lib/solGS/AnalysisReport.pm

   1 package solGS::AnalysisReport;
   2
   3 use Moose;
   4 use namespace::autoclean;
   5
   6 use Email::Sender::Simple qw /sendmail/;
   7 use Email::Simple;
   8 use Email::Simple::Creator;
   9 use File::Spec::Functions qw /catfile catdir/;
  10 use File::Slurp qw /write_file read_file/;
  11 use Storable qw/ nstore retrieve /;
  12
  13
  14 with 'MooseX::Getopt';
  15 with 'MooseX::Runnable';
  16
  17 has 'output_details_file' => (
  18     is       => 'ro',
  19     isa      => 'Str',
  20     required => 1,
  21     );
  22
  23
  24
  25 sub run {
  26  my $self = shift;
  27
  28  my $output_details = retrieve($self->output_details_file);
  29  $self->check_analysis_status($output_details);
  30
  31 }
  32
  33
  34 sub check_analysis_status {
  35     my ($self, $output_details) = @_;
  36
  37     $output_details = $self->check_success($output_details);
  38
  39     $self->log_analysis_status($output_details);
  40     $self->report_status($output_details);
  41
  42 }
  43
  44
  45 sub check_success {
  46     my ($self, $output_details) = @_;
  47
  48     my $analysis_profile = $output_details->{analysis_profile};
  49
  50     if ( $analysis_profile->{analysis_type} =~ /population download/ )
  51     {
  52         $output_details = $self->check_population_download($output_details);
  53     }
  54     elsif ( $analysis_profile->{analysis_type} =~ /(single|multiple) model/ )
  55     {
  56         if ($output_details->{data_set_type} =~ /combined populations/)
  57         {
  58             $output_details = $self->check_combined_pops_trait_modeling($output_details);
  59         }
  60         elsif ($output_details->{data_set_type} =~ /single population/)
  61         {
  62             $output_details = $self->check_trait_modeling($output_details);
  63         }
  64     }
  65     elsif ( $analysis_profile->{analysis_type} =~ /combine populations/ )
  66     {
  67         $output_details = $self->check_multi_pops_data_download($output_details);
  68     }
  69     elsif ( $analysis_profile->{analysis_type} =~ /selection prediction/ )
  70     {
  71         if ($output_details->{data_set_type} =~ /combined populations/)
  72         {
  73           # $output_details = $self->check_combined_pops_trait_modeling($output_details);
  74            $output_details = $self->check_selection_prediction($output_details);
  75         }
  76         elsif ($output_details->{data_set_type} =~ /single population/)
  77         {
  78             $output_details = $self->check_selection_prediction($output_details);
  79         }
  80
  81     }
  82
  83     return $output_details;
  84 }
  85
  86
  87 sub check_combined_pops_trait_modeling {
  88     my ($self, $output_details) = @_;
  89
  90     $output_details = $self->check_pops_trait_data_combination($output_details);
  91     $output_details = $self->check_trait_modeling($output_details);
  92
  93     return $output_details;
  94 }
  95
  96
  97 sub check_pops_trait_data_combination {
  98     my ($self, $output_details) = @_;
  99
 100     my $job_tempdir = $output_details->{r_job_tempdir};
 101
 102     foreach my $k (keys %{$output_details})
 103     {
 104         if ($k =~ /population_id/)
 105         {
 106             my $pheno_file;
 107             my $geno_file;
 108
 109             if (ref $output_details->{$k} eq 'HASH')
 110             {
 111                 $pheno_file = $output_details->{$k}->{phenotype_file};
 112                 $geno_file  = $output_details->{$k}->{genotype_file};
 113             }
 114
 115             if ($geno_file || $pheno_file)
 116             {
 117                 my $pheno_size;
 118                 my $geno_size;
 119                 my $died_file;
 120
 121                 while (1)
 122                 {
 123                     sleep 60;
 124                     $pheno_size = -s $pheno_file;
 125                     $geno_size  = -s $geno_file;
 126
 127                     if ($pheno_size)
 128                     {
 129                         $output_details->{$k}->{pheno_success} = 'pheno success';
 130                     }
 131
 132                     if ($geno_size)
 133                     {
 134                         $output_details->{$k}->{geno_success} = 'geno success';
 135                     }
 136
 137                     if ($pheno_size && $geno_size)
 138                     {
 139                         $output_details->{$k}->{success} = 1;
 140                         $output_details->{status} = 'Done';
 141                         last;
 142                     }
 143                     else
 144                     {
 145                         if ($job_tempdir)
 146                         {
 147                             $died_file = $self->get_file($job_tempdir, 'died');
 148                             if ($died_file)
 149                             {
 150                                 $output_details->{$k}->{pheno_success}   = 0;
 151                                 $output_details->{$k}->{geno_success}    = 0;
 152                                 $output_details->{$k}->{success} = 0;
