lib/CXGN/Fieldbook/TraitInfo.pm

   1 package CXGN::Fieldbook::TraitInfo;
   2
   3 =head1 NAME
   4
   5 CXGN::Fieldbook::TraitInfo - a module to get information from a trait to build the fieldbook trait file.
   6
   7 =head1 USAGE
   8
   9  my $trait_info_lookup = CXGN::Fieldbook::TraitInfo->new({ chado_schema => $chado_schema, db_name => $db_name, trait_accession => $trait_accession });
  10  my $trait_info = $trait_info_lookup->get_trait_info();  #returns a string to use for the fieldbook trait file or returns false if not found
  11
  12 =head1 DESCRIPTION
  13
  14 Looks up a trait and builds a string to use in the fieldbook trait file.
  15
  16 =head1 AUTHORS
  17
  18  Jeremy D. Edwards (jde22@cornell.edu)
  19  Naama Menda (nm249@cornell.edu)
  20
  21 =cut
  22
  23 use Moose;
  24 use MooseX::FollowPBP;
  25 use Moose::Util::TypeConstraints;
  26
  27 has 'chado_schema' => (
  28                  is       => 'ro',
  29                  isa      => 'DBIx::Class::Schema',
  30                  required => 1,
  31                 );
  32 has 'db_name' => (
  33                   is => 'ro',
  34                   isa => 'Str',
  35                   required => 1,
  36                  );
  37 has 'trait_accession' => (
  38                   is => 'ro',
  39                   isa => 'Str',
  40                   required => 1,
  41                  );
  42
  43 sub get_trait_info {
  44   my $self = shift;
  45         my $trait_name = shift;
  46   my $chado_schema = $self->get_chado_schema();
  47   my $trait_info_string;
  48
  49   my $db_rs = $chado_schema->resultset("General::Db")->search( { 'me.name' => $self->get_db_name() });
  50
  51   if (!$db_rs) {
  52     print STDERR "Could not find trait ontology database: ".$self->get_db_name()."\n";
  53     return;
  54   }
  55
  56   my $trait_cvterm = $chado_schema->resultset("Cv::Cvterm")
  57     ->find( {
  58              'dbxref.db_id'     => $db_rs->first()->db_id(),
  59              'dbxref.accession' => $self->get_trait_accession(),
  60             },
  61             {
  62              'join' => 'dbxref'
  63             }
  64           );
  65
  66
  67   if (!$trait_cvterm) {
  68     print STDERR "Could not find trait name: ".$trait_name."\n";
  69     return;
  70   }
  71
  72   #get cvtermprops
  73   my $cvtermprops = $trait_cvterm->search_related('cvtermprops');
  74
  75         # add full name in detail field, plus scale info if it's available
  76         my $trait_details = $trait_name;
  77         my $trait_def = $trait_cvterm->definition();
  78         $trait_def =~ s/([^\.]*\.\s{1})//;
  79         if ($trait_def =~ /=/) { $trait_details .= "\n" . $trait_def; }
  80         #print STDERR "trait details = $trait_details\n";
  81
  82   my $cvterms = $self->_get_cvterms();
  83
  84   my %trait_props;
  85   #set default values
  86   $trait_props{'trait_format'}='numeric';
  87   $trait_props{'trait_default_value'}='';
  88   $trait_props{'trait_minimum'}='';
  89   $trait_props{'trait_maximum'}='';
  90   $trait_props{'trait_details'}=$trait_details;
  91   $trait_props{'trait_categories'}='';
  92
  93
  94         print STDERR "trait name = $trait_name\n";
  95         # change from default numeric based on trait name
  96         if ($trait_name =~ m/percent/) {
  97                 $trait_props{'trait_format'}='percent';
  98                 $trait_props{'trait_minimum'}='0';
  99                 $trait_props{'trait_maximum'}='100';
 100                 $trait_props{'trait_default_value'}='50';
 101         }
 102 #       elsif ($trait_name =~ m/counting/) {
 103 #               $trait_props{'trait_format'}='counter';
 104 #       }
 105         elsif ($trait_name =~ m/image/) {
 106                 $trait_props{'trait_format'}='photo';
 107         }
 108         elsif ($trait_name =~ m/([0-9])-([0-9]+)/) {
 109                 print STDERR "matched categorical trait with scale $1 to $2\n";
 110
 111                 if (($2-$1) >= 12) { #leave categorical traits as numeric if they exceed fieldbook's max of 12 categories
 112                         $trait_props{'trait_minimum'}=$1;
 113                         $trait_props{'trait_maximum'}=$2;
 114                 } else {
 115                         $trait_props{'trait_format'}='categorical';
 116                         my $categories;
 117                         foreach (my $i=$1; $i < $2; $i++ ) {
 118                                 $categories .= $i . "/";
 119                         }
 120                         $categories .= $2;
 121                         print STDERR "categories = $categories\n";
 122                         $trait_props{'trait_categories'}= $categories;
 123                 }
 124         }
 125
 126         #change from default numeric based on properties stored in the database
 127   foreach my $property_name (keys %{$cvterms}) {
 128     my $prop_cvterm = $cvterms->{$property_name};
 129     my $prop = $cvtermprops->find({'type_id' => $prop_cvterm->cvterm_id()});
 130     if ($prop  && $prop->value()) {
 131       $trait_props{$property_name}=$prop->value();
 132     }
 133   }
 134
 135   #build trait_info_string
 136   #order for trait file is: format,defaultValue,minimum,maximum,details,categories
 137   $trait_info_string .= '"'.$trait_props{'trait_format'}.'",';
 138   $trait_info_string .= '"'.$trait_props{'trait_default_value'}.'",';
 139   $trait_info_string .= '"'.$trait_props{'trait_minimum'}.'",';
 140   $trait_info_string .= '"'.$trait_props{'trait_maximum'}.'",';
 141   $trait_info_string .= '"'.$trait_props{'trait_details'}.'",';
 142   $trait_info_string .= '"'.$trait_props{'trait_categories'}.'"';
 143
 144   return $trait_info_string;
 145 }
 146
 147 sub _get_cvterms {
 148   my $self = shift;
 149   my $chado_schema = $self->get_chado_schema();
 150   my %cvterms;
 151
 152   my @trait_property_names = qw(
 153                              trait_format
 154                              trait_default_value
 155                              trait_minimum
 156                              trait_maximum
 157                              trait_details
 158                              trait_categories
 159                           );
 160
 161   # my $cv = $chado_schema->resultset("Cv::Cv")
 162   #   ->find_or_create({
 163   #                name => 'trait_property',
 164   #               });
 165   # $cv->insert;
 166
 167   foreach my $property_name (@trait_property_names) {
 168
 169     $cvterms{$property_name} = $chado_schema->resultset("Cv::Cvterm")
 170       ->create_with({
 171                      name   => $property_name,
 172                      cv     => 'trait_property',
 173                     });
 174   }
 175
 176   return \%cvterms;
 177
 178 }
 179
 180
 181 #######
 182 1;
 183 #######