t/unit_fixture/CXGN/Trial.t

   1 #This script should test all functions in CXGN::Trial, CXGN::Trial::TrialLayout, CXGN::Trial::TrialDesign, CXGN::Trial::TrialCreate
   2
   3 use strict;
   4 use lib 't/lib';
   5
   6 use Test::More;
   7 use SGN::Test::Fixture;
   8 use SimulateC;
   9
  10 use Data::Dumper;
  11
  12 use CXGN::Trial;
  13 use CXGN::Trial::TrialLayout;
  14 use CXGN::Trial::TrialDesign;
  15 use CXGN::Trial::TrialCreate;
  16 use CXGN::Trial::Folder;
  17 use CXGN::Phenotypes::StorePhenotypes;
  18 use CXGN::Trial::Search;
  19 use SGN::Model::Cvterm;
  20
  21 my $f = SGN::Test::Fixture->new();
  22 my $schema = $f->bcs_schema;
  23
  24 my $trial_search = CXGN::Trial::Search->new({
  25     bcs_schema=>$schema,
  26 });
  27 my ($result, $total_count) = $trial_search->search();
  28 print STDERR "ALL TRIAL =".Dumper($result)."\n";
  29 is_deeply($result, [
  30           {
  31             'design' => 'RCBD',
  32             'breeding_program_id' => 134,
  33             'genotyping_facility_status' => undef,
  34             'genotyping_plate_sample_type' => undef,
  35             'genotyping_facility_submitted' => undef,
  36             'project_harvest_date' => '',
  37             'location_id' => '23',
  38             'breeding_program_description' => 'test',
  39             'location_name' => 'test_location',
  40             'breeding_program_name' => 'test',
  41             'genotyping_plate_format' => undef,
  42             'year' => '2017',
  43             'description' => 'Copy of trial with postcomposed phenotypes from cassbase.',
  44             'trial_name' => 'CASS_6Genotypes_Sampling_2015',
  45                 'trial_type' => 'Preliminary Yield Trial',
  46                 'trial_type_value' => 'Preliminary Yield Trial',
  47             'trial_type_name' => 'Preliminary Yield Trial',
  48             'trial_type_id' => 76515,
  49             'folder_description' => undef,
  50             'genotyping_facility_plate_id' => undef,
  51             'folder_id' => undef,
  52             'genotyping_facility' => undef,
  53             'project_planting_date' => '',
  54             'folder_name' => undef,
  55             'trial_id' => 165,
  56             'sampling_facility' => undef,
  57                 'sampling_trial_sample_type' => undef,
  58                 'additional_info' => undef
  59
  60           },
  61           {
  62             'genotyping_facility_status' => undef,
  63             'genotyping_plate_sample_type' => undef,
  64             'genotyping_facility_submitted' => undef,
  65             'breeding_program_id' => 134,
  66             'design' => 'Alpha',
  67             'description' => 'This trial was loaded into the fixture to test solgs.',
  68             'year' => '2014',
  69             'genotyping_plate_format' => undef,
  70             'trial_type_name' => 'Clonal Evaluation',
  71             'trial_name' => 'Kasese solgs trial',
  72                 'trial_type' => 'Clonal Evaluation',
  73                 'trial_type_value' => '1',
  74             'folder_description' => undef,
  75             'trial_type_id' => 77106,
  76             'project_planting_date' => '',
  77             'genotyping_facility' => undef,
  78             'folder_name' => undef,
  79             'folder_id' => undef,
  80             'trial_id' => 139,
  81             'genotyping_facility_plate_id' => undef,
  82             'breeding_program_description' => 'test',
  83             'location_name' => 'test_location',
  84             'location_id' => '23',
  85             'project_harvest_date' => '',
  86             'breeding_program_name' => 'test',
  87             'sampling_facility' => undef,
  88                 'sampling_trial_sample_type' => undef,
  89                 'additional_info' => undef
  90
  91           },
  92           {
  93             'description' => 'new_test_cross',
  94             'year' => undef,
  95             'genotyping_plate_format' => undef,
  96             'trial_type_name' => undef,
  97                 'trial_type' => undef,
  98                 'trial_type_value' => undef,
  99             'trial_name' => 'new_test_cross',
 100             'folder_description' => undef,
 101             'trial_type_id' => undef,
 102             'trial_id' => 135,
 103             'genotyping_facility' => undef,
 104             'project_planting_date' => '',
 105             'folder_name' => undef,
 106             'folder_id' => undef,
 107             'genotyping_facility_plate_id' => undef,
 108             'breeding_program_description' => 'test',
 109             'location_name' => '',
 110             'project_harvest_date' => '',
 111             'location_id' => undef,