 153                                 $output_details->{status} = 'Failed';
 154                                 last;
 155                             }
 156                         }
 157                     }
 158                 }
 159             }
 160             else
 161             {
 162                 if (ref $output_details->{$k} eq 'HASH')
 163                 {
 164                     $output_details->{$k}->{pheno_success}   = 0;
 165                     $output_details->{$k}->{geno_success}    = 0;
 166                     $output_details->{$k}->{success} = 0;
 167                     $output_details->{status} = 'Failed';
 168                 }
 169             }
 170         }
 171     }
 172
 173     return $output_details;
 174 }
 175
 176
 177
 178 sub check_multi_pops_data_download {
 179     my ($self, $output_details) = @_;
 180
 181     my $job_tempdir = $output_details->{r_job_tempdir};
 182
 183     my $no_match = $output_details->{no_match};
 184
 185     foreach my $k (keys %{$output_details})
 186     {
 187         my $pheno_file;
 188         my $geno_file;
 189         if ($k =~ /population_id/)
 190         {
 191             if (ref $output_details->{$k} eq 'HASH')
 192             {
 193                 $pheno_file = $output_details->{$k}->{phenotype_file};
 194                 $geno_file  = $output_details->{$k}->{genotype_file};
 195                 print STDERR "\n $k - pheno_file: $pheno_file -- geno_file: $geno_file\n";
 196             }
 197
 198             if ($geno_file && $pheno_file)
 199             {
 200                 my $pheno_size;
 201                 my $geno_size;
 202                 my $died_file;
 203
 204                 while (1)
 205                 {
 206                     sleep 60;
 207                     $pheno_size = -s $pheno_file;
 208                     $geno_size  = -s $geno_file;
 209
 210                     if ($pheno_size)
 211                     {
 212                         $output_details->{$k}->{pheno_success} = 'pheno success';
 213                     }
 214
 215                     if ($geno_size)
 216                     {
 217                         $output_details->{$k}->{geno_success} = 'geno success';
 218                     }
 219
 220                     if ($pheno_size && $geno_size)
 221                     {
 222                         $output_details->{$k}->{success} = 1;
 223                         $output_details->{status} = 'Done';
 224                         last;
 225                     }
 226                     else
 227                     {
 228                         if ($job_tempdir)
 229                         {
 230                             print STDERR "\n job_tempdir: $job_tempdir\n";
 231                             $died_file = $self->get_file($job_tempdir, 'died');
 232                             if ($died_file)
 233                             {
 234                                 $output_details->{$k}->{pheno_success} = 0;
 235                                 $output_details->{$k}->{geno_success}  = 0;
 236                                 $output_details->{$k}->{success} = 0;
 237                                 $output_details->{status} = 'Failed';
 238                                 last;
 239                             }
 240                         }
 241                     }
 242                 }
 243             }
 244             else
 245             {
 246                 if (ref $output_details->{$k} eq 'HASH')
 247                 {
 248                     $output_details->{$k}->{pheno_success} = 0;
 249                     $output_details->{$k}->{geno_success}  = 0;
 250                     $output_details->{$k}->{success} = 0;
 251                     $output_details->{status} = 'Failed';
 252                 }
 253             }
 254         }
 255     }
 256
 257     return $output_details;
 258 }
 259
 260
 261 sub check_selection_prediction {
 262     my ($self, $output_details) = @_;
 263
 264     my $job_tempdir = $output_details->{r_job_tempdir};
 265
 266     foreach my $k (keys %{$output_details})
 267     {
 268         if ($k =~ /trait_id/)
 269         {
 270             my $gebv_file;
 271             if (ref $output_details->{$k} eq 'HASH')
 272             {
 273                 if ($output_details->{$k}->{trait_id})
 274                 {
 275                     $gebv_file = $output_details->{$k}->{gebv_file};
 276                 }
 277
 278                 if ($gebv_file)
 279                 {
 280                     my $gebv_size;
 281                     my $died_file;
 282
 283                     while (1)
 284                     {
 285                         sleep 60;
 286                         $gebv_size = -s $gebv_file;
 287
 288                         if ($gebv_size)
 289                         {
 290                             $output_details->{$k}->{success} = 1;
 291                             $output_details->{status} = 'Done';
 292                             last;
 293                         }
 294                         else
 295                         {
