lib/CXGN/Dataset/File.pm

   1
   2 package CXGN::Dataset::File;
   3
   4 use Moose;
   5 use File::Slurp qw | write_file |;
   6 use JSON::Any;
   7
   8 extends 'CXGN::Dataset';
   9
  10 has 'file_name' => ( isa => 'Str',
  11                      is => 'rw',
  12                      default => '/tmp/dataset_file',
  13     );
  14
  15 override('retrieve_genotypes',
  16          sub {
  17              my $self = shift;
  18              my $protocol_id = shift;
  19              my $file = shift || $self->file_name()."_genotype.txt";
  20              my $genotypes = $self->SUPER::retrieve_genotypes($protocol_id);
  21              my $genotype_string = "";
  22              my $genotype_example = $genotypes->[0];
  23              foreach my $key (sort keys %{$genotype_example->{genotype_hash}}) {
  24                  $genotype_string .= $key."\t";
  25              }
  26              $genotype_string .= "\n";
  27              foreach my $element (@$genotypes) {
  28                  my $genotype_id = $element->{germplasmDbId};
  29                  my $genotype_data_string = "";
  30                  foreach my $key (sort keys %{$element->{genotype_hash}}) {
  31                      my $value = $element->{genotype_hash}->{$key};
  32                      my $current_genotype = $value;
  33                      $genotype_data_string .= $current_genotype."\t";
  34                  }
  35                  my $s = join "\t", $genotype_id;
  36                  $genotype_string .= $s."\t".$genotype_data_string."\n";
  37              }
  38              write_file($file, $genotype_string);
  39
  40
  41 #            my $genotype_json = JSON::Any->encode($genotypes);
  42 #            write_file($file, $genotype_json);
  43              return $genotypes;
  44          });
  45
  46 override('retrieve_phenotypes',
  47          sub {
  48              my $self = shift;
  49              my $file = shift || $self->file_name()."_phenotype.txt";
  50              my $phenotypes = $self->SUPER::retrieve_phenotypes();
  51              my $phenotype_string = "";
  52              foreach my $line (@$phenotypes) {
  53                  my $s = join "\t", @$line;
  54                  $phenotype_string .= $s."\n";
  55              }
  56              write_file($file, $phenotype_string);
  57              return $phenotypes;
  58          });
  59
  60 override('retrieve_accessions',
  61          sub {
  62              my $self = shift;
  63              my $file = shift || $self->file_name()."_accessions.txt";
  64              my $accessions = $self->SUPER::retrieve_accessions();
  65              my $accession_json = JSON::Any->encode($accessions);
  66              write_file($file, $accession_json);
  67              return $accessions;
  68          });
  69
  70 override('retrieve_plots',
  71          sub {
  72              my $self = shift;
  73              my $file = shift || $self->file_name()."_plots.txt";
  74              my $plots = $self->SUPER::retrieve_plots();
  75              my $plot_json = JSON::Any->encode($plots);
  76              write_file($file, $plot_json);
  77              return $plots;
  78          });
  79
  80 override('retrieve_trials',
  81          sub {
  82              my $self = shift;
  83              my $file = shift || $self->file_name()."_trials.txt";
  84              my $trials = $self->SUPER::retrieve_trials();
  85              my $trial_json = JSON::Any->encode($trials);
  86              write_file($file, $trial_json);
  87              return $trials;
  88          });
  89
  90 override('retrieve_traits',
  91          sub {
  92              my $self = shift;
  93              my $file = shift || $self->file_name()."_traits.txt";
  94              my $traits = $self->SUPER::retrieve_traits();
  95              my $trait_json = JSON::Any->encode($traits);
  96              write_file($file, $trait_json);
  97              return $traits;
  98          });
  99
 100 override('retrieve_years',
 101          sub {
 102              my $self = shift;
 103              my $file = shift || $self->file_name()."_years.txt";
 104              my $years = $self->SUPER::retrieve_years();
 105              my $year_json = JSON::Any->encode($years);
 106              write_file($file, $year_json);
 107              return $years;
 108          });
 109
 110 1;