 112             'breeding_program_name' => 'test',
 113             'genotyping_plate_sample_type' => undef,
 114             'genotyping_facility_status' => undef,
 115             'genotyping_facility_submitted' => undef,
 116             'breeding_program_id' => 134,
 117             'design' => undef,
 118             'sampling_facility' => undef,
 119                 'sampling_trial_sample_type' => undef,
 120                 'additional_info' => undef
 121
 122           },
 123           {
 124             'genotyping_facility_plate_id' => undef,
 125             'genotyping_facility' => undef,
 126             'folder_name' => undef,
 127             'project_planting_date' => '',
 128             'folder_id' => undef,
 129             'trial_id' => 144,
 130             'trial_type_id' => undef,
 131             'folder_description' => undef,
 132             'trial_name' => 'test_t',
 133                 'trial_type' => undef,
 134                 'trial_type_value' => undef,
 135             'trial_type_name' => undef,
 136             'year' => '2016',
 137             'genotyping_plate_format' => undef,
 138             'description' => 'test tets',
 139             'breeding_program_name' => 'test',
 140             'project_harvest_date' => '',
 141             'location_id' => '23',
 142             'location_name' => 'test_location',
 143             'breeding_program_description' => 'test',
 144             'genotyping_facility_submitted' => undef,
 145             'genotyping_plate_sample_type' => undef,
 146             'genotyping_facility_status' => undef,
 147             'design' => 'CRD',
 148             'breeding_program_id' => 134,
 149             'sampling_facility' => undef,
 150                 'sampling_trial_sample_type' => undef,
 151                 'additional_info' => undef
 152
 153           },
 154           {
 155             'genotyping_facility_status' => undef,
 156             'genotyping_plate_sample_type' => undef,
 157             'genotyping_facility_submitted' => undef,
 158             'breeding_program_id' => 134,
 159             'design' => 'CRD',
 160             'trial_type_name' => undef,
 161             'trial_name' => 'test_trial',
 162                 'trial_type' => undef,
 163                 'trial_type_value' => undef,
 164             'description' => 'test trial',
 165             'year' => '2014',
 166             'genotyping_plate_format' => undef,
 167             'genotyping_facility' => undef,
 168             'folder_name' => undef,
 169             'project_planting_date' => '2017-July-04',
 170             'folder_id' => undef,
 171             'trial_id' => 137,
 172             'genotyping_facility_plate_id' => undef,
 173             'folder_description' => undef,
 174             'trial_type_id' => undef,
 175             'breeding_program_name' => 'test',
 176             'breeding_program_description' => 'test',
 177             'location_name' => 'test_location',
 178             'project_harvest_date' => '2017-July-21',
 179             'location_id' => '23',
 180             'sampling_facility' => undef,
 181                 'sampling_trial_sample_type' => undef,
 182                 'additional_info' => undef
 183
 184           },
 185           {
 186             'genotyping_facility_submitted' => undef,
 187             'genotyping_facility_status' => undef,
 188             'genotyping_plate_sample_type' => undef,
 189             'breeding_program_id' => 134,
 190             'design' => 'CRD',
 191             'folder_description' => undef,
 192                 'trial_type_id' => undef,
 193                 'trial_type_value' => undef,
 194             'folder_name' => undef,
 195             'genotyping_facility' => undef,
 196             'project_planting_date' => '',
 197             'folder_id' => undef,
 198             'trial_id' => 141,
 199             'genotyping_facility_plate_id' => undef,
 200             'description' => 'another trial for solGS',
 201             'genotyping_plate_format' => undef,
 202             'year' => '2014',
 203             'trial_type_name' => undef,
 204             'trial_name' => 'trial2 NaCRRI',
 205             'trial_type' => undef,
 206             'breeding_program_description' => 'test',
 207             'location_name' => 'test_location',
 208             'location_id' => '23',
 209             'project_harvest_date' => '',
 210             'breeding_program_name' => 'test',
 211             'sampling_facility' => undef,
 212                 'sampling_trial_sample_type' => undef,
 213                 'additional_info' => undef
 214
 215           }
 216         ], 'trial search test 1');
 217
 218 $trial_search = CXGN::Trial::Search->new({
 219     bcs_schema=>$schema,