 296                             if ($job_tempdir)
 297                             {
 298                                 $died_file = $self->get_file($job_tempdir, 'died');
 299                                 if ($died_file)
 300                                 {
 301                                     $output_details->{$k}->{success} = 0;
 302                                     $output_details->{status} = 'Failed';
 303                                     last;
 304                                 }
 305                             }
 306                         }
 307                     }
 308                 }
 309             }
 310             else
 311             {
 312                 if (ref $output_details->{$k} eq 'HASH')
 313                 {
 314                     $output_details->{$k}->{success} = 0;
 315                     $output_details->{status} = 'Failed';
 316                 }
 317             }
 318         }
 319     }
 320
 321     return $output_details;
 322 }
 323
 324
 325
 326 sub check_trait_modeling {
 327     my ($self, $output_details) = @_;
 328
 329     my $job_tempdir = $output_details->{r_job_tempdir};
 330
 331     foreach my $k (keys %{$output_details})
 332     {
 333         if ($k =~ /trait_id/)
 334 {
 335         my $gebv_file;
 336         if (ref $output_details->{$k} eq 'HASH')
 337         {
 338              if ($output_details->{$k}->{trait_id})
 339             {
 340                 $gebv_file = $output_details->{$k}->{gebv_file};
 341             }
 342
 343              if ($gebv_file)
 344              {
 345                  my $gebv_size;
 346                  my $died_file;
 347
 348                  while (1)
 349                  {
 350                      sleep 60;
 351                      $gebv_size = -s $gebv_file;
 352
 353                      if ($gebv_size)
 354                      {
 355                          $output_details->{$k}->{success} = 1;
 356                          $output_details->{status} = 'Done';
 357                          last;
 358                      }
 359                      else
 360                      {
 361                          if ($job_tempdir)
 362                          {
 363                              $died_file = $self->get_file($job_tempdir, 'died');
 364                              if ($died_file)
 365                              {
 366                                  $output_details->{$k}->{success} = 0;
 367                                  $output_details->{status} = 'Failed';
 368                                  last;
 369                              }
 370                          }
 371                      }
 372                  }
 373              }
 374         }
 375         else
 376         {
 377             if (ref $output_details->{$k} eq 'HASH')
 378             {
 379                 $output_details->{$k}->{success} = 0;
 380                 $output_details->{status} = 'Failed';
 381             }
 382         }
 383 }
 384     }
 385
 386     return $output_details;
 387 }
 388
 389
 390 sub check_population_download {
 391     my ($self, $output_details) = @_;
 392
 393     my $job_tempdir = $output_details->{r_job_tempdir};
 394
 395     foreach my $k (keys %{$output_details})
 396     {
 397         if ($k =~ /population_id/)
 398         {
 399             my $pheno_file;
 400             my $geno_file;
 401
 402             if (ref $output_details->{$k} eq 'HASH')
 403             {
 404                 if ($output_details->{$k}->{population_id})
 405                 {
 406                     $pheno_file = $output_details->{$k}->{phenotype_file};
 407                     $geno_file  = $output_details->{$k}->{genotype_file};
 408
 409                     if ($pheno_file && $geno_file)
 410                     {
 411                         my $pheno_size;
 412                         my $geno_size;
 413                         my $died_file;
 414
 415                         while (1)
 416                         {
 417                             sleep 60;
 418                             $pheno_size = -s $pheno_file;
 419                             $geno_size  = -s $geno_file;
 420
 421                             unless (!$pheno_size)
 422                             {
 423                                 $output_details->{$k}->{pheno_success} = 1;
 424                             }
 425
 426                             unless (!$geno_size)
 427                             {
 428                                 $output_details->{$k}->{geno_success} = 1;
 429                             }
 430
 431                             if ($pheno_size && $geno_size)
 432                             {
 433                                 $output_details->{$k}->{success} = 1;
 434                                 $output_details->{status} = 'Done';
 435                                 last;
 436                             }
 437                             else
 438                             {
 439                                 if ($job_tempdir)
 440                                 {
