lib/SGN/Controller/solGS/Download.pm

   1 package SGN::Controller::solGS::Download;
   2
   3
   4 use Moose;
   5 use namespace::autoclean;
   6
   7
   8 BEGIN { extends 'Catalyst::Controller::REST' }
   9
  10
  11 __PACKAGE__->config(
  12     default   => 'application/json',
  13     stash_key => 'rest',
  14     map       => { 'application/json' => 'JSON' },
  15     );
  16
  17
  18 sub download_training_pop_data :Path('/solgs/download/training/pop/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         $c->stash->{rest}{training_pop_raw_geno_file} = $self->download_raw_geno_data_file($c);
  25         $c->stash->{rest}{training_pop_raw_pheno_file} = $self->download_raw_pheno_data_file($c);
  26         $c->stash->{rest}{traits_acronym_file} = $self->download_traits_acronym_file($c);
  27
  28 }
  29
  30
  31 sub download_selection_pop_data :Path('/solgs/download/selection/pop/data') Args(0) {
  32         my ($self, $c) = @_;
  33
  34         my $args = $c->req->param('arguments');
  35     $c->controller('solGS::Utils')->stash_json_args($c, $args);
  36
  37         my $geno_file = $self->download_selection_pop_filtered_geno_data_file($c);
  38         my $log_file = $self->download_selection_prediction_report_file($c);
  39
  40         $c->stash->{rest}{selection_pop_filtered_geno_file} = $geno_file;
  41         $c->stash->{rest}{selection_prediction_report_file} = $log_file;
  42 }
  43
  44 sub download_model_input_data :Path('/solgs/download/model/input/data') Args(0) {
  45         my ($self, $c) = @_;
  46
  47         my $args = $c->req->param('arguments');
  48     $c->controller('solGS::Utils')->stash_json_args($c, $args);
  49
  50         my $geno_file = $self->download_model_geno_data_file($c);
  51         my $pheno_file = $self->download_model_pheno_data_file($c);
  52         my $log_file = $self->download_model_analysis_report_file($c);
  53
  54         $c->stash->{rest}{model_geno_data_file} = $geno_file;
  55         $c->stash->{rest}{model_pheno_data_file} = $pheno_file;
  56         $c->stash->{rest}{model_analysis_report_file} = $log_file;
  57
  58 }
  59
  60
  61 sub download_gebvs :Path('/solgs/download/gebvs/pop') Args(0) {
  62     my ($self, $c) = @_;
  63
  64         my $args = $c->req->param('arguments');
  65     $c->controller('solGS::Utils')->stash_json_args($c, $args);
  66
  67         my $gebvs_file;
  68         my $type;
  69         if ($c->stash->{selection_pop_id})
  70         {
  71                 $type = 'selection';
  72                 $gebvs_file = $self->download_selection_gebvs_file($c);
  73         }
  74         else
  75         {
  76                 $type = 'training';
  77                 $gebvs_file = $self->download_training_gebvs_file($c);
  78         }
  79
  80         my $file_id = $c->controller('solGS::Files')->gebvs_file_id($c, $type);
  81
  82         $c->stash->{rest}{gebvs_file} = $gebvs_file;
  83         $c->stash->{rest}{gebvs_file_id} = $file_id;
  84
  85 }
  86
  87
  88 sub download_marker_effects :Path('/solgs/download/model/marker/effects') Args(0) {
  89     my ($self, $c) = @_;
  90
  91     my $args = $c->req->param('arguments');
  92     $c->controller('solGS::Utils')->stash_json_args($c, $args);
  93
  94         my $marker_effects_file = $self->download_marker_effects_file($c);
  95         $c->stash->{rest}{marker_effects_file} = $marker_effects_file;
  96
  97 }
  98
  99 sub download_traits_acronym :Path('/solgs/download/traits/acronym') Args(0) {
 100     my ($self, $c) = @_;
 101
 102     my $args = $c->req->param('arguments');
 103     $c->controller('solGS::Utils')->stash_json_args($c, $args);
 104
 105         my $acronyms_file = $self->download_traits_acronym_file($c);
 106         $c->stash->{rest}{traits_acronym_file} = $acronyms_file;
 107
 108 }
 109
 110
 111 sub selection_prediction_download_urls {
 112     my ($self, $c, $training_pop_id, $selection_pop_id) = @_;
 113
 114     my $selected_model_traits = $c->stash->{training_traits_ids} || [$c->stash->{trait_id}];
 115     my $protocol_id = $c->stash->{genotyping_protocol_id};
 116
 117     no warnings 'uninitialized';
 118
 119         my $url_args = {
 120           'training_pop_id' => $training_pop_id,
 121           'selection_pop_id' => $selection_pop_id,
 122           'genotyping_protocol_id' => $protocol_id,
 123         };
 124
 125         my $selection_traits_ids;
 126
 127     if ($selection_pop_id)
 128     {
