lib/SGN/Controller/solGS/Histogram.pm

   1 package SGN::Controller::solGS::Histogram;
   2
   3 use Moose;
   4 use namespace::autoclean;
   5
   6 use Carp qw/ carp confess croak /;
   7 use File::Spec::Functions qw / catfile catdir/;
   8 use File::Path qw / mkpath  /;
   9 use File::Copy;
  10 use File::Basename;
  11 use File::Temp qw / tempfile tempdir /;
  12 use JSON;
  13 use Storable qw/ nstore retrieve /;
  14
  15 BEGIN { extends 'Catalyst::Controller' }
  16
  17
  18 sub trait_pheno_means_data :Path('/trait/pheno/means/data/') Args(0) {
  19     my ($self, $c) = @_;
  20
  21     my $args = $c->req->param('arguments');
  22     $c->controller('solGS::Utils')->stash_json_args($c, $args);
  23
  24     my $trait_id = $c->stash->{'trait_id'};
  25     $c->controller('solGS::Trait')->get_trait_details($c, $c->stash->{trait_id});
  26
  27     my $data = $self->get_trait_pheno_means_data($c);
  28     my $raw_data = $self->get_trait_pheno_raw_data($c);
  29     $c->controller('solGS::solGS')->model_phenotype_stat($c);
  30     my $stat = $c->stash->{descriptive_stat};
  31
  32     my $ret->{status} = 'failed';
  33
  34     if (@$data)
  35     {
  36         $ret->{data} = $data;
  37         $ret->{stat} = $stat;
  38         $ret->{status} = 'success';
  39     }
  40
  41     $ret = to_json($ret);
  42
  43     $c->res->content_type('application/json');
  44     $c->res->body($ret);
  45
  46 }
  47
  48 sub trait_pheno_raw_data :Path('/trait/pheno/raw/data/') Args(0) {
  49     my ($self, $c) = @_;
  50
  51     my $args = $c->req->param('arguments');
  52     $c->controller('solGS::Utils')->stash_json_args($c, $args);
  53
  54     my $trait_id = $c->stash->{'trait_id'};
  55     $c->controller('solGS::Trait')->get_trait_details($c, $c->stash->{trait_id});
  56
  57     my $data = $self->get_trait_pheno_raw_data($c);
  58
  59     $c->controller('solGS::solGS')->model_phenotype_stat($c);
  60     my $stat = $c->stash->{descriptive_stat};
  61
  62     my $ret->{status} = 'failed';
  63
  64     if (@$data)
  65     {
  66         $ret->{data} = $data;
  67         $ret->{stat} = $stat;
  68         $ret->{status} = 'success';
  69     }
  70
  71     $ret = to_json($ret);
  72
  73     $c->res->content_type('application/json');
  74     $c->res->body($ret);
  75
  76 }
  77
  78
  79 sub get_trait_pheno_means_data {
  80     my ($self, $c) = @_;
  81
  82     my $trait_id = $c->stash->{trait_id};
  83     $c->controller('solGS::Trait')->get_trait_details($c, $trait_id);
  84     $c->controller('solGS::Files')->model_phenodata_file($c);
  85     my $model_pheno_file = $c->stash->{model_phenodata_file};
  86
  87     my $data = $c->controller('solGS::Utils')->read_file_data($model_pheno_file);
  88
  89    return $data;
  90
  91 }
  92
  93
  94 sub get_trait_pheno_raw_data {
  95     my ($self, $c) = @_;
  96
  97     my $trait_id = $c->stash->{trait_id};
  98     $c->controller('solGS::Trait')->get_trait_details($c, $trait_id);
  99     $c->controller('solGS::Files')->trait_raw_phenodata_file($c);
 100     my $trait_raw_pheno_file = $c->stash->{trait_raw_phenodata_file};
 101     my $trait_abbr = $c->stash->{trait_abbr};
 102     my @cols = ('observationUnitName', $trait_abbr);
 103     my $data = $c->controller('solGS::Utils')->read_file_data_cols($trait_raw_pheno_file, \@cols);
 104
 105    return $data;
 106
 107 }
 108
 109
 110
 111 sub run_histogram {
 112     my ($self, $c) = @_;
 113
 114     $self->histogram_r_jobs_file($c);
 115     $c->stash->{dependent_jobs} = $c->stash->{histogram_r_jobs_file};
 116
 117     $c->controller('solGS::AsyncJob')->run_async($c);
 118
 119 }
 120
 121
 122 sub histogram_r_jobs {
 123     my ($self, $c) = @_;
 124
 125     my $pop_id = $c->stash->{pop_id} ? $c->stash->{pop_id} : $c->stash->{combo_pops_id};
 126     my $trait_abbr = $c->stash->{trait_abbr};
 127
 128     $c->stash->{analysis_tempfiles_dir} = $c->stash->{histogram_temp_dir};
 129
 130     my $input_file = $self->histogram_input_files($c);
 131     my $output_file = $self->histogram_output_files($c);