 441                                     $died_file = $self->get_file($job_tempdir, 'died');
 442                                     if ($died_file)
 443                                     {
 444                                         $output_details->{$k}->{pheno_success}   = 0;
 445                                         $output_details->{$k}->{geno_success}    = 0;
 446                                         $output_details->{$k}->{success} = 0;
 447                                         $output_details->{status} = 'Failed';
 448                                         last;
 449                                     }
 450                                 }
 451                             }
 452                         }
 453                     }
 454                     else
 455                     {
 456                         if (ref $output_details->{$k} eq 'HASH')
 457                         {
 458                             $output_details->{$k}->{pheno_success}   = 0;
 459                             $output_details->{$k}->{geno_success}    = 0;
 460                             $output_details->{$k}->{success} = 0;
 461                             $output_details->{status} = 'Failed';
 462                         }
 463                     }
 464                 }
 465             }
 466         }
 467     }
 468
 469     return $output_details;
 470
 471 }
 472
 473
 474 sub get_file {
 475     my ($self, $dir, $exp) = @_;
 476
 477     opendir my $dh, $dir
 478         or die "can't open $dir: $!\n";
 479
 480     my ($file)  = grep { /$exp/ && -f "$dir/$_" }  readdir($dh);
 481     close $dh;
 482
 483     if ($file)
 484     {
 485         $file = catfile($dir, $file);
 486     }
 487
 488     return $file;
 489 }
 490
 491
 492 sub report_status {
 493     my ($self, $output_details) = @_;
 494
 495     my $analysis_profile = $output_details->{analysis_profile};
 496     my $user_email = $analysis_profile->{user_email};
 497     my $user_name  = $analysis_profile->{user_name};
 498
 499     my $analysis_page = $analysis_profile->{analysis_page};
 500     my $analysis_name = $analysis_profile->{analysis_name};
 501     my $analysis_type = $analysis_profile->{analysis_type};
 502
 503     my $analysis_result;
 504
 505     if ($analysis_type =~ /multiple models/)
 506     {
 507         $analysis_result = $self->multi_modeling_message($output_details);
 508     }
 509     elsif ($analysis_type =~ /single model/)
 510     {
 511         $analysis_result = $self->single_modeling_message($output_details);
 512     }
 513     elsif ($analysis_type =~ /population download/  )
 514     {
 515         $analysis_result = $self->population_download_message($output_details);
 516     }
 517     elsif ($analysis_type =~ /combine populations/  )
 518     {
 519         $analysis_result = $self->combine_populations_message($output_details);
 520     }
 521     elsif ($analysis_type =~ /selection prediction/  )
 522     {
 523         $analysis_result = $self->selection_prediction_message($output_details);
 524     }
 525
 526     my $closing = "If you have any remarks, please contact us:\n"
 527         . $output_details->{contact_page}
 528         ."\n\nThanks and regards,\nsolGS M Tool";
 529
 530     my $body = "Dear $user_name,\n"
 531         . "\n$analysis_result"
 532         . "$closing";
 533
 534     my $email_from;
 535     my $email_to;
 536     my $email_cc;
 537
 538     if ($output_details->{host} =~ /localhost/)
 539     {
 540         my $uid = getpwuid($<);
 541         $email_from = '"' . $uid .'" <' . $uid . '@localhost.localdomain>';
 542         $email_to   = '"' . $uid .'" <' . $uid . '@localhost.localdomain>';
 543     }
 544     else
 545     {
 546         $email_from = '"solGS M Tool" <cluster-jobs@solgenomics.net>';
 547         $email_to   = "$user_name <$user_email>";
 548         $email_cc   = 'solGS Job <cluster-jobs@solgenomics.net>';
 549     }
 550
 551     my $email = Email::Simple->create(
 552         header => [
 553             From    => $email_from,
 554             To      => $email_to,
 555             Cc      => $email_cc,
 556             Subject => "Analysis result of $analysis_name",
 557         ],
 558         body => $body,
 559         );
 560
 561     sendmail($email);
 562
 563 }
 564
 565
 566 sub multi_modeling_message {
 567     my ($self, $output_details) = @_;
 568
 569     my $message;
 570     my $cnt = 0;
 571
 572     foreach my $k (keys %{$output_details})
 573     {
 574         if ($k =~ /trait_id/)
 575         {
 576             my $all_success;
 577
 578             if (ref $output_details->{$k} eq 'HASH')
 579             {
 580                 if ($output_details->{$k}->{trait_id})
 581                 {
 582                     if ($output_details->{$k}->{success})
 583                     {
 584                         $cnt++;
 585                         $all_success = 1;
 586                         my $trait_name = uc($output_details->{$k}->{trait_name});
 587                         my $trait_page = $output_details->{$k}->{trait_page};
 588                         $message .= "The analysis for $trait_name is done."
