lib/SGN/Controller/solGS/CachedResult.pm

   1 =head1 AUTHOR
   2
   3 Isaak Y Tecle <iyt2@cornell.edu>
   4
   5 =head1 Name
   6
   7 SGN::Controller::solGS::CachedResult - a controller related to cached result.
   8
   9 =cut
  10
  11
  12 package SGN::Controller::solGS::CachedResult;
  13
  14 use Moose;
  15 use namespace::autoclean;
  16 use JSON;
  17
  18
  19 BEGIN { extends 'Catalyst::Controller::REST' }
  20
  21
  22 __PACKAGE__->config(
  23     default   => 'application/json',
  24     stash_key => 'rest',
  25     map       => { 'application/json' => 'JSON',
  26                    'text/html' => 'JSON' },
  27     );
  28
  29
  30 sub check_cached_result :Path('/solgs/check/cached/result') Args(0) {
  31     my ($self, $c) = @_;
  32
  33     my $req_page = $c->req->param('page');
  34     my $args     = $c->req->param('args');
  35     my $json     = JSON->new();
  36     $args        = $json->decode($args);
  37
  38     $self->_check_cached_output($c, $req_page, $args);
  39
  40 }
  41
  42
  43 sub _check_cached_output {
  44     my ($self, $c, $req_page, $args) = @_;
  45
  46     $c->stash->{rest}{cached} = undef;
  47
  48     if ($req_page =~ /solgs\/population\//)
  49     {
  50         my $pop_id = $args->{training_pop_id}[0];
  51
  52         if ($pop_id !~ /uploaded/)
  53         {
  54             $self->_check_single_trial_training_data($c, $pop_id);
  55         }
  56     }
  57     elsif ($req_page =~ /solgs\/populations\/combined\//)
  58     {
  59         my $pop_id = $args->{training_pops_id}[0] || $args->{combo_pops_id}[0];
  60         $c->stash->{data_set_type} = $args->{data_set_type};
  61
  62         $self->_check_combined_trials_data($c, $pop_id);
  63     }
  64     elsif ($req_page =~ /solgs\/trait\//)
  65     {
  66         my $pop_id   = $args->{training_pop_id}[0];
  67         my $trait_id = $args->{trait_id}[0];
  68
  69         $self->_check_single_trial_model_output($c, $pop_id, $trait_id);
  70     }
  71     elsif ($req_page =~ /solgs\/model\/combined\/trials\//)
  72     {
  73         my $pop_id   = $args->{training_pop_id}[0];
  74         my $trait_id = $args->{trait_id}[0];
  75
  76         $c->stash->{data_set_type} = $args->{data_set_type};
  77
  78         $self->_check_combined_trials_model_output($c, $pop_id, $trait_id);
  79     }
  80     elsif ($req_page =~ /solgs\/model\/\d+\/prediction\//)
  81     {
  82         my $tr_pop_id  = $args->{training_pop_id}[0];
  83         my $sel_pop_id = $args->{selection_pop_id}[0];
  84         my $trait_id   = $args->{trait_id}[0];
  85
  86         $c->stash->{data_set_type} = $args->{data_set_type};
  87
  88         my $referer = $c->req->referer;
  89
  90         if ($referer =~ /solgs\/traits\/all\//)
  91         {
  92             $self->_check_selection_pop_all_traits_output($c, $tr_pop_id, $sel_pop_id);
  93         }
  94         elsif ($referer =~ /solgs\/models\/combined\/trials\//)
  95         {
  96           $self->_check_selection_pop_all_traits_output($c, $tr_pop_id, $sel_pop_id);
  97         }
  98         else
  99         {
 100             $self->_check_selection_pop_output($c, $tr_pop_id, $sel_pop_id, $trait_id);
 101         }
 102     }
