lib/CXGN/Trait.pm

   1
   2 package CXGN::Trait;
   3
   4 use Moose;
   5
   6 ## to do: add concept of trait short name; provide alternate constructors for term, shortname, and synonyms etc.
   7
   8 has 'bcs_schema' => ( isa => 'Bio::Chado::Schema',
   9                   is => 'rw',
  10                   required => 1,
  11     );
  12
  13 has 'cvterm_id' => (isa => 'Int',
  14                     is => 'rw',
  15                     required => 1,
  16     );
  17
  18 has 'cvterm' => ( isa => 'Bio::Chado::Schema::Result::Cv::Cvterm',
  19                   is => 'rw');
  20
  21
  22 has 'name' => ( isa => 'Str',
  23                 is => 'ro',
  24                 lazy => 1,
  25                 default => sub {
  26                     my $self = shift;
  27                     return $self->cvterm->name();
  28                 },
  29
  30     );
  31
  32 has 'display_name' => (isa => 'Str',
  33                        is => 'ro',
  34                        lazy => 1,
  35                        default => sub {
  36                            my $self = shift;
  37                            my $db = $self->db();
  38                            my $name = $self->name();
  39                            my $accession = $self->accession();
  40                            #print STDERR $db." ".$name." ".$accession."\n";
  41                            if ($db && $name && $accession ) {
  42                                return $name ."|".$db.":".$accession;
  43                            }
  44                            return "";
  45                        }
  46     );
  47
  48 has 'accession' => (isa => 'Str',
  49                     is => 'ro',
  50                     lazy => 1,
  51                     default => sub {
  52                         my $self = shift;
  53                         my $rs = $self->bcs_schema()->resultset("Cv::Cvterm")
  54                             -> search( { cvterm_id => $self->cvterm_id() })
  55                             -> search_related("dbxref");
  56                         if ($rs->count() ==1) {
  57                             my $accession = $rs->first()->get_column("accession");
  58                             return $accession;
  59                         }
  60                         return "";
  61                     }
  62
  63     );
  64
  65 has 'term' => (isa => 'Str',
  66                is => 'ro',
  67                lazy => 1,
  68                default => sub {
  69                    my $self = shift;
  70                    my $accession = $self->accession();
  71                    my $db = $self->db();
  72                    if ($accession && $db) {
  73                        return "$db:$accession";
  74                    }
  75                    return "";
  76                }
  77     );
  78
  79 has 'db'   => ( isa => 'Str',
  80                 is => 'ro',
  81                 lazy => 1,
  82                 default => sub {
  83                     my $self = shift;
  84                     my $rs = $self->bcs_schema()->resultset("Cv::Cvterm")->search( { cvterm_id => $self->cvterm_id()})->search_related("dbxref")->search_related("db");
  85                     if ($rs->count() == 1) {
  86                         my $db_name =  $rs->first()->get_column("name");
  87                         #print STDERR "DBNAME = $db_name\n";
  88                         return $db_name;
  89                     }
  90                     return "";
  91
  92                 }
  93     );
  94
  95 has 'db_id'   => (
  96         isa => 'Int',
  97         is => 'ro',
  98         lazy => 1,
  99         default => sub {
 100                 my $self = shift;
 101                 my $rs = $self->cvterm->search_related("dbxref");
 102                 if ($rs->count() == 1) {
 103                         my $db_id =  $rs->first()->get_column("db_id");
 104                         #print STDERR "DBID = $db_id\n";
 105                         return $db_id;
 106                 }
 107                 return "";
 108         }
 109 );
 110
 111 has 'definition' => (isa => 'Maybe[Str]',
 112                      is => 'ro',
 113                      lazy => 1,
 114                      default => sub {
 115                          my $self = shift;
 116                          return $self->cvterm->definition();
 117                      },
 118
 119     );
 120
 121 has 'format' => (isa => 'Str',
 122                  is => 'ro',