 220     location_list=>['test_location'],
 221     program_list=>['test'],
 222 });
 223 ($result, $total_count) = $trial_search->search();
 224 print STDERR "SELECTED TRIAL =".Dumper($result)."\n";
 225 is_deeply($result, [
 226           {
 227             'genotyping_facility_status' => undef,
 228             'genotyping_plate_sample_type' => undef,
 229             'genotyping_facility_submitted' => undef,
 230             'design' => 'RCBD',
 231             'breeding_program_id' => 134,
 232             'trial_type_name' => 'Preliminary Yield Trial',
 233             'trial_type' => 'Preliminary Yield Trial',
 234             'trial_name' => 'CASS_6Genotypes_Sampling_2015',
 235             'description' => 'Copy of trial with postcomposed phenotypes from cassbase.',
 236             'year' => '2017',
 237             'genotyping_plate_format' => undef,
 238             'project_planting_date' => '',
 239             'genotyping_facility' => undef,
 240             'folder_id' => undef,
 241             'folder_name' => undef,
 242             'trial_id' => 165,
 243             'genotyping_facility_plate_id' => undef,
 244             'folder_description' => undef,
 245             'trial_type_id' => 76515,
 246             'breeding_program_name' => 'test',
 247             'breeding_program_description' => 'test',
 248                 'location_name' => 'test_location',
 249                 'trial_type_value' => 'Preliminary Yield Trial',
 250             'location_id' => '23',
 251             'project_harvest_date' => '',
 252             'sampling_facility' => undef,
 253                 'sampling_trial_sample_type' => undef,
 254                 'additional_info' => undef
 255           },
 256           {
 257             'project_harvest_date' => '',
 258             'location_id' => '23',
 259             'location_name' => 'test_location',
 260             'breeding_program_description' => 'test',
 261             'breeding_program_name' => 'test',
 262             'genotyping_plate_format' => undef,
 263             'year' => '2014',
 264             'description' => 'This trial was loaded into the fixture to test solgs.',
 265             'trial_type' => 'Clonal Evaluation',
 266             'trial_name' => 'Kasese solgs trial',
 267                 'trial_type_name' => 'Clonal Evaluation',
 268                 'trial_type_value' => '1',
 269             'trial_type_id' => 77106,
 270             'folder_description' => undef,
 271             'genotyping_facility_plate_id' => undef,
 272             'project_planting_date' => '',
 273             'genotyping_facility' => undef,
 274             'trial_id' => 139,
 275             'folder_id' => undef,
 276             'folder_name' => undef,
 277             'design' => 'Alpha',
 278             'breeding_program_id' => 134,
 279             'genotyping_facility_status' => undef,
 280             'genotyping_plate_sample_type' => undef,
 281             'genotyping_facility_submitted' => undef,
 282             'sampling_facility' => undef,
 283                 'sampling_trial_sample_type' => undef,
 284                 'additional_info' => undef
 285           },
 286           {
 287             'genotyping_facility_plate_id' => undef,
 288             'folder_id' => undef,
 289             'genotyping_facility' => undef,
 290             'project_planting_date' => '',
 291             'trial_id' => 135,
 292             'folder_name' => undef,
 293             'trial_type_id' => undef,
 294             'folder_description' => undef,
 295             'trial_type' => undef,
 296             'trial_name' => 'new_test_cross',
 297             'trial_type_name' => undef,
 298             'year' => undef,
 299             'genotyping_plate_format' => undef,
 300             'description' => 'new_test_cross',
 301             'breeding_program_name' => 'test',
 302             'project_harvest_date' => '',
 303             'location_id' => undef,
 304             'location_name' => '',
 305             'breeding_program_description' => 'test',
 306             'genotyping_facility_submitted' => undef,
 307             'genotyping_plate_sample_type' => undef,
 308             'genotyping_facility_status' => undef,
 309             'breeding_program_id' => 134,
 310             'design' => undef,
 311             'sampling_facility' => undef,
 312                 'sampling_trial_sample_type' => undef,
 313                 'trial_type_value' => undef,
 314                 'additional_info' => undef
 315           },
 316           {
 317             'design' => 'CRD',
 318             'breeding_program_id' => 134,
 319             'genotyping_plate_sample_type' => undef,
 320             'genotyping_facility_status' => undef,
