lib/SGN/Controller/solGS/Correlation.pm

   1 package SGN::Controller::solGS::Correlation;
   2
   3 use Moose;
   4 use namespace::autoclean;
   5
   6 use Carp qw/ carp confess croak /;
   7 use Cache::File;
   8 use CXGN::Tools::Run;
   9 use File::Temp qw / tempfile tempdir /;
  10 use File::Spec::Functions qw / catfile catdir/;
  11 use File::Slurp qw /write_file read_file/;
  12 use File::Path qw / mkpath  /;
  13 use File::Copy;
  14 use File::Basename;
  15 use CXGN::Phenome::Population;
  16 use JSON;
  17 use Try::Tiny;
  18 use Scalar::Util qw /weaken reftype/;
  19 use Storable qw/ nstore retrieve /;
  20
  21
  22 BEGIN { extends 'Catalyst::Controller' }
  23
  24 sub cluster_analysis : Path('/correlation/analysis/') Args() {
  25     my ( $self, $c, $id ) = @_;
  26
  27     if ( $id && !$c->user ) {
  28         $c->controller('solGS::Utils')->require_login($c);
  29     }
  30
  31     $c->stash->{template} = '/solgs/tools/correlation/analysis.mas';
  32
  33 }
  34
  35
  36 sub pheno_correlation_analysis :Path('/phenotypic/correlation/analysis') Args(0) {
  37     my ($self, $c) = @_;
  38
  39     my $args = $c->req->param('arguments');
  40     $c->controller('solGS::Utils')->stash_json_args($c, $args);
  41
  42     $self->cache_pheno_corr_output_files($c);
  43     my $corre_json_file = $c->stash->{pheno_corr_json_file};
  44
  45     my $ret->{status} = 'Correlation analysis failed.';
  46
  47     if (!-s $corre_json_file)
  48     {
  49             $c->controller('solGS::Utils')->save_metadata($c);
  50         $self->run_correlation_analysis($c);
  51     }
  52
  53     if (-s $corre_json_file)
  54     {
  55         $ret->{status}   = 'success';
  56         $ret->{data}     = read_file($corre_json_file, {binmode => ':utf8'});
  57         $ret->{corre_table_file} = $self->download_pheno_correlation_file($c);
  58     }
  59
  60     $ret = to_json($ret);
  61
  62     $c->res->content_type('application/json');
  63     $c->res->body($ret);
  64
  65 }
  66
  67
  68 sub genetic_correlation_analysis :Path('/genetic/correlation/analysis') Args() {
  69     my ($self, $c) = @_;
  70
  71     my $args = $c->req->param('arguments');
  72     $c->controller('solGS::Utils')->stash_json_args($c, $args);
  73
  74     my $corr_pop_id = $c->stash->{corr_pop_id};
  75     my $pop_type = $c->stash->{pop_type};
  76     $c->stash->{selection_pop_id} = $corr_pop_id if $pop_type =~ /selection/;
  77
  78     $self->cache_genetic_corr_output_files($c);
  79     my $corre_json_file = $c->stash->{genetic_corr_json_file};
  80
  81     if (!-s $corre_json_file)
  82     {
  83         $c->controller('solGS::Gebvs')->run_combine_traits_gebvs($c);
  84     }
  85
  86     $c->controller('solGS::Gebvs')->combined_gebvs_file($c);
  87     my $combined_gebvs_file = $c->stash->{combined_gebvs_file};
  88
  89     my $ret->{status} = undef;
  90     my $json = JSON->new();
  91     if ( !-s $combined_gebvs_file )
  92     {
  93         $ret->{status} = "There is no GEBVs input. Error occured combining the GEBVs of the traits.";
  94     }
  95     else
  96     {
  97         $self->run_correlation_analysis($c);
  98     }
  99
 100     if (-s $corre_json_file)
 101     {
 102         $ret->{status}   = 'success';
 103         $ret->{data}     = read_file($corre_json_file, {binmode => ':utf8'});
 104         $ret->{corre_table_file} = $self->download_genetic_correlation_file($c);
 105     }
 106     else
 107     {
 108         $ret->{status}   = 'There is no correlation output. Error occured running the correlation. ';
 109     }
 110
 111     $ret = $json->encode($ret);
 112     $c->res->content_type('application/json');
 113     $c->res->body($ret);
 114
 115 }
 116
