lib/SGN/Controller/Genefamily.pm

   1
   2 package SGN::Controller::Genefamily;
   3
   4 use Moose;
   5
   6 use Data::Dumper;
   7
   8 BEGIN { extends 'Catalyst::Controller'; }
   9
  10 sub genefamily_index :Path('/tools/genefamily') Args(0) {
  11     my $self = shift;
  12     my $c = shift;
  13
  14     $c->stash->{template} = '/tools/genefamily/index.mas';
  15 }
  16
  17
  18 sub search : Path('/tools/genefamily/search') Args(0) {
  19     my $self = shift;
  20     my $c = shift;
  21
  22 #    if ($c->user()) {
  23 #       if (grep(/curator|genefamily_editor/, $c->user->get_object()->get_roles() )) {
  24
  25             $c->stash->{genefamily_id} = $c->req->param("genefamily_id") || '';
  26             $c->stash->{build} = $c->req->param("build") || '';
  27             $c->stash->{member_id} = $c->req->param("member_id") || '';
  28             $c->stash->{action} = $c->req->param("action") || '';
  29
  30             $c->stash->{template} = '/tools/genefamily/search.mas';
  31 #       }
  32 #       else {
  33 #           $c->stash->{message} = "You do not have the necessary privileges to access this page.";
  34 #           $c->stash->{template} = "/generic_message.mas";
  35 #       }
  36
  37  #   }
  38   #  else {
  39 #       $c->stash->{message} = "You need to be logged in to access this page.";
  40 #       $c->stash->{template} = "/generic_message.mas";
  41  #   }
  42
  43 }
  44
  45 sub sequence_details :Path('/tools/genefamily/seq') Args(3) {
  46     my $self = shift;
  47     my $c = shift;
  48     my $build = shift;
  49     my $family = shift;
  50     my $sequence = shift;
  51
  52     my $gf = SGN::Genefamily->new(
  53         name      => $family,
  54         build   => $build,
  55         files_dir => $c->config()->{genefamily_dir},
  56         );
  57
  58     print STDERR "Trying to locate sequence $sequence\n";
  59
  60     my $seq_info  = $gf->get_sequence($sequence);
  61
  62     my ($seq_id, $desc, $seq) = @$seq_info;
  63     $c->stash->{build} = $build;
  64     $c->stash->{family} = $family;
  65     $c->stash->{seq_id} = $seq_id;
  66     $c->stash->{desc} = $desc || "[ no description provided ]";
  67     $c->stash->{seq} = $seq;
  68
  69     $c->stash->{template} = '/tools/genefamily/sequence.mas';
  70
  71
  72 }
  73
  74 sub get_family_fasta :Path('/tools/genefamily/fasta/') Args(2) {
  75     my $self = shift;
  76     my $c = shift;
  77     my $build = shift;
  78     my $family = shift;
  79
  80     my $gf = SGN::Genefamily->new(
  81         name      => $family,
  82         build   => $build,
  83         files_dir => $c->config()->{genefamily_dir},
  84         );
  85
  86     my $fasta_seq = $gf -> get_fasta();
  87
  88     $c->stash->{build} = $build;
  89     $c->stash->{family} = $family;
  90     $c->stash->{fasta} = $fasta_seq;
  91
  92     $c->stash->{template} = '/tools/genefamily/fasta.mas';
  93 }
  94
  95 sub genefamily_details :Path('/tools/genefamily/details') Args(2) {
  96     my $self = shift;
  97     my $c = shift;
  98     my $build = shift;
  99     my $family = shift;
 100
 101     my $gf = SGN::Genefamily->new(
 102         name      => $family,
 103         build   => $build,
 104         files_dir => $c->config()->{genefamily_dir},
 105         );
 106
 107     my $seq_data ="";
 108     my $fasta_data = "";
 109     my $tree_data = "";
 110     my $annot_data = "";
 111     my $exp_data = "";
 112
 113     my $align_link_disabled = "";
 114     my $fasta_link_disabled = "";
 115     my $tree_link_disabled = "";
 116     my $exp_link_disabled = "";
 117
 118     my $errors = "";
 119     my $big_errors = 0;
 120
 121     if (!$family) {
 122         $c->stash->{template} = '/generic_message.mas';
 123         $c->stash->{message} = 'Need a family to display!';
 124         return;
 125     }
 126
 127     $c->stash->{genefamily_id} = $family;
 128
 129     my $members = $gf->get_members($family);
 130
 131     print STDERR "Members: ".Dumper($members);
 132
 133     $c->stash->{member_count} = scalar(@$members);
 134     $c->stash->{members} = join(", ", @$members);
 135
 136
 137     eval {
 138       $c->stash->{seq_data} = $gf->get_alignment();
 139     };
 140
 141     if ($@) {
 142       $errors .= "Alignment data not available. ";
 143       $big_errors++;
 144       $align_link_disabled="disabled";
 145     }
 146
 147     eval {
 148       $c->stash->{fasta_data} = $gf->get_fasta();
 149
 150     };
 151
 152     if ($@) {
 153       $errors .= "Sequence data not available. ";
 154       $big_errors++;
 155       $fasta_link_disabled = "disabled";
 156     }
 157     eval {
 158       $c->stash->{tree_data} = $gf->get_tree();
 159     };
 160     if ($@) {
 161       $errors .= "Tree data not available. ";
 162       $c->stash->{tree_link_disabled} = "disabled"
 163     }
 164     eval {
 165       $c->stash->{annot_data} = $gf->get_annotation();
 166     };
 167     if ($@) {
 168       $errors .= "Annotation data not available. ";
 169       $c->stash->{annot_data} = "(No annotation data available)";
 170     }
 171     eval {
 172       $errors .= "Expression data not available. ";
 173       $c->stash->{exp_data} = $gf->get_expression();
 174     };
 175     if ($@) {
 176       $c->stash->{exp_link_disabled} = "disabled";
 177     }
 178
 179     if ($big_errors > 0) {
 180       $errors = "This family does not seem to exist!\n";
 181     }
 182
 183     $c->stash->{template} = '/tools/genefamily/details.mas';
 184
 185 }
 186
 187 1;