 103     elsif ($req_page =~ /solgs\/analyze\/traits\/population\//)
 104     {
 105         my $tr_pop_id  = $args->{training_pop_id}[0];
 106         my $sel_pop_id = $args->{selection_pop_id}[0];
 107         my $traits_ids = $args->{trait_id};
 108
 109         $self->_check_single_trial_model_all_traits_output($c, $tr_pop_id, $traits_ids);
 110     }
 111     elsif ($req_page =~ /solgs\/models\/combined\/trials\//)
 112     {
 113         my $tr_pop_id  = $args->{training_pop_id}[0];
 114         my $sel_pop_id = $args->{selection_pop_id}[0];
 115         my $traits     = $args->{trait_id};
 116
 117         $c->stash->{data_set_type} = $args->{data_set_type};
 118
 119         $self->_check_combined_trials_model_all_traits_output($c, $tr_pop_id, $traits);
 120     }
 121
 122 }
 123
 124
 125 sub _check_single_trial_training_data {
 126     my ($self, $c, $pop_id) = @_;
 127
 128     $c->stash->{rest}{cached} = $self->check_single_trial_training_data($c, $pop_id);
 129
 130 }
 131
 132
 133 sub _check_single_trial_model_output {
 134     my ($self, $c, $pop_id, $trait_id) =@_;
 135
 136     my $cached_pop_data  = $self->check_single_trial_training_data($c, $pop_id);
 137
 138     if ($cached_pop_data)
 139     {
 140         $c->stash->{rest}{cached} =  $self->check_single_trial_model_output($c, $pop_id, $trait_id);
 141     }
 142 }
 143
 144
 145 sub _check_single_trial_model_all_traits_output {
 146     my ($self, $c, $pop_id, $traits_ids) =@_;
 147
 148     my $cached_pop_data  = $self->check_single_trial_training_data($c, $pop_id);
 149
 150     $self->check_single_trial_model_all_traits_output($c, $pop_id, $traits_ids);
 151
 152     foreach my $tr (@$traits_ids)
 153     {
 154         my $tr_cache = $c->stash->{$tr}{cached};
 155
 156         if (!$tr_cache)
 157         {
 158             $c->stash->{rest}{cached} = undef;
 159             last;
 160         }
 161         else
 162         {
 163                $c->stash->{rest}{cached} = 1;
 164         }
 165     }
 166 }
 167
 168
 169 sub _check_combined_trials_data {
 170     my ($self, $c, $pop_id) =@_;
 171
 172     $c->stash->{combo_pops_id} = $pop_id;
 173     $c->controller('solGS::combinedTrials')->get_combined_pops_arrayref($c);
 174     my $trials = $c->stash->{arrayref_combined_pops_ids};
 175
 176     foreach my $trial (@$trials)
 177     {
 178         $self->_check_single_trial_training_data($c, $trial);
 179         my $cached = $c->stash->{rest}{cached};
 180
 181         last if !$c->stash->{rest}{cached};
 182     }
 183 }
 184
 185
 186 sub _check_combined_trials_model_output {
 187     my ($self, $c, $pop_id, $trait_id) =@_;
 188
 189     my $cached_pop_data  = $self->check_combined_trials_training_data($c, $pop_id, $trait_id);
 190
 191     if ($cached_pop_data)
 192     {
 193         $c->stash->{rest}{cached} =  $self->check_single_trial_model_output($c, $pop_id, $trait_id);
 194     }
 195
 196 }
 197
 198
 199 sub _check_combined_trials_model_all_traits_output {
 200     my ($self, $c, $pop_id, $traits) = @_;
 201
 202     $self->check_combined_trials_model_all_traits_output($c, $pop_id, $traits);
 203
 204     foreach my $tr (@$traits)
 205     {
 206         my $tr_cache = $c->stash->{$tr}{cached};
 207
 208         if (!$tr_cache)
 209         {