 117 sub cache_pheno_corr_output_files {
 118     my ($self, $c) = @_;
 119
 120     my $pop_id = $c->stash->{corr_pop_id};
 121     my $corre_cache_dir = $c->stash->{correlation_cache_dir};
 122
 123     my $table_cache_data = {key    => 'pheno_corr_table_' . $pop_id,
 124                       file      => "pheno_corr_table_${pop_id}" . '.txt',
 125                       stash_key => 'pheno_corr_table_file',
 126                       cache_dir => $corre_cache_dir
 127     };
 128
 129     $c->controller('solGS::Files')->cache_file($c, $table_cache_data);
 130
 131     my $json_cache_data = {key    => 'pheno_corr_json_' . $pop_id,
 132                       file      => "pheno_corr_json_${pop_id}" . '.txt',
 133                       stash_key => 'pheno_corr_json_file',
 134                       cache_dir => $corre_cache_dir
 135     };
 136
 137    $c->controller('solGS::Files')->cache_file($c, $json_cache_data);
 138
 139 }
 140
 141
 142 sub cache_genetic_corr_output_files {
 143     my ($self, $c) = @_;
 144
 145     my $corr_pop_id = $c->stash->{corr_pop_id};
 146     my $pop_type         = $c->stash->{pop_type};
 147     my $traits_code = $c->stash->{training_traits_code};
 148     my $sindex_name = $c->stash->{sindex_name};
 149
 150     my $model_id    = $c->stash->{training_pop_id};
 151     my $identifier;
 152     if ($sindex_name)
 153     {
 154         $identifier  =  $sindex_name;
 155     }
 156     else
 157     {
 158         $identifier  =  $pop_type =~ /selection/ ? "$model_id-${corr_pop_id}-${traits_code}" :  "${corr_pop_id}-${traits_code}";
 159     }
 160
 161     my $corre_cache_dir = $c->stash->{correlation_cache_dir};
 162
 163     my $table_cache_data = {key    => 'genetic_corr_table_' . $identifier,
 164                       file      => "genetic_corr_table_${identifier}",
 165                       stash_key => 'genetic_corr_table_file',
 166                       cache_dir => $corre_cache_dir
 167     };
 168
 169     $c->controller('solGS::Files')->cache_file($c, $table_cache_data);
 170
 171     my $json_cache_data = {key    => 'genetic_corr_json_' . $identifier,
 172                       file      => "genetic_corr_json_${identifier}",
 173                       stash_key => 'genetic_corr_json_file',
 174                       cache_dir => $corre_cache_dir
 175     };
 176
 177    $c->controller('solGS::Files')->cache_file($c, $json_cache_data);
 178
 179 }
 180
 181
 182 sub download_pheno_correlation_file {
 183     my ($self, $c) = @_;
 184
 185     $self->cache_pheno_corr_output_files($c);
 186     my $file = $c->stash->{pheno_corr_table_file};
 187
 188     $file = $c->controller('solGS::Files')->copy_to_tempfiles_subdir($c, $file, 'correlation');
 189
 190     return $file;
 191 }
 192
 193
 194 sub download_genetic_correlation_file {
 195     my ($self, $c) = @_;
 196
 197     $self->cache_genetic_corr_output_files($c);
 198     my $file = $c->stash->{genetic_corr_table_file};
 199
 200     $file = $c->controller('solGS::Files')->copy_to_tempfiles_subdir($c, $file, 'correlation');
 201
 202     return $file;
 203 }
 204
 205
 206 sub pheno_corr_output_files {
 207     my ($self, $c) = @_;
 208
 209     my $pop_id = $c->stash->{corr_pop_id};
 210     $self->cache_pheno_corr_output_files($c);
 211
 212     my $output_files = join ("\t",
 213                           $c->stash->{pheno_corr_table_file},
 214                           $c->stash->{pheno_corr_json_file},
 215         );
 216
 217     my $tmp_dir = $c->stash->{correlation_temp_dir};
 218     my $name = "pheno_corr_output_files_${pop_id}";
 219     my $tempfile =  $c->controller('solGS::Files')->create_tempfile($tmp_dir, $name);
 220     write_file($tempfile, {binmode => ':utf8'}, $output_files);
 221