 321             'genotyping_facility_submitted' => undef,
 322             'breeding_program_name' => 'test',
 323             'location_id' => '23',
 324             'project_harvest_date' => '',
 325             'breeding_program_description' => 'test',
 326             'location_name' => 'test_location',
 327             'trial_type' => undef,
 328             'trial_name' => 'test_t',
 329                 'trial_type_name' => undef,
 330                 'trial_type_value' => undef,
 331             'genotyping_plate_format' => undef,
 332             'year' => '2016',
 333             'description' => 'test tets',
 334             'genotyping_facility_plate_id' => undef,
 335             'folder_id' => undef,
 336             'genotyping_facility' => undef,
 337             'project_planting_date' => '',
 338             'trial_id' => 144,
 339             'folder_name' => undef,
 340             'trial_type_id' => undef,
 341             'folder_description' => undef,
 342             'sampling_facility' => undef,
 343                 'sampling_trial_sample_type' => undef,
 344                 'additional_info' => undef
 345           },
 346           {
 347             'design' => 'CRD',
 348             'breeding_program_id' => 134,
 349             'genotyping_facility_submitted' => undef,
 350             'genotyping_facility_status' => undef,
 351             'genotyping_plate_sample_type' => undef,
 352                 'breeding_program_name' => 'test',
 353                 'trial_type_value' => undef,
 354             'breeding_program_description' => 'test',
 355             'location_name' => 'test_location',
 356             'location_id' => '23',
 357             'project_harvest_date' => '2017-July-21',
 358             'genotyping_facility' => undef,
 359             'project_planting_date' => '2017-July-04',
 360             'folder_id' => undef,
 361             'folder_name' => undef,
 362             'trial_id' => 137,
 363             'genotyping_facility_plate_id' => undef,
 364             'folder_description' => undef,
 365             'trial_type_id' => undef,
 366             'trial_type_name' => undef,
 367             'trial_name' => 'test_trial',
 368             'trial_type' => undef,
 369             'description' => 'test trial',
 370             'genotyping_plate_format' => undef,
 371             'year' => '2014',
 372             'sampling_facility' => undef,
 373                 'sampling_trial_sample_type' => undef,
 374                 'additional_info' => undef
 375           },
 376           {
 377             'breeding_program_description' => 'test',
 378             'location_name' => 'test_location',
 379             'location_id' => '23',
 380             'project_harvest_date' => '',
 381                 'breeding_program_name' => 'test',
 382                  'trial_type_value' => undef,
 383             'description' => 'another trial for solGS',
 384             'year' => '2014',
 385             'genotyping_plate_format' => undef,
 386             'trial_type_name' => undef,
 387             'trial_name' => 'trial2 NaCRRI',
 388             'trial_type' => undef,
 389             'folder_description' => undef,
 390             'trial_type_id' => undef,
 391             'genotyping_facility' => undef,
 392             'project_planting_date' => '',
 393             'trial_id' => 141,
 394             'folder_name' => undef,
 395             'folder_id' => undef,
 396             'genotyping_facility_plate_id' => undef,
 397             'design' => 'CRD',
 398             'breeding_program_id' => 134,
 399             'genotyping_facility_status' => undef,
 400             'genotyping_plate_sample_type' => undef,
 401             'genotyping_facility_submitted' => undef,
 402             'sampling_facility' => undef,
 403                 'sampling_trial_sample_type' => undef,
 404                 'additional_info' => undef
 405           }
 406         ], 'trial search test 2');
 407
 408
 409
 410 #CXGN::Trial Class METHODS
 411 my $locations = CXGN::Trial::get_all_locations($f->bcs_schema());
 412 #print STDERR Dumper $locations;
 413 my @all_location_names;
 414 foreach (@$locations) {
 415     push @all_location_names, $_->[1];
 416 }
 417 @all_location_names = sort @all_location_names;
 418 #print STDERR Dumper \@all_location_names;
 419 my %all_location_names = map {$_=>1} @all_location_names;
 420 ok(exists($all_location_names{'Cornell Biotech'}));
 421 ok(exists($all_location_names{'test_location'}));
 422
 423 my @project_types = CXGN::Trial::get_all_project_types($f->bcs_schema());
 424 my @all_project_types;
 425 foreach (@project_types) {
 426     push @all_project_types, $_->[1];
 427 }
 428 @all_project_types = sort @all_project_types;
