103         if (!$bcs_cvterm) { return; }
 104         my $cvtermprops = $bcs_cvterm->search_related("cvtermprops");
 105         while ( my $prop =  $cvtermprops->next ) {
 106             push @{ $properties->{$prop->type->name} } ,   $prop->value ;
 107         }
 108     }
 109     return $properties;
 110 }
 111 ####
 112 1;##
 113 ####