 589                             ." You can view the model output here:"
 590                             ."\n\n$trait_page\n\n";
 591                     }
 592                     else
 593                     {
 594                         $all_success = 0;
 595                         my $trait_name = uc($output_details->{$k}->{trait_name});
 596                         $message .= "The analysis for $trait_name failed.\n\n";
 597                     }
 598                 }
 599             }
 600         }
 601     }
 602     if ($cnt > 1 )
 603     {
 604         $message .= "You can also view the summary of all the analyses in the page below."
 605             ."\nAdditionally, you may find the analytical features in the page useful.\n"
 606             . $output_details->{analysis_profile}->{analysis_page} ."\n\n";
 607     }
 608
 609     return  $message;
 610 }
 611
 612
 613 sub single_modeling_message {
 614     my ($self, $output_details) = @_;
 615
 616     my $message;
 617     foreach my $k (keys %{$output_details})
 618     {
 619
 620         if ($k =~ /trait_id/)
 621         {
 622             my $gebv_file;
 623             if (ref $output_details->{$k} eq 'HASH')
 624             {
 625                 if ($output_details->{$k}->{trait_id})
 626                 {
 627                     my $trait_name = uc($output_details->{$k}->{trait_name});
 628                     my $trait_page = $output_details->{$k}->{trait_page};
 629                     $gebv_file = $output_details->{$k}->{gebv_file};
 630
 631                     if ($output_details->{$k}->{success})
 632                     {
 633                         $message = "The analysis for $trait_name is done."
 634                             ."\nYou can view the model output here:"
 635                             ."\n\n$trait_page\n\n";
 636                     }
 637                     else
 638                     {
 639                         $message = "The analysis for $trait_name failed."
 640                             ."\n\nWe are troubleshooting the cause. "
 641                             . "We will contact you when we find out more.";
 642                     }
 643                 }
 644             }
 645         }
 646     }
 647
 648     return  $message;
 649 }
 650
 651
 652 sub selection_prediction_message {
 653     my ($self, $output_details) = @_;
 654
 655     my $message;
 656     my $cnt = 0;
 657     foreach my $k (keys %{$output_details})
 658     {
 659         if ($k =~ /trait_id/)
 660         {
 661             my $gebv_file;
 662             if (ref $output_details->{$k} eq 'HASH')
 663             {
 664                 if ($output_details->{$k}->{trait_id})
 665                 {
 666                     my $trait_name          = uc($output_details->{$k}->{trait_name});
 667                     my $training_pop_page   = $output_details->{$k}->{training_pop_page};
 668                     my $model_page          = $output_details->{$k}->{model_page};
 669                     my $prediction_pop_name = $output_details->{$k}->{prediction_pop_name};
 670
 671                     if ($output_details->{$k}->{success})
 672                     {
 673                         $cnt++;
 674                         if($cnt == 1)
 675                         {
 676                             $message .= "The prediction of selection population $prediction_pop_name is done."
 677                                 . "\nYou can view the prediction output by clicking the trait name "
 678                                 . "\nat the bottom of the model page(s):\n\n";
 679                         }
 680
 681                         $message .= "$model_page\n\n";
 682                     }
 683                     else
 684                     {
 685                         $message .= "The analysis for $trait_name failed."