 429 print STDERR Dumper \@all_project_types;
 430 is_deeply(\@all_project_types, [
 431           'Advanced Yield Trial',
 432           'Clonal Evaluation',
 433           'Preliminary Yield Trial',
 434           'Screen House',
 435           'Seed Multiplication',
 436           'Seedling Nursery',
 437           'Sensory Trial',
 438           'Specialty Trial',
 439           'Uniform Yield Trial',
 440           'Variety Release Trial',
 441           'activity_record',
 442           'crossing_block_trial',
 443           'crossing_trial',
 444           'genetic_gain_trial',
 445           'genotyping_project',
 446           'genotyping_trial',
 447           'grafting_trial',
 448           'health_status_trial',
 449           'heterosis_trial',
 450           'misc_trial',
 451           'phenotyping_trial',
 452           'pollinating_trial',
 453           'storage_trial',
 454           'transformation_project'
 455       ], "check get_all_project_types");
 456
 457
 458 my $stock_count_rs = $f->bcs_schema()->resultset("Stock::Stock")->search( { } );
 459 my $initial_stock_count = $stock_count_rs->count();
 460
 461 my $number_of_reps = 3;
 462 my $stock_list = [ 'test_accession1', 'test_accession2', 'test_accession3' ];
 463 # print STDERR "\n\n Before creating trial design\n\n";
 464 my $td = CXGN::Trial::TrialDesign->new(
 465     {
 466         schema => $f->bcs_schema(),
 467         trial_name => "anothertrial",
 468         stock_list => $stock_list,
 469         number_of_reps => $number_of_reps,
 470         block_size => 2,
 471         design_type => 'RCBD',
 472         number_of_blocks => 3,
 473     });
 474
 475 # print STDERR "\n\n After creating trial design\n\n";
 476
 477 my $number_of_plots = $number_of_reps * scalar(@$stock_list);
 478 # print STDERR "\n\n before calculating design! \n\n";
 479
 480 $td->calculate_design();
 481 # print STDERR "\n\nGot passed calculating design! \n\n";
 482
 483 my $trial_design = $td->get_design();
 484 # print STDERR "\n\nTrial Design  :".Dumper($trial_design)."\n\n";
 485
 486
 487 my $breeding_program_row = $f->bcs_schema->resultset("Project::Project")->find( { name => 'test' });
 488 my $trial_type_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($f->bcs_schema, 'Advanced Yield Trial', 'project_type')->cvterm_id();
 489
 490 my $new_trial = CXGN::Trial::TrialCreate->new(
 491   {
 492     dbh => $f->dbh(),
 493     chado_schema => $f->bcs_schema(),
 494     user_name => 'janedoe', #not implemented
 495     program => 'test',
 496     trial_year => 2014,
 497
 498     trial_description => 'another test trial...',
 499     design_type => 'RCBD',
 500     trial_type => $trial_type_cvterm_id,
 501     trial_location => 'test_location',
 502     trial_name => "anothertrial",
 503     design => $trial_design,
 504     owner_id => 41,
 505     operator => 'janedoe'
 506   });
 507
 508 my $save = $new_trial->save_trial();
 509
 510 my $after_design_creation_count = $stock_count_rs->count();
 511
 512 is($number_of_plots + $initial_stock_count, $after_design_creation_count, "check stock table count after trial creation.");
 513
 514 my $trial_rs = $f->bcs_schema->resultset("Project::Project")->search( { name => 'anothertrial' });
 515
 516 my $trial_id = 0;
 517
 518 if ($trial_rs->count() > 0) {
 519     $trial_id = $trial_rs->first()->project_id();
 520 }
 521
 522 if (!$trial_id) { die "Test failed... could not retrieve trial\n"; }
 523
 524 my $trial = CXGN::Trial->new( { bcs_schema => $f->bcs_schema(),
 525                                 trial_id => $trial_id });
 526
 527 my $breeding_programs = $trial->get_breeding_programs();
 528 #print STDERR Dumper $breeding_programs;
 529 my @breeding_program_names;
 530 foreach (@$breeding_programs){
 531     push @breeding_program_names, $_->[1];
 532 }
 533 @breeding_program_names = sort @breeding_program_names;
 534 #print STDERR Dumper \@breeding_program_names;
 535 is_deeply(\@breeding_program_names, ['test'], "check breeding_program_names");
 536
 537 print STDERR Dumper($trial_design);
 538 my $plot_name = $trial_design->{9}->{plot_name};
 539 print STDERR "PLOT NAME = $plot_name\n";
 540 my $rs = $f->bcs_schema()->resultset("Stock::Stock")->search( { name => $plot_name });
 541 is($rs->count(), 1, "check that a single plot was saved for a single name.");
 542 is($rs->first->name(), $plot_name, 'check that plot name was saved correctly');
 543
 544 if ($rs->count() > 0) {
 545     print STDERR "antohertrial1 has id ".$rs->first()->stock_id()."\n";
 546 }
 547 else {
 548     print STDERR "anothertrial1 does not exist!\n";
 549 }
 550
 551 # Test addition and deletion of phenotypic data
 552 #
 553 my $phenotype_count_before_store = $trial->phenotype_count();
 554