 123                  lazy => 1,
 124                  default => sub {
 125                      my $self = shift;
 126
 127                      my $row = $self->bcs_schema()->resultset("Cv::Cvtermprop")->find(
 128                          {
 129                              cvterm_id => $self->cvterm_id(), 'type.name' => 'trait_format'
 130                          },
 131                          { join => 'type'}
 132                          );
 133
 134                      if ($row) {
 135                          return $row->value();
 136                      }
 137                      return "";
 138                  }
 139     );
 140
 141 has 'default_value' => (
 142         isa => 'Str',
 143         is => 'ro',
 144         lazy => 1,
 145         default => sub {
 146                 my $self = shift;
 147                 my $row = $self->bcs_schema()->resultset("Cv::Cvtermprop")->find(
 148                         { cvterm_id => $self->cvterm_id(), 'type.name' => 'trait_default_value' },
 149                         { join => 'type'}
 150                 );
 151
 152                 if ($row) {
 153                         return $row->value();
 154                 }
 155                 return "";
 156         }
 157 );
 158
 159 has 'minimum' => (
 160         isa => 'Str',
 161         is => 'ro',
 162         lazy => 1,
 163         default => sub {
 164                 my $self = shift;
 165                 my $row = $self->bcs_schema()->resultset("Cv::Cvtermprop")->find(
 166                         { cvterm_id => $self->cvterm_id(), 'type.name' => 'trait_minimum' },
 167                         { join => 'type'}
 168                 );
 169
 170                 if ($row) {
 171                         return $row->value();
 172                 }
 173                 return "";
 174         }
 175 );
 176
 177 has 'maximum' => (
 178         isa => 'Str',
 179         is => 'ro',
 180         lazy => 1,
 181         default => sub {
 182                 my $self = shift;
 183                 my $row = $self->bcs_schema()->resultset("Cv::Cvtermprop")->find(
 184                         { cvterm_id => $self->cvterm_id(), 'type.name' => 'trait_maximum' },
 185                         { join => 'type'}
 186                 );
 187
 188                 if ($row) {
 189                         return $row->value();
 190                 }
 191                 return "";
 192         }
 193 );
 194
 195 has 'categories' => (
 196         isa => 'Str',
 197         is => 'ro',
 198         lazy => 1,
 199         default => sub {
 200                 my $self = shift;
 201                 my $row = $self->bcs_schema()->resultset("Cv::Cvtermprop")->find(
 202                         { cvterm_id => $self->cvterm_id(), 'type.name' => 'trait_categories' },
 203                         { join => 'type'}
 204                 );
 205
 206                 if ($row) {
 207                         return $row->value();
 208                 }
 209                 return "";
 210         }
 211 );
 212
 213 has 'associated_plots' => ( isa => 'Str',
 214                             is => 'ro',
 215                             lazy => 1,
 216                             default => sub { "not yet implemented" }
 217     );
 218
 219 has 'associated_accessions' =>  ( isa => 'Str',
 220                                   is => 'ro',
 221                                   lazy => 1,
 222                                   default => sub { "not yet implemented" }
 223     );
 224
 225 has 'uri' => (isa => 'Str',
 226         is            => 'ro',
 227         lazy          => 1,
 228         default => sub {
 229                 my $self = shift;
 230                 my $row = $self->bcs_schema()->resultset("Cv::Cvtermprop")->find(
 231                         {cvterm_id => $self->cvterm_id(), 'type.name' => 'uri'},
 232                         { join => 'type'}
 233                 );
 234
 235                 if ($row) {
 236                         return $row->value();
 237                 }
 238                 return "";
 239         }
 240 );
 241
 242 sub BUILD {
 243     #print STDERR "BUILDING...\n";
 244     my $self = shift;
 245     my $cvterm = $self->bcs_schema()->resultset("Cv::Cvterm")->find( { cvterm_id => $self->cvterm_id() });
 246     if ($cvterm) {
 247         #print STDERR "Cvterm with ID ".$self->cvterm_id()." was found!\n";
 248     }
 249     $self->cvterm($cvterm);
 250 }
 251
 252
 253 1;