 210             $c->stash->{rest}{cached} = undef;
 211             last;
 212         }
 213         else
 214         {
 215                $c->stash->{rest}{cached} = 1;
 216         }
 217     }
 218
 219 }
 220
 221
 222 sub _check_selection_pop_all_traits_output {
 223     my ($self, $c, $tr_pop_id, $sel_pop_id) =@_;
 224
 225     #$self->check_selection_pop_all_traits_output($c, $tr_pop_id, $sel_pop_id);
 226
 227     $c->controller('solGS::solGS')->prediction_pop_analyzed_traits($c, $tr_pop_id, $sel_pop_id);
 228     my $sel_traits_ids = $c->stash->{prediction_pop_analyzed_traits_ids};
 229
 230     $c->stash->{training_pop_id} = $tr_pop_id;
 231     $c->controller("solGS::solGS")->traits_with_valid_models($c);
 232     my $training_models_traits = $c->stash->{traits_ids_with_valid_models};
 233
 234     if (sort(@$sel_traits_ids) ~~ sort(@$training_models_traits))
 235     {
 236         $c->stash->{rest}{cached} = 1;
 237     }
 238
 239 }
 240
 241
 242 sub _check_selection_pop_output {
 243     my ($self, $c, $tr_pop_id, $sel_pop_id, $trait_id) = @_;
 244
 245     my $data_set_type = $c->stash->{data_set_type};
 246
 247     if ($data_set_type =~ 'combined populations')
 248     {
 249         $self->_check_combined_trials_model_selection_output($c, $tr_pop_id, $sel_pop_id, $trait_id);
 250     }
 251     else
 252     {
 253         $self->_check_single_trial_model_selection_output($c, $tr_pop_id, $sel_pop_id, $trait_id);
 254     }
 255
 256 }
 257
 258
 259 sub _check_single_trial_model_selection_output {
 260     my ($self, $c, $tr_pop_id, $sel_pop_id, $trait_id) = @_;
 261
 262     my $cached_pop_data = $self->check_single_trial_training_data($c, $tr_pop_id);
 263
 264     if ($cached_pop_data)
 265     {
 266         my $cached_model_out = $self->check_single_trial_model_output($c, $tr_pop_id, $trait_id);
 267
 268         if ($cached_model_out)
 269         {
 270             $c->stash->{rest}{cached} = $self->check_selection_pop_output($c, $tr_pop_id, $sel_pop_id, $trait_id);
 271         }
 272     }
 273
 274 }
 275
 276
 277 sub _check_combined_trials_model_selection_output {
 278     my ($self, $c, $tr_pop_id, $sel_pop_id, $trait_id) = @_;
 279
 280     my $cached_tr_data = $self->check_combined_trials_training_data($c, $tr_pop_id, $trait_id);
 281
 282     if ($cached_tr_data)
 283     {
 284         my $cached_model_out = $self->_check_combined_trials_model_output($c, $tr_pop_id, $trait_id);
 285
 286         if ($cached_model_out)
 287         {
 288             $c->stash->{rest}{cached} = $self->check_selection_pop_output($c, $tr_pop_id, $sel_pop_id, $trait_id);
 289         }
 290     }
 291
 292 }
 293
 294
 295 sub check_single_trial_training_data {
 296     my ($self, $c, $pop_id) = @_;
 297
 298     $c->controller('solGS::solGS')->phenotype_file_name($c, $pop_id);
 299     my $cached_pheno = -s $c->stash->{phenotype_file_name};
 300
 301     $c->controller('solGS::solGS')->genotype_file_name($c, $pop_id);
 302     my $cached_geno = -s $c->stash->{genotype_file_name};
 303
 304     if ($cached_pheno && $cached_geno)
 305     {
 306         return  1;
 307     }
 308     else
 309     {
 310         return 0;
 311     }
 312
 313 }
 314
 315
 316 sub check_single_trial_model_output {