 555 ok($trial->phenotype_count() == 0, "trial has no phenotype data");
 556 my $plotlist_ref = [ $trial_design->{7}->{plot_name}, $trial_design->{8}->{plot_name}, $trial_design->{9}->{plot_name} ];
 557
 558 my $traitlist_ref = [ 'root number|CO_334:0000011', 'dry yield|CO_334:0000014' ];
 559
 560 my %plot_trait_value = ( $trial_design->{7}->{plot_name} => { 'root number|CO_334:0000011'  => [0,''], 'dry yield|CO_334:0000014' => [30,''] },
 561                            $trial_design->{8}->{plot_name} => { 'root number|CO_334:0000011'  => [10,''], 'dry yield|CO_334:0000014' => [40,''] },
 562                            $trial_design->{9}->{plot_name} => { 'root number|CO_334:0000011'  => [20,''], 'dry yield|CO_334:0000014' => [50,''] },
 563     );
 564
 565
 566 my %metadata = ( operator => 'johndoe', date => '20141223' );
 567
 568 my $total_phenotypes_before_store = $trial->total_phenotypes();
 569
 570 my $lp = CXGN::Phenotypes::StorePhenotypes->new(
 571     basepath=>$f->config->{basepath},
 572     dbhost=>$f->config->{dbhost},
 573     dbname=>$f->config->{dbname},
 574     dbuser=>$f->config->{dbuser},
 575     dbpass=>$f->config->{dbpass},
 576     temp_file_nd_experiment_id=>$f->config->{cluster_shared_tempdir}."/test_temp_nd_experiment_id_delete",
 577     bcs_schema=>$f->bcs_schema,
 578     metadata_schema=>$f->metadata_schema,
 579     phenome_schema=>$f->phenome_schema,
 580     user_id=>41,
 581     stock_list=>$plotlist_ref,
 582     trait_list=>$traitlist_ref,
 583     values_hash=>\%plot_trait_value,
 584     has_timestamps=>0,
 585     overwrite_values=>0,
 586     metadata_hash=>\%metadata,
 587     composable_validation_check_name=>$f->config->{composable_validation_check_name}
 588 );
 589
 590 $lp->store();
 591
 592 my $total_phenotypes = $trial->total_phenotypes();
 593
 594 my $trial_phenotype_count = $trial->phenotype_count();
 595
 596 #print STDERR "Total phentoypes: $total_phenotypes\n";
 597 #print STDERR "Trial phentoypes: $trial_phenotype_count\n";
 598 is($total_phenotypes, $total_phenotypes_before_store + 6, "total phenotype data");
 599 is($trial_phenotype_count, 6, "trial has phenotype data");
 600
 601 my $tn = CXGN::Trial->new( { bcs_schema => $f->bcs_schema(),
 602                                 trial_id => $trial_id });
 603
 604 my $traits_assayed  = $tn->get_traits_assayed();
 605 my @traits_assayed_names;
 606 #print STDERR Dumper $traits_assayed;
 607 foreach (@$traits_assayed) {
 608     push @traits_assayed_names, $_->[1];
 609 }
 610 @traits_assayed_names = sort @traits_assayed_names;
 611 #print STDERR Dumper \@traits_assayed_names;
 612 is_deeply(\@traits_assayed_names, ['dry yield|CO_334:0000014', 'root number counting|CO_334:0000011'], 'check traits assayed' );
 613
 614 my @pheno_for_trait = $tn->get_phenotypes_for_trait(70727);
 615 my @pheno_for_trait_sorted = sort {$a <=> $b} @pheno_for_trait;
 616 #print STDERR Dumper \@pheno_for_trait_sorted;
 617 is_deeply(\@pheno_for_trait_sorted, ['30','40','50'], 'check traits assayed' );
 618
 619 my $plot_pheno_for_trait = $tn->get_stock_phenotypes_for_traits([70727], 'all', ['plot_of','plant_of'], 'accession', 'subject');
 620 print STDERR Dumper "PHENO FOR TRAIT: $plot_pheno_for_trait\n";
 621 my @phenotyped_stocks;
 622 my @phenotyped_stocks_values;
 623 foreach (@$plot_pheno_for_trait) {
 624     push @phenotyped_stocks, $_->[1];
 625     push @phenotyped_stocks_values, $_->[7];
 626 }
 627 @phenotyped_stocks = sort @phenotyped_stocks;
 628 @phenotyped_stocks_values = sort @phenotyped_stocks_values;
 629 my @expected_sorted_stocks = sort ($trial_design->{7}->{plot_name}, $trial_design->{8}->{plot_name}, $trial_design->{9}->{plot_name});
 630 print STDERR Dumper \@phenotyped_stocks;
 631 print STDERR Dumper \@expected_sorted_stocks;
 632 is_deeply(\@phenotyped_stocks, \@expected_sorted_stocks, "check phenotyped stocks");
 633 is_deeply(\@phenotyped_stocks_values, ['30', '40', '50'], "check phenotyped stocks 2");
 634
 635 my $trial_experiment_count = $trial->get_experiment_count();
 636 print STDERR $trial_experiment_count."\n";
 637 is($trial_experiment_count, 4, "check get_experiment_count");
 638
 639 my $location_type_id = $trial->get_location_type_id();
 640 #print STDERR $location_type_id."\n";
 641 is($location_type_id, 76462, "check get_location_type_id");
 642
 643 my $year_type_id = $trial->get_year_type_id();
 644 #print STDERR $year_type_id."\n";
 645 is($year_type_id, 76395, "check get_year_type_id");
 646
 647 my $bp_trial_rel_cvterm_id = $trial->get_breeding_program_trial_relationship_cvterm_id();
 648 #print STDERR $bp_trial_rel_cvterm_id,"\n";
 649 is($bp_trial_rel_cvterm_id, 76448, "check get_breeding_program_trial_relationship_cvterm_id");
 650