 222     $c->stash->{pheno_corr_output_files} = $tempfile;
 223
 224 }
 225
 226
 227 sub pheno_corr_input_files {
 228     my ($self, $c) = @_;
 229
 230     my $pop_id = $c->stash->{corr_pop_id};
 231     my $data_type = $c->stash->{data_type} || 'phenotype';
 232     my $input_files;
 233
 234     if ( $data_type =~ /phenotype/i )
 235     {
 236         $input_files = $c->stash->{phenotype_files_list}
 237         || $c->stash->{phenotype_file_name};
 238
 239         if (!$input_files)
 240         {
 241             if ($c->stash->{data_set_type} =~ /combined_populations/)
 242             {
 243                 $c->controller('solGS::combinedTrials')->get_combined_pops_list( $c, $pop_id );
 244                 $c->controller('solGS::combinedTrials')->multi_pops_pheno_files($c, $c->stash->{combined_pops_list});
 245             }
 246             else
 247             {
 248                 $c->controller('solGS::Files')->phenotype_file_name( $c, $pop_id);
 249             }
 250         }
 251         $c->controller('solGS::Files')->phenotype_metadata_file($c);
 252         my $metadata_file = $c->stash->{phenotype_metadata_file};
 253         $input_files .= "\t" . $metadata_file;
 254     }
 255
 256     my $tmp_dir = $c->stash->{correlation_temp_dir};
 257     my $name = "pheno_corr_input_files_${pop_id}";
 258     my $tempfile =  $c->controller('solGS::Files')->create_tempfile($tmp_dir, $name);
 259     write_file($tempfile, {binmode => ':utf8'}, $input_files);
 260     $c->stash->{pheno_corr_input_files} = $tempfile;
 261
 262 }
 263
 264
 265 sub geno_corr_output_files {
 266     my ($self, $c) = @_;
 267
 268     my $pop_id = $c->stash->{corr_pop_id};
 269     $self->cache_genetic_corr_output_files($c);
 270
 271     my $output_files = join ("\t",
 272         $c->stash->{genetic_corr_table_file},
 273         $c->stash->{genetic_corr_json_file},
 274         );
 275
 276     my $tmp_dir = $c->stash->{correlation_temp_dir};
 277     my $name = "genetic_corr_output_files_${pop_id}";
 278     my $tempfile =  $c->controller('solGS::Files')->create_tempfile($tmp_dir, $name);
 279     write_file($tempfile, {binmode => ':utf8'}, $output_files);
 280
 281     $c->stash->{geno_corr_output_files} = $tempfile;
 282
 283 }
 284
 285
 286 sub geno_corr_input_files {
 287     my ($self, $c) = @_;
 288
 289     my $pop_id = $c->stash->{corr_pop_id};
 290     my $gebvs_file = $c->stash->{combined_gebvs_file};
 291     my $index_file = $c->stash->{selection_index_file};
 292
 293     my $input_files = join ("\t",
 294                       $gebvs_file,
 295                       $index_file
 296         );
 297
 298     my $tmp_dir = $c->stash->{correlation_temp_dir};
 299     my $name = "genetic_corr_input_files_${pop_id}";
 300     my $tempfile =  $c->controller('solGS::Files')->create_tempfile($tmp_dir, $name);
 301     write_file($tempfile, {binmode => ':utf8'}, $input_files);
 302
 303     $c->stash->{geno_corr_input_files} = $tempfile;
 304
 305 }
 306
 307 sub corr_input_files {
 308     my ($self, $c) = @_;
 309
 310      $c->stash->{correlation_script} = "R/solGS/correlation.r";
 311     if ($c->stash->{correlation_type} =~ /pheno/)
 312     {
 313     $self->pheno_corr_input_files($c);
 314     $c->stash->{corre_input_files}  = $c->stash->{pheno_corr_input_files};
 315     }
 316     elsif ($c->stash->{correlation_type} =~ /genetic/)
 317     {
 318     $self->geno_corr_input_files($c);
 319     $c->stash->{corre_input_files}  = $c->stash->{geno_corr_input_files};
 320     }
 321
 322 }
 323
 324 sub corr_output_files {
 325     my ($self, $c) = @_;
 326
 327     if ($c->stash->{correlation_type} =~ /pheno/)
 328     {
 329     $self->pheno_corr_output_files($c);