 129         $c->controller('solGS::Gebvs')->selection_pop_analyzed_traits($c, $training_pop_id, $selection_pop_id);
 130         $selection_traits_ids = $c->stash->{selection_pop_analyzed_traits_ids};
 131     }
 132
 133     my @selection_traits_ids = sort(@$selection_traits_ids) if $selection_traits_ids->[0];
 134     my @selected_model_traits = sort(@$selected_model_traits) if $selected_model_traits->[0];
 135
 136         my $page = $c->req->referer;
 137         my $data_set_type = $page =~ /combined/ ? 'combined_populations' : 'single_population';
 138         $url_args->{data_set_type} = $data_set_type;
 139
 140         my $sel_pop_page;
 141         my $download_url;
 142
 143     if (@selected_model_traits ~~ @selection_traits_ids)
 144     {
 145                 foreach my $trait_id (@selection_traits_ids)
 146                 {
 147
 148                         $url_args->{trait_id} = $trait_id;
 149
 150                     $c->controller('solGS::Trait')->get_trait_details($c, $trait_id);
 151                     my $trait_abbr = $c->stash->{trait_abbr};
 152
 153                         $sel_pop_page =  $c->controller('solGS::Path')->selection_page_url($url_args);
 154
 155                         if ($page =~ /solgs\/traits\/all\/|solgs\/models\/combined\//)
 156                     {
 157                                 $download_url .= " | " if $download_url;
 158                     }
 159
 160                         $download_url .= qq |<a href="$sel_pop_page">$trait_abbr</a> |;
 161                 }
 162     }
 163
 164     if (!$download_url)
 165     {
 166                 my $trait_id = $selected_model_traits[0];
 167                 $url_args->{trait_id} = $trait_id;
 168
 169                 $sel_pop_page =  $c->controller('solGS::Path')->selection_page_url($url_args);
 170                 $download_url = qq | <a href ="$sel_pop_page"  onclick="solGS.waitPage(this.href); return false;">[ Predict ]</a>|;
 171     }
 172
 173     $c->stash->{selection_prediction_download} = $download_url;
 174
 175 }
 176
 177 sub download_raw_pheno_data_file {
 178         my ($self, $c) = @_;
 179
 180         my $pop_id = $c->stash->{training_pop_id};
 181         my $data_set_type = $c->stash->{data_set_type};
 182
 183         my @trials_ids;
 184         if ($data_set_type =~ /combined_populations/)
 185         {
 186                 my $trials_ids = $c->controller('solGS::combinedTrials')->get_combined_pops_list($c, $pop_id);
 187                 @trials_ids = @$trials_ids;
 188         }
 189         else
 190         {
 191                 push @trials_ids, $pop_id;
 192         }
 193
 194         my @files;
 195
 196         foreach my $trial_id (@trials_ids)
 197         {
 198                 my $file = $c->controller('solGS::Files')->phenotype_file_name($c, $trial_id);
 199                 $file = $c->controller('solGS::Files')->copy_to_tempfiles_subdir($c, $file, 'solgs');
 200
 201                 push @files, $file;
 202         }
 203
 204         return \@files;
 205
 206 }
 207
 208
 209 sub download_raw_geno_data_file {
 210         my ($self, $c) = @_;
 211
 212         my $pop_id = $c->stash->{training_pop_id};
 213         my $protocol_id = $c->stash->{genotyping_protocol_id};
 214         my $data_set_type = $c->stash->{data_set_type};
 215
 216         my @trials_ids;
 217         if ($data_set_type =~ /combined_populations/)
 218         {
 219                 my $trials_ids = $c->controller('solGS::combinedTrials')->get_combined_pops_list($c, $pop_id);
 220                 @trials_ids = @$trials_ids;
 221         }
 222         else
 223         {
 224                 push @trials_ids, $pop_id;
 225         }
 226
 227         my @files;
 228
 229         foreach my $trial_id (@trials_ids)
 230         {
 231                 my $file = $c->controller('solGS::Files')->genotype_file_name($c, $trial_id, $protocol_id);
 232                 $file = $c->controller('solGS::Files')->copy_to_tempfiles_subdir($c, $file, 'solgs');
 233
 234                 push @files, $file;
 235         }
 236
 237         return \@files;
 238
 239 }
 240
 241 sub download_selection_pop_filtered_geno_data_file {
 242         my ($self, $c) = @_;
 243
 244         $c->controller('solGS::Files')->filtered_selection_genotype_file($c);
 245         my $file = $c->stash->{filtered_selection_genotype_file};
 246         $file = $c->controller('solGS::Files')->copy_to_tempfiles_subdir($c, $file, 'solgs');
