lib/SGN/Controller/solGS/Histogram.pm

   1 package SGN::Controller::solGS::Histogram;
   2
   3 use Moose;
   4 use namespace::autoclean;
   5 use CXGN::Tools::Run;
   6 use File::Spec::Functions qw / catfile catdir/;
   7 use File::Path qw / mkpath  /;
   8 use File::Copy;
   9 use File::Basename;
  10 use File::Temp qw / tempfile tempdir /;
  11 use JSON;
  12 use Try::Tiny;
  13
  14 BEGIN { extends 'Catalyst::Controller' }
  15
  16
  17 sub histogram_phenotype_data :Path('/histogram/phenotype/data/') Args(0) {
  18     my ($self, $c) = @_;
  19
  20     my $pop_id   = $c->req->param('population_id');
  21     my $trait_id = $c->req->param('trait_id');
  22     my $referer  = $c->req->referer;
  23
  24     if ($referer =~ /combined/)
  25     {
  26         $c->stash->{data_set_type} = 'combined populations';
  27         $c->stash->{combo_pops_id} = $pop_id;
  28     }
  29
  30     $c->stash->{pop_id} = $pop_id;
  31
  32     $c->controller('solGS::solGS')->get_trait_details($c, $trait_id);
  33     my $trait_abbr = $c->stash->{trait_abbr};
  34
  35     $c->controller('solGS::solGS')->trait_phenodata_file($c);
  36     my $trait_pheno_file = $c->stash->{trait_phenodata_file};
  37     $c->stash->{histogram_trait_file} = $c->stash->{trait_phenodata_file};
  38
  39     if (!$trait_pheno_file || -z $trait_pheno_file)
  40     {
  41         $self->create_population_phenotype_data($c);
  42     }
  43
  44     unless (!$c->stash->{phenotype_file} || -s $trait_pheno_file)
  45     {
  46         $self->create_trait_phenodata($c);
  47     }
  48
  49     my $data = $self->format_plot_data($c);
  50
  51     $c->controller('solGS::solGS')->trait_phenotype_stat($c);
  52     my $stat = $c->stash->{descriptive_stat};
  53
  54     my $ret->{status} = 'failed';
  55
  56     if (@$data)
  57     {
  58         $ret->{data} = $data;
  59         $ret->{stat} = $stat;
  60         $ret->{status} = 'success';
  61     }
  62
  63     $ret = to_json($ret);
  64
  65     $c->res->content_type('application/json');
  66     $c->res->body($ret);
  67
  68 }
  69
  70
  71 sub format_plot_data {
  72    my ($self, $c) = @_;
  73
  74    my $file = $c->stash->{histogram_trait_file};
  75    my $data = $c->controller('solGS::solGS')->convert_to_arrayref_of_arrays($c, $file);
  76
  77    return $data;
  78
  79 }
  80
  81
  82 sub create_population_phenotype_data {
  83     my ($self, $c) = @_;
  84
  85     $c->controller("solGS::solGS")->phenotype_file($c);
  86
  87 }
  88
  89
  90 sub create_histogram_dir {
  91     my ($self, $c) = @_;
  92
  93     $c->controller("solGS::solGS")->get_solgs_dirs($c);
  94 }
  95
  96
  97 sub create_trait_phenodata {
  98     my ($self, $c) = @_;
  99
 100     my $combo_id = $c->stash->{combo_pops_id};
 101
 102     my $pop_id = $c->stash->{pop_id} ? $c->stash->{pop_id} : $c->stash->{combo_pops_id};
 103
 104     $self->create_histogram_dir($c);
 105     my $histogram_dir = $c->stash->{histogram_dir};
 106
 107     my $pheno_file = $c->stash->{phenotype_file};
 108     my $trait_file = $c->controller("solGS::solGS")->trait_phenodata_file($c);
 109     my $trait_abbr = $c->stash->{trait_abbr};
 110
 111     if (-s $pheno_file)
 112     {
 113         CXGN::Tools::Run->temp_base($histogram_dir);
 114
 115         my ( $histogram_commands_temp, $histogram_output_temp ) =
 116             map
 117         {
 118             my (undef, $filename ) =
 119                 tempfile(
 120                     catfile(
 121                         CXGN::Tools::Run->temp_base(),
 122                         "histogram_analysis_${pop_id}_${trait_abbr}-$_-XXXXXX",
 123                          ),
 124                 );
 125             $filename
 126         } qw / in out /;
 127
 128         {
 129             my $histogram_commands_file = $c->path_to('/R/histogram.r');
 130             copy( $histogram_commands_file, $histogram_commands_temp )
 131             or die "could not copy '$histogram_commands_file' to '$histogram_commands_temp'";
 132         }
 133         try
 134         {
 135             print STDERR "\nsubmitting histogram job to the cluster..\n";
 136             my $r_process = CXGN::Tools::Run->run_cluster(
 137                 'R', 'CMD', 'BATCH',
 138                 '--slave',
 139                 "--args  input_file=$pheno_file trait_name=$trait_abbr output_file=$trait_file",
 140                 $histogram_commands_temp,
 141                 $histogram_output_temp,
 142                 {
 143                     working_dir => $histogram_dir,
 144                     max_cluster_jobs => 1_000_000_000,
 145                 },
 146                 );
 147
 148             $r_process->wait;
 149             print STDERR "\ndone with histogram analysis..\n";
 150         }
 151         catch
 152         {
 153             my $err = $_;
 154             $err =~ s/\n at .+//s; #< remove any additional backtrace
 155             #     # try to append the R output
 156             try
 157             {
 158                 $err .= "\n=== R output ===\n".file($histogram_output_temp)->slurp."\n=== end R output ===\n"
 159             };
 160
 161             $c->stash->{script_error} =  "There is a problem running the histogram r script on this dataset.";
 162
 163         };
 164
 165         $c->stash->{histogram_trait_file} = $trait_file;
 166     }
 167     else
 168     {
 169         $c->stash->{script_error} =  "There is no phenotype for this trait.";
 170     }
 171
 172 }
 173
 174
 175 sub begin : Private {
 176     my ($self, $c) = @_;
 177
 178     $c->controller("solGS::solGS")->get_solgs_dirs($c);
 179
 180 }
 181 ####
 182 1;
 183 ####