 330     $c->stash->{corre_output_files} = $c->stash->{pheno_corr_output_files};
 331     }
 332     elsif ($c->stash->{correlation_type} =~ /genetic/)
 333     {
 334     $self->geno_corr_output_files($c);
 335     $c->stash->{corre_output_files} = $c->stash->{geno_corr_output_files};
 336     }
 337
 338 }
 339
 340 sub run_correlation_analysis {
 341     my ($self, $c) = @_;
 342
 343     my $queries_file;
 344     if ($c->stash->{correlation_type} =~ /pheno/)
 345     {
 346         $self->corr_query_jobs_file($c);
 347         $queries_file = $c->stash->{corr_query_jobs_file};
 348     }
 349
 350     $self->corr_r_jobs_file($c);
 351     my $r_jobs_file = $c->stash->{corr_r_jobs_file};
 352     $c->stash->{prerequisite_jobs} = $queries_file if $queries_file;
 353     $c->stash->{dependent_jobs} = $r_jobs_file;
 354
 355     $c->controller('solGS::AsyncJob')->run_async($c);
 356
 357 }
 358
 359
 360 sub corr_r_jobs {
 361     my ($self, $c) = @_;
 362
 363     $self->corr_input_files($c);
 364     $c->stash->{input_files} = $c->stash->{corre_input_files};
 365
 366     $self->corr_output_files($c);
 367     $c->stash->{output_files} = $c->stash->{corre_output_files};
 368
 369     my $corre_type = $c->stash->{correlation_type};
 370     my $pop_id = $c->stash->{corr_pop_id};
 371
 372     $c->stash->{r_temp_file}  = "${corre_type}-${pop_id}";
 373     $c->stash->{r_script}     = $c->stash->{correlation_script};
 374
 375     $c->stash->{analysis_tempfiles_dir} = $c->stash->{correlation_temp_dir};
 376
 377     $c->controller('solGS::AsyncJob')->get_cluster_r_job_args($c);
 378     my $jobs  = $c->stash->{cluster_r_job_args};
 379
 380     if (reftype $jobs ne 'ARRAY')
 381     {
 382         $jobs = [$jobs];
 383     }
 384
 385     $c->stash->{corr_r_jobs} = $jobs;
 386
 387 }
 388
 389
 390 sub corr_r_jobs_file {
 391     my ($self, $c) = @_;
 392
 393     $self->corr_r_jobs($c);
 394     my $jobs = $c->stash->{corr_r_jobs};
 395
 396     my $temp_dir = $c->stash->{correlation_temp_dir};
 397     my $jobs_file =  $c->controller('solGS::Files')->create_tempfile($temp_dir, 'corre-r-jobs-file');
 398
 399     nstore $jobs, $jobs_file
 400         or croak "correlation r jobs : $! serializing correlation r jobs to $jobs_file";
 401
 402     $c->stash->{corr_r_jobs_file} = $jobs_file;
 403
 404 }
 405
 406 sub corr_query_jobs {
 407     my ($self, $c) = @_;
 408
 409     my $corr_pop_id = $c->stash->{corr_pop_id};
 410     my $data_set_type = $c->stash->{data_set_type};
 411     my $data_str = $c->stash->{data_structure};
 412     my $trials_ids = [];
 413
 414     my $jobs = $c->controller('solGS::AsyncJob')->create_phenotype_data_query_jobs($c, $corr_pop_id);
 415
 416     if (reftype $jobs ne 'ARRAY')
 417     {
 418             $jobs = [$jobs];
 419     }
 420
 421     $c->stash->{corr_query_jobs} = $jobs;
 422
 423 }
 424
 425
 426 sub corr_query_jobs_file {
 427     my ($self, $c) = @_;
 428
 429     $self->corr_query_jobs($c);
 430     my $jobs = $c->stash->{corr_query_jobs};
 431
 432     my $corr_type = $c->stash->{correlation_type};
 433     my $jobs_file;
 434
 435     if ($jobs->[0])
 436     {
 437         my $temp_dir = $c->stash->{correlation_temp_dir};
 438         $jobs_file =  $c->controller('solGS::Files')->create_tempfile($temp_dir, "${corr_type}-query-jobs-file");
 439
 440         nstore $jobs, $jobs_file
 441             or croak "correlation pheno query jobs : $! serializing correlation ${corr_type} query jobs to $jobs_file";
 442     }
 443
 444     $c->stash->{corr_query_jobs_file} = $jobs_file;
 445
 446 }
 447
 448
 449 sub begin : Private {
 450     my ($self, $c) = @_;
 451
 452     $c->controller('solGS::Files')->get_solgs_dirs($c);
 453
 454 }
 455
 456
 457
 458 ####
 459 1;
 460 ####