lib/SGN/Controller/Ontology.pm

   1
   2 package SGN::Controller::Ontology;
   3
   4 use CXGN::Chado::Cvterm;
   5 use CXGN::People::Roles;
   6 use URI::FromHash 'uri';
   7 use CXGN::Page::FormattingHelpers qw | simple_selectbox_html |;
   8 use CXGN::Onto;
   9 use Data::Dumper;
  10
  11 use Moose;
  12
  13 BEGIN { extends 'Catalyst::Controller' };
  14 with 'Catalyst::Component::ApplicationAttribute';
  15
  16
  17 sub onto_browser : Path('/tools/onto') :Args(0) {
  18     my $self = shift;
  19     my $c = shift;
  20
  21     my $root_nodes = $c->config->{onto_root_namespaces};
  22     my @namespaces = split ",", $root_nodes;
  23     foreach my $n (@namespaces) {
  24         $n =~ s/\s*(\w+)\s*\(.*\)/$1/g;
  25         print STDERR "Adding node $n\n";
  26     }
  27     #$c->stash->{root_nodes} = $c->req->param("root_nodes");
  28     $c->stash->{root_nodes} = join " ", @namespaces;
  29     $c->stash->{db_name} = $c->req->param("db_name");
  30     $c->stash->{expand} = $c->req->param("expand");
  31
  32     $c->stash->{template} = '/ontology/standalone.mas';
  33
  34 }
  35
  36 sub compose_trait : Path('/tools/compose') :Args(0) {
  37     my $self = shift;
  38     my $c = shift;
  39
  40     if (!$c->user()) {
  41       # redirect to login page
  42       $c->res->redirect( uri( path => '/user/login', query => { goto_url => $c->req->uri->path_query } ) );
  43       return;
  44     }
  45
  46     my @composable_cvs = split ",", $c->config->{composable_cvs};
  47     my $dbh = $c->dbc->dbh();
  48     my $sp_person_id = $c->user() ? $c->user->get_object()->get_sp_person_id() : undef;
  49     my $onto = CXGN::Onto->new( { schema => $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado', $sp_person_id) } );
  50     my %html_hash;
  51     foreach my $name (@composable_cvs) {
  52         $name =~ s/^\s+|\s+$//g; # remove whitespace
  53         if ($name eq 'time' || $name eq 'tod' || $name eq 'toy' || $name eq 'gen' || $name eq 'evt' ) {
  54             print STDERR "Skipping time-related cv\n";
  55             next;
  56         }
  57         my $cv_type = $name."_ontology";
  58         #print STDERR "cv_type = $cv_type\n";
  59
  60
  61         my @root_nodes = $onto->get_root_nodes($cv_type);
  62         #print STDERR Dumper \@root_nodes;
  63         if (scalar @root_nodes > 1) {
  64             #create simple selectbox of root_nodes
  65             my $id = $name."_root_select";
  66             my $name = $name."_root_select";
  67             my $html = simple_selectbox_html(
  68                name => $name,
  69                id => $id,
  70                choices => \@root_nodes,
  71                size => '10',
  72                default => 'Pick an Ontology'
  73             );
  74             #put html in hash
  75             $html_hash{$cv_type} = $html;
  76         }
  77         else {
  78             my $cv_id = $root_nodes[0][0];
  79            my @components = $onto->get_terms($cv_id);
  80
  81            my $id = $name."_select";
  82            my $name = $name."_select";
  83            my $default = 0;
  84            if ($default) { unshift @components, [ '', $default ]; }
  85
  86            my $html = simple_selectbox_html(
  87               name => $name,
  88               multiple => 1,
  89               id => $id,
  90               choices => \@components,
  91               size => '10'
  92            );
  93            #put html in hash
  94            $html_hash{$cv_type} = $html;
  95        }
  96     }
  97
  98     $c->stash->{object_select} = $html_hash{'object_ontology'};
  99     $c->stash->{attribute_select} = $html_hash{'attribute_ontology'};
 100     $c->stash->{method_select} = $html_hash{'method_ontology'};
 101     $c->stash->{unit_select} = $html_hash{'unit_ontology'};
 102     $c->stash->{trait_select} = $html_hash{'trait_ontology'};
 103
 104     $c->stash->{composable_cvs} = $c->config->{composable_cvs};
 105     $c->stash->{composable_cvs_allowed_combinations} = $c->config->{composable_cvs_allowed_combinations};
 106     $c->stash->{composable_tod_root_cvterm} = $c->config->{composable_tod_root_cvterm};
 107     $c->stash->{composable_toy_root_cvterm} = $c->config->{composable_toy_root_cvterm};
 108     $c->stash->{composable_gen_root_cvterm} = $c->config->{composable_gen_root_cvterm};
 109     $c->stash->{composable_evt_root_cvterm} = $c->config->{composable_evt_root_cvterm};
 110
 111     $c->stash->{user} = $c->user();
 112     $c->stash->{template} = '/ontology/compose_trait.mas';
 113
 114 }
 115
 116 1;