 686                             ."\n\nWe are troubleshooting the cause. "
 687                             . "We will contact you when we find out more.";
 688                     }
 689
 690                     if ($cnt > 1)
 691                     {
 692                         $message .= "You can also view the summary of all the analyses in the page below."
 693                             ."\nAdditionally, you may find the analytical features in the page useful.\n"
 694                             . $output_details->{referer} . "\n\n";
 695                     }
 696                 }
 697             }
 698         }
 699     }
 700
 701     return  $message;
 702 }
 703
 704
 705 sub population_download_message {
 706     my ($self, $output_details) = @_;
 707
 708     my $message;
 709
 710     foreach my $k (keys %{$output_details})
 711     {
 712         if ($k =~ /population_id/)
 713         {
 714             if (ref $output_details->{$k} eq 'HASH')
 715             {
 716                 if ($output_details->{$k}->{population_id})
 717                 {
 718                     my $pop_name = uc($output_details->{$k}->{population_name});
 719                     my $pop_page = $output_details->{$k}->{population_page};
 720
 721                     if ($output_details->{$k}->{success})
 722                     {
 723                         $message = "The phenotype and genotype data for $pop_name is ready for analysis."
 724                             ."\nYou can view the training population page here:\n"
 725                             ."\n$pop_page.\n\n";
 726                     }
 727                     else
 728                     {
 729                         $message = "Downloading phenotype and genotype data for $pop_name failed."
 730                             ."\nWe are troubleshooting the cause. "
 731                             . "We will contact you when we find out more.";
 732                     }
 733                 }
 734             }
 735         }
 736     }
 737
 738     return  $message;
 739 }
 740
 741
 742 sub combine_populations_message {
 743     my ($self, $output_details) = @_;
 744
 745     my $no_match = $output_details->{no_match};
 746
 747     my $message;
 748
 749     if ($no_match)
 750     {
 751         $message = $no_match
 752             . " can not be combined.\n"
 753             . "Possibly the the populations were genotyped\n"
 754             . "with different marker sets or querying the data for one or more of the\n"
 755             . "populations failed. See details below:\n\n";
 756
 757         my $troost_mededeling;
 758
 759         foreach my $k (keys %{$output_details})
 760         {
 761             if ($k =~ /population_id/)
 762             {
 763                 if (ref $output_details->{$k} eq 'HASH')
 764                 {
 765                     if ($output_details->{$k}->{population_id})
 766                     {
 767                         my $pop_name = uc($output_details->{$k}->{population_name});
 768                         my $pop_page = $output_details->{$k}->{population_page};
 769
 770                         if ($output_details->{$k}->{success})
 771                         {
 772                             $message .= "The phenotype and genotype data for $pop_name is succesfuly downloaded."
 773                             ."\nYou can view the population here:"
 774                             ."\n$pop_page.\n\n";
 775                         }
 776                         else
 777                         {
 778                             $message .= "Downloading phenotype and genotype data for $pop_name failed.";
 779                             $troost_mededeling = "\n\nWe are troubleshooting the cause. "
 780                                 . "We will contact you when we find out more.";
 781                         }
 782                     }
 783                 }
 784             }
 785         }
 786
 787         $message .= $troost_mededeling;
 788     }
 789     else
 790     {
 791         my $combined_pops_page = $output_details->{combined_pops_page};
 792         $message .= "Your combined training population is ready for analysis."
 793             ."You can view it here:\n\n$combined_pops_page\n\n";
 794     }
 795
 796     return  $message;
 797 }
 798
 799
 800 sub log_analysis_status {
 801     my ($self, $output_details) = @_;
 802
 803     my $log_file = $output_details->{analysis_log_file};
 804
 805     my $analysis_profile = $output_details->{analysis_profile};
 806     my $analysis_name    = $analysis_profile->{analysis_name};
 807
 808     my $status = $output_details->{status};
 809
 810     my @contents = read_file($log_file);
 811
 812     map{ $contents[$_] =~ m/\t$analysis_name\t/
 813              ? $contents[$_] =~ s/error|submitted/$status/ig
 814              : $contents[$_] } 0..$#contents;
 815
 816     write_file($log_file, @contents);
 817
 818 }
 819
 820
 821
 822
 823
 824 __PACKAGE__->meta->make_immutable;
 825
 826
 827
 828
 829 ####
 830 1; #
 831 ####