 651 my $bp_cvterm_id = $trial->get_breeding_program_cvterm_id();
 652 #print STDERR $bp_cvterm_id."\n";
 653 is($bp_cvterm_id, 76440, "check get_breeding_program_cvterm_id");
 654
 655 my $folder = $trial->get_folder();
 656 #print STDERR $folder->name."\n";
 657 is($folder->name, 'test', 'check get_folder when no folder associated. should return bp name');
 658
 659 my $folder = CXGN::Trial::Folder->create({
 660   bcs_schema => $f->bcs_schema(),
 661   parent_folder_id => 0,
 662   name => 'F1',
 663   breeding_program_id => $breeding_program_row->project_id(),
 664 });
 665 my $folder_id = $folder->folder_id();
 666
 667 my $folder = CXGN::Trial::Folder->new({
 668     bcs_schema => $f->bcs_schema(),
 669     folder_id => $trial_id
 670 });
 671
 672 $folder->associate_parent($folder_id);
 673
 674 my $folder = $trial->get_folder();
 675 #print STDERR $folder->name."\n";
 676 is($folder->name, 'F1', 'check get_folder after folder associated');
 677
 678 my $harvest_date_cvterm_id = $trial->get_harvest_date_cvterm_id();
 679 #print STDERR $harvest_date_cvterm_id."\n";
 680 is($harvest_date_cvterm_id, 76495, "check get_harvest_date_cvterm_id");
 681
 682 my $planting_date_cvterm_id = $trial->get_planting_date_cvterm_id();
 683 #print STDERR $planting_date_cvterm_id."\n";
 684 is($planting_date_cvterm_id, 76496, "check get_planting_date_cvterm_id");
 685
 686 my $design_type = $trial->get_design_type();
 687 #print STDERR $design_type."\n";
 688 is($design_type, 'RCBD', 'check get_design_type');
 689
 690 my $trial_accessions = $trial->get_accessions();
 691 #print STDERR Dumper $trial_accessions;
 692 my @trial_accession_names;
 693 foreach (@$trial_accessions) {
 694     push @trial_accession_names, $_->{'accession_name'};
 695 }
 696 @trial_accession_names = sort @trial_accession_names;
 697 is_deeply(\@trial_accession_names, ['test_accession1', 'test_accession2', 'test_accession3'], "check get_accessions");
 698
 699 my $trial_plots = $trial->get_plots();
 700 my @trial_plot_names;
 701 foreach (@$trial_plots){
 702     push @trial_plot_names, $_->[1];
 703 }
 704 @trial_plot_names = sort @trial_plot_names;
 705 print STDERR "Num plots: ".scalar(@trial_plot_names)."\n";
 706 is(scalar(@trial_plot_names), 9, 'check number of plots');
 707
 708 print STDERR "DESIGN NOW: ".Dumper($trial_design);
 709
 710
 711 #my @expected_sorted_plots = sort ($trial_design->{11}->{plot_name}, $trial_design->{12}->{plot_name}, $trial_design->{13}->{plot_name}, $trial_design->{21}->{plot_name}, $trial_design->{22}->{plot_name}, $trial_design->{23}->{plot_name}, $trial_design->{31}->{plot_name}, $trial_design->{32}->{plot_name}, $trial_design->{33}->{plot_name});
 712 my @expected_sorted_plots = sort ($trial_design->{1}->{plot_name}, $trial_design->{2}->{plot_name}, $trial_design->{3}->{plot_name}, $trial_design->{4}->{plot_name}, $trial_design->{5}->{plot_name}, $trial_design->{6}->{plot_name}, $trial_design->{7}->{plot_name}, $trial_design->{8}->{plot_name}, $trial_design->{9}->{plot_name});
 713 print STDERR "TRIAL PLOT NAMES: ". Dumper \@trial_plot_names;
 714 print STDERR "TRIAL SORTED PLOTS: ".Dumper \@expected_sorted_plots;
 715 is_deeply(\@trial_plot_names, \@expected_sorted_plots, 'Check get_plots 1');
 716
 717 my $trial_controls = $trial->get_controls();
 718 #print STDERR Dumper $trial_controls;
 719 is_deeply($trial_controls, [], "check get_controls");
 720
 721 #add plant entries
 722 my $num_plants_add = 3;
 723 $trial->create_plant_entities($num_plants_add);
 724 #print STDERR Dumper($trial);
 725 ok($trial->has_plant_entries(), "check if plant entries created.");
 726
 727 my $trial = CXGN::Trial->new( { bcs_schema => $f->bcs_schema(), trial_id => $trial_id });
 728 my $plants = $trial->get_plants();
 729 #print STDERR Dumper $plants;
 730 is(scalar(@$plants), $number_of_plots*3, "check if the right number of plants was created");
 731
 732 my $plantlist_ref = [ $trial_design->{7}->{plot_name}.'_plant_2', $trial_design->{8}->{plot_name}.'_plant_2', $trial_design->{9}->{plot_name}.'_plant_1' ];
 733
 734 my $traitlist_ref = [ 'root number|CO_334:0000011', 'dry yield|CO_334:0000014', 'harvest index|CO_334:0000015' ];
 735
 736 my %plant_trait_value = ( $trial_design->{7}->{plot_name}.'_plant_2' => { 'root number|CO_334:0000011'  => [12,''], 'dry yield|CO_334:0000014' => [30,''], 'harvest index|CO_334:0000015' => [2,''] },
 737     $trial_design->{8}->{plot_name}.'_plant_2' => { 'root number|CO_334:0000011'  => [10,''], 'dry yield|CO_334:0000014' => [40,''], 'harvest index|CO_334:0000015' => [3,''] },
 738     $trial_design->{9}->{plot_name}.'_plant_1' => { 'root number|CO_334:0000011'  => [20,''], 'dry yield|CO_334:0000014' => [50,''], 'harvest index|CO_334:0000015' => [7,''] },
 739 );
 740
 741 my %metadata = ( operator => 'johndoe', date => '20141225' );