 317     my ($self, $c, $pop_id, $trait_id) = @_;
 318
 319     $c->controller('solGS::solGS')->get_trait_details($c, $trait_id);
 320     my $trait_abbr = $c->stash->{trait_abbr};
 321
 322     $c->stash->{trait_abbr} = $trait_abbr;
 323     $c->stash->{pop_id}     = $pop_id;
 324
 325     $c->controller('solGS::solGS')->gebv_kinship_file($c);
 326     my $cached_gebv = -s $c->stash->{gebv_kinship_file};
 327
 328     if ($cached_gebv)
 329     {
 330         return  1;
 331     }
 332     else
 333     {
 334         return 0;
 335     }
 336
 337 }
 338
 339
 340 sub check_single_trial_model_all_traits_output {
 341     my ($self, $c, $pop_id, $traits_ids) =@_;
 342
 343     my $cached_pop_data  = $self->check_single_trial_training_data($c, $pop_id);
 344
 345     if ($cached_pop_data)
 346     {
 347         foreach my $tr (@$traits_ids)
 348         {
 349             $c->stash->{$tr}{cached} = $self->check_single_trial_model_output($c, $pop_id, $tr);
 350         }
 351     }
 352
 353 }
 354
 355
 356 sub check_combined_trials_model_all_traits_output {
 357     my ($self, $c, $pop_id, $traits_ids) =@_;
 358
 359     foreach my $tr (@$traits_ids)
 360     {
 361         my $cached_tr_data = $self->check_combined_trials_training_data($c, $pop_id, $tr);
 362
 363         if ($cached_tr_data)
 364         {
 365             $c->stash->{$tr}{cached} = $self->check_single_trial_model_output($c, $pop_id, $tr);
 366         }
 367     }
 368
 369 }
 370
 371
 372 sub check_selection_pop_output {
 373     my ($self, $c, $tr_pop_id, $sel_pop_id, $trait_id) = @_;
 374
 375     my $identifier = $tr_pop_id . '_' . $sel_pop_id;
 376     $c->controller('solGS::solGS')->prediction_pop_gebvs_file($c, $identifier, $trait_id);
 377
 378     my $cached_gebv = -s $c->stash->{prediction_pop_gebvs_file};
 379
 380     if ($cached_gebv)
 381     {
 382         return  1;
 383     }
 384     else
 385     {
 386         return 0;
 387     }
 388
 389 }
 390
 391
 392 sub check_selection_pop_all_traits_output {
 393     my ($self, $c, $tr_pop_id, $sel_pop_id) =@_;
 394
 395     $c->controller('solGS::solGS')->prediction_pop_analyzed_traits($c, $tr_pop_id, $sel_pop_id);
 396     my $traits_ids = $c->stash->{prediction_pop_analyzed_traits_ids};
 397
 398     foreach my $tr (@$traits_ids)
 399     {
 400         $c->stash->{$tr}{cached} = $self->check_selection_pop_output($c, $tr_pop_id, $sel_pop_id, $tr);
 401     }
 402
 403 }
 404
 405
 406 sub check_combined_trials_training_data {
 407     my ($self, $c, $combo_pops_id, $trait_id) = @_;
 408
 409     $c->controller('solGS::solGS')->get_trait_details($c, $trait_id);
 410      $c->stash->{combo_pops_id} = $combo_pops_id;
 411
 412     $c->controller('solGS::solGS')->cache_combined_pops_data($c);
 413
 414     my $cached_pheno = -s $c->stash->{trait_combined_pheno_file};
 415     my $cached_geno  = -s $c->stash->{trait_combined_geno_file};
 416
 417     if ($cached_pheno && $cached_geno)
 418     {
 419         return  1;
 420     }
 421     else
 422     {
 423         return 0;
 424     }
 425
 426 }
 427
 428
 429 sub begin : Private {
 430     my ($self, $c) = @_;
 431
 432     $c->controller("solGS::solGS")->get_solgs_dirs($c);
 433
 434 }
 435
 436
 437 #####
 438 1;###
 439 ####