lib/SGN/Controller/Genefamily/Manual.pm

   1 package SGN::Controller::Genefamily::Manual;
   2
   3
   4 =head1 NAME
   5
   6 SGN::Controller::Genefamily::Manual - Catalyst controller for pages dealing with
   7 manually curated gene families (aka 'locusgroup')
   8
   9 =cut
  10
  11 use Moose;
  12
  13 BEGIN { extends "Catalyst::Controller"; }
  14 with 'Catalyst::Component::ApplicationAttribute';
  15
  16
  17 has 'schema' => (
  18     is       => 'rw',
  19     isa      => 'DBIx::Class::Schema',
  20     lazy_build => 1,
  21 );
  22
  23 sub _build_schema {
  24     shift->_app->dbic_schema( 'CXGN::Phenome::Schema' )
  25 }
  26
  27 =head2 view_genefamily
  28
  29 Public path: /genefamily/manual/<locusgroup_id>/view
  30
  31 View a gene family (locusgroup) detail page.
  32
  33 Chained off of L</get_genefamily> below.
  34
  35 =cut
  36
  37 sub view_genefamily : Chained('get_genefamily') PathPart('view') Args(0) {
  38     my ( $self, $c, $action) = @_;
  39     my $genefamily = $c->stash->{genefamily};
  40     if( $genefamily ) {
  41         $c->forward('get_genefamily_extended_info');
  42     }
  43
  44     my $logged_user = $c->user;
  45     my $person_id   = $logged_user->get_object->get_sp_person_id if $logged_user;
  46     my $curator     = $logged_user->check_roles('curator') if $logged_user;
  47     my $submitter   = $logged_user->check_roles('submitter') if $logged_user;
  48     my $sequencer   = $logged_user->check_roles('sequencer') if $logged_user;
  49     my $dbh = $c->dbc->dbh;
  50
  51     ##################
  52
  53     ###Check if a gene family page can be printed###
  54     my $genefamily_id = $genefamily ? $genefamily->get_locusgroup_id : undef ;
  55
  56     # print message if locusgroup_id is not valid
  57     unless ( $genefamily_id =~ m /^\d+$/ )  {
  58         $c->throw_404( "No gene family exists for that identifier." );
  59     }
  60     unless ( $genefamily ) {
  61         $c->throw_404( "No gene family  exists for that identifier." );
  62     }
  63     ####################
  64     my $is_owner;
  65     my $owner_id = $c->stash->{owner_id} || undef ;
  66     if ( $genefamily && ($curator || $person_id && ( $person_id == $owner_id ) ) ) {
  67         $is_owner = 1;
  68     }
  69     my $members = $genefamily->get_locusgroup_members;
  70     #########
  71     ################
  72     $c->stash(
  73         template => '/genefamily/manual/index.mas',
  74         hashref => {
  75             action    => $action,
  76             genefamily => $genefamily,
  77             curator   => $curator,
  78             submitter => $submitter,
  79             sequencer => $sequencer,
  80             person_id => $person_id,
  81             user      => $logged_user,
  82             genefamily     => $genefamily,
  83             dbh       => $dbh,
  84             is_owner  => $is_owner,
  85             members   => $members,
  86         },
  87         locus_add_uri  => $c->uri_for( '/ajax/locus/associate_locus' ),
  88         );
  89 }
  90
  91
  92 =head1 PRIVATE ACTIONS
  93
  94 =head2 get_genefamily
  95
  96 Chain root for fetching a locusgroup object to operate on.
  97
  98 Path part: /genefamily/manual/<locusgroup_id>
  99
 100 =cut
 101
 102 sub get_genefamily : Chained('/')  PathPart('genefamily/manual')  CaptureArgs(1) {
 103     my ($self, $c, $locusgroup_id) = @_;
 104     $c->stash->{genefamily} = CXGN::Phenome::LocusGroup->new($self->schema, $locusgroup_id);
 105 }
 106
 107
 108 sub get_genefamily_extended_info : Private {
 109     my ( $self, $c ) = @_;
 110     #$c->forward('get_genefamily_members');
 111 }
 112
 113
 114 __PACKAGE__->meta->make_immutable;