 247
 248         return $file;
 249
 250 }
 251
 252
 253 sub download_model_geno_data_file {
 254         my ($self, $c) = @_;
 255
 256         $c->controller('solGS::Trait')->get_trait_details($c, $c->stash->{trait_id});
 257
 258         my $file = $c->controller('solGS::Files')->model_genodata_file($c);
 259         $file = $c->controller('solGS::Files')->copy_to_tempfiles_subdir($c, $file, 'solgs');
 260
 261         return $file;
 262
 263 }
 264
 265
 266 sub download_model_pheno_data_file {
 267         my ($self, $c) = @_;
 268
 269         $c->controller('solGS::Trait')->get_trait_details($c, $c->stash->{trait_id});
 270
 271         my $file = $c->controller('solGS::Files')->model_phenodata_file($c);
 272         $file = $c->controller('solGS::Files')->copy_to_tempfiles_subdir($c, $file, 'solgs');
 273
 274         return $file;
 275
 276 }
 277
 278 sub download_model_analysis_report_file {
 279         my ($self, $c) = @_;
 280
 281         $c->controller('solGS::Trait')->get_trait_details($c, $c->stash->{trait_id});
 282
 283         my $page = $c->controller('solGS::Path')->page_type($c, $c->req->referer);
 284
 285         if ($page =~ /training_model/)
 286         {
 287                 $c->stash->{analysis_type} =  'training_model';
 288         }
 289
 290         my $file = $c->controller('solGS::Files')->analysis_report_file($c);
 291         #$file = $c->controller('solGS::Files')->convert_txt_pdf($file);
 292
 293         $file = $c->controller('solGS::Files')->copy_to_tempfiles_subdir($c, $file, 'solgs');
 294
 295         return $file;
 296
 297 }
 298
 299 sub download_selection_prediction_report_file {
 300         my ($self, $c) = @_;
 301
 302         $c->controller('solGS::Trait')->get_trait_details($c, $c->stash->{trait_id});
 303
 304         my $referer = $c->req->referer;
 305         $c->stash->{analysis_type} = $c->controller('solGS::Path')->page_type($c, $referer);
 306
 307         my $file = $c->controller('solGS::Files')->analysis_report_file($c);
 308         $file = $c->controller('solGS::Files')->copy_to_tempfiles_subdir($c, $file, 'solgs');
 309
 310         return $file;
 311
 312 }
 313
 314 sub download_training_gebvs_file {
 315         my ($self, $c) = @_;
 316
 317         my $training_pop_id = $c->stash->{training_pop_id};
 318         my $trait_id = $c->stash->{trait_id};
 319         my $protocol_id = $c->stash->{genotyping_protocol_id};
 320
 321         $c->controller('solGS::Files')->rrblup_training_gebvs_file($c, $training_pop_id, $trait_id, $protocol_id);
 322         my $gebvs_file = $c->stash->{rrblup_training_gebvs_file};
 323
 324         $gebvs_file = $c->controller('solGS::Files')->copy_to_tempfiles_subdir($c, $gebvs_file, 'solgs');
 325
 326         return $gebvs_file;
 327
 328 }
 329
 330
 331 sub download_selection_gebvs_file {
 332         my ($self, $c) = @_;
 333
 334         my $training_pop_id = $c->stash->{training_pop_id};
 335         my $selection_pop_id = $c->stash->{selection_pop_id};
 336         my $trait_id = $c->stash->{trait_id};
 337         my $protocol_id = $c->stash->{genotyping_protocol_id};
 338
 339         $c->controller('solGS::Files')->rrblup_selection_gebvs_file($c, $training_pop_id, $selection_pop_id, $trait_id, $protocol_id);
 340         my $gebvs_file = $c->stash->{rrblup_selection_gebvs_file};
 341
 342         $gebvs_file = $c->controller('solGS::Files')->copy_to_tempfiles_subdir($c, $gebvs_file, 'solgs');
 343
 344         return $gebvs_file;
 345
 346 }
 347
 348
 349 sub download_marker_effects_file {
 350         my ($self, $c) = @_;
 351
 352         $c->controller('solGS::Trait')->get_trait_details($c, $c->stash->{trait_id});
 353
 354         my $file = $c->controller('solGS::Files')->marker_effects_file($c);
 355         $file = $c->controller('solGS::Files')->copy_to_tempfiles_subdir($c, $file, 'solgs');
 356
 357         return $file;
 358 }
 359
 360 sub download_traits_acronym_file {
 361         my ($self, $c) = @_;
 362
 363
 364          $c->controller('solGS::Files')->traits_acronym_file($c, $c->stash->{training_pop_id});
 365     my $file = $c->stash->{traits_acronym_file};
 366
 367         $file = $c->controller('solGS::Files')->copy_to_tempfiles_subdir($c, $file, 'solgs');
 368
 369         return $file;
 370 }
 371
 372 sub begin : Private {
 373     my ($self, $c) = @_;
 374
 375     $c->controller('solGS::Files')->get_solgs_dirs($c);
 376
 377 }
 378
 379 #####
 380 1;
 381 #####