 132     #my $trait_file = $c->controller('solGS::Files')->model_phenodata_file($c);
 133
 134     $c->stash->{r_temp_file}  = "histogram-data-${pop_id}-${trait_abbr}";
 135     $c->stash->{r_script}     = 'R/solGS/histogram.r';
 136     $c->stash->{input_file} = $input_file;
 137     $c->stash->{output_file} = $output_file;
 138
 139     $c->controller('solGS::AsyncJob')->get_cluster_r_job_args($c);
 140     my $jobs  = $c->stash->{cluster_r_job_args};
 141
 142     if (reftype $jobs ne 'ARRAY')
 143     {
 144         $jobs = [$jobs];
 145     }
 146
 147     $c->stash->{histogram_r_jobs} = $jobs;
 148
 149 }
 150
 151
 152 sub histogram_r_jobs_file {
 153     my ($self, $c) = @_;
 154
 155     $self->histogram_r_jobs($c);
 156     my $jobs = $c->stash->{histogram_r_jobs};
 157
 158     my $temp_dir = $c->stash->{histogram_temp_dir};
 159     my $jobs_file =  $c->controller('solGS::Files')->create_tempfile($temp_dir, 'histo-r-jobs-file');
 160
 161     nstore $jobs, $jobs_file
 162         or croak "histogram r jobs : $! serializing histogram r jobs to $jobs_file";
 163
 164     $c->stash->{histogram_r_jobs_file} = $jobs_file;
 165
 166 }
 167
 168
 169 sub histogram_input_files {
 170     my ($self, $c) = @_;
 171
 172     my $pop_id = $c->stash->{pop_id} || $c->stash->{combo_pops_id};
 173     my $trait_id = $c->stash->{trait_id};
 174
 175     $c->controller('solGS::Files')->phenotype_file_name($c);
 176     my $pheno_file = $c->stash->{phenotype_file_name};
 177
 178     $self->histogram_traits_file($c);
 179     my $traits_file = $c->stash->{histogram_traits_file};
 180
 181     $c->controller("solGS::Files")->phenotype_metadata_file($c);
 182     my $metadata_file = $c->stash->{phenotype_metadata_file};
 183
 184     my $file_list = join ("\t",
 185                           $pheno_file,
 186                           $traits_file,
 187                           $metadata_file
 188         );
 189
 190     my $tmp_dir = $c->stash->{histogram_temp_dir};
 191     my $name = "histogram_input_files_${pop_id}_${trait_id}";
 192     my $tempfile =  $c->controller('solGS::Files')->create_tempfile($tmp_dir, $name);
 193     write_file($tempfile, {binmode => ':utf8'}, $file_list);
 194
 195     $c->stash->{histogram_input_files} = $tempfile;
 196
 197 }
 198
 199
 200 sub histogram_output_files {
 201     my ($self, $c) = @_;
 202
 203     my $pop_id = $c->stash->{training_pop_id} || $c->stash->{combo_pops_id};
 204     my $trait_id = $c->stash->{trait_id};
 205
 206     $c->controller('solGS::Trait')->get_trait_details($c, $trait_id);
 207
 208     $c->controller('solGS::Files')->trait_raw_phenodata_file($c);
 209     my $raw_pheno_file = $c->stash->{trait_raw_phenodata_file};
 210
 211     my $means_pheno_file = $c->controller('solGS::Files')->model_phenodata_file($c);
 212
 213     my $file_list = join ("\t",
 214                           $raw_pheno_file,
 215                           $means_pheno_file,
 216         );
 217
 218     my $tmp_dir = $c->stash->{histogram_temp_dir};
 219     my $name = "histogram_output_files_${pop_id}_${trait_id}";
 220     my $tempfile =  $c->controller('solGS::Files')->create_tempfile($tmp_dir, $name);
 221     write_file($tempfile, {binmode => ':utf8'}, $file_list);
 222
 223     $c->stash->{histogram_output_files} = $tempfile;
 224
 225 }
 226
 227
 228 sub histogram_traits_file {
 229     my ($self, $c) = @_;
 230
 231     my $pop_id = $c->stash->{pop_id} || $c->stash->{combo_pops_id};
 232
 233     my $traits   = $c->stash->{trait_abbr};
 234
 235     my $tmp_dir = $c->stash->{histogram_temp_dir};
 236     my $name    = "histogram_traits_file_${pop_id}";
 237     my $traits_file =  $c->controller('solGS::Files')->create_tempfile($tmp_dir, $name);
 238     write_file($traits_file, {binmode => ':utf8'}, $traits);
 239
 240     $c->stash->{histogram_traits_file} = $traits_file;
 241
 242 }
 243
 244
 245
 246 sub begin : Private {
 247     my ($self, $c) = @_;
 248
 249     $c->controller('solGS::Files')->get_solgs_dirs($c);
 250
 251 }
 252 ####
 253 1;
 254 ####