 742
 743 my $total_phenotype_count_before_save2 = $trial->total_phenotypes();
 744
 745 my $lp = CXGN::Phenotypes::StorePhenotypes->new({
 746     basepath=>$f->config->{basepath},
 747     dbhost=>$f->config->{dbhost},
 748     dbname=>$f->config->{dbname},
 749     dbuser=>$f->config->{dbuser},
 750     dbpass=>$f->config->{dbpass},
 751     temp_file_nd_experiment_id=>$f->config->{cluster_shared_tempdir}."/test_temp_nd_experiment_id_delete",
 752     bcs_schema=>$f->bcs_schema,
 753     metadata_schema=>$f->metadata_schema,
 754     phenome_schema=>$f->phenome_schema,
 755     user_id=>41,
 756     stock_list=>$plantlist_ref,
 757     trait_list=>$traitlist_ref,
 758     values_hash=>\%plant_trait_value,
 759     has_timestamps=>0,
 760     overwrite_values=>0,
 761     metadata_hash=>\%metadata,
 762     composable_validation_check_name=>$f->config->{composable_validation_check_name}
 763 });
 764 $lp->store();
 765
 766 my $total_phenotypes = $trial->total_phenotypes();
 767
 768 my $trial_phenotype_count = $trial->phenotype_count();
 769
 770 print STDERR "Total phentoypes: $total_phenotypes\n";
 771 print STDERR "Trial phentoypes: $trial_phenotype_count\n";
 772 is($total_phenotypes, $total_phenotype_count_before_save2 + 9, "total phenotype data");
 773 is($trial_phenotype_count, 15, "trial has phenotype data");
 774
 775 my $tn = CXGN::Trial->new( { bcs_schema => $f->bcs_schema(),
 776                                 trial_id => $trial_id });
 777
 778 my $traits_assayed  = $tn->get_traits_assayed();
 779 my @traits_assayed_sorted = sort {$a->[0] cmp $b->[0]} @$traits_assayed;
 780 #print STDERR Dumper \@traits_assayed_sorted;
 781
 782 my @traits_assayed_check = (['70668','Harvest index variable'],['70706','Root number counting'],['70727','Dry yield']);
 783
 784 #is_deeply(\@traits_assayed_sorted, \@traits_assayed_check, 'check traits assayed' );
 785
 786 my @pheno_for_trait = $tn->get_phenotypes_for_trait(70706);
 787 my @pheno_for_trait_sorted = sort {$a <=> $b} @pheno_for_trait;
 788 #print STDERR Dumper \@pheno_for_trait_sorted;
 789 my @pheno_for_trait_check = (0, 10, 10, 12, 20, 20);
 790 is_deeply(\@pheno_for_trait_sorted, \@pheno_for_trait_check, 'check traits assayed' );
 791
 792 my @pheno_for_trait = $tn->get_phenotypes_for_trait(70668);
 793 my @pheno_for_trait_sorted = sort {$a <=> $b} @pheno_for_trait;
 794 #print STDERR Dumper \@pheno_for_trait_sorted;
 795 my @pheno_for_trait_check = (2,3,7);
 796 is_deeply(\@pheno_for_trait_sorted, \@pheno_for_trait_check, 'check traits assayed' );
 797
 798 my @pheno_for_trait = $tn->get_phenotypes_for_trait(70727);
 799 my @pheno_for_trait_sorted = sort {$a <=> $b} @pheno_for_trait;
 800 #print STDERR Dumper \@pheno_for_trait_sorted;
 801 my @pheno_for_trait_check = (30,30,40,40,50,50);
 802 is_deeply(\@pheno_for_trait_sorted, \@pheno_for_trait_check, 'check traits assayed' );
 803
 804
 805 my $retrieve_accessions = $trial->get_accessions();
 806 #print STDERR Dumper $retrieve_accessions;
 807 my @get_accessions_names;
 808 foreach (@$retrieve_accessions){
 809     push @get_accessions_names, $_->{'accession_name'};
 810 }
 811 @get_accessions_names = sort @get_accessions_names;
 812 #print STDERR Dumper \@get_accessions_names;
 813 is_deeply(\@get_accessions_names, [
 814           'test_accession1',
 815           'test_accession2',
 816           'test_accession3'
 817         ], 'check get_accessions');
 818
 819 my $retrieve_plots = $trial->get_plots();
 820 #print STDERR Dumper $retrieve_plots;
 821 my @get_plot_names;
 822 foreach (@$retrieve_plots){
 823     push @get_plot_names, $_->[1];
 824 }
 825 @get_plot_names = sort @get_plot_names;
 826 print STDERR "PLOT NAMES NOW: ". Dumper \@get_plot_names;
 827 print STDERR "EXPECTED PLOT NAMES NOW: ".Dumper \@expected_sorted_plots;
 828 is_deeply(\@get_plot_names, \@expected_sorted_plots, "check get_plots 2");
 829
 830 my @expected_plants;
 831 foreach (@expected_sorted_plots) {
 832     for my $i (1..$num_plants_add){
 833         push @expected_plants, $_."_plant_".$i;
 834     }
 835 }
 836 my @expected_sorted_plants = sort @expected_plants;
 837
 838 my $retrieve_plants = $trial->get_plants();
 839 #print STDERR Dumper $retrieve_plants;
 840 my @get_plant_names;
 841 foreach (@$retrieve_plants){
 842     push @get_plant_names, $_->[1];
 843 }
 844 @get_plant_names = sort @get_plant_names;
 845 print STDERR Dumper \@get_plant_names;
 846 is_deeply(\@get_plant_names, \@expected_sorted_plants, "check get_plants()");
 847
 848
 849 # check trial deletion - first, delete associated phenotypes
 850 #
 851 my $del_ret = $trial->delete_phenotype_data($f->config->{basepath}, $f->config->{dbhost}, $f->config->{dbname}, $f->config->{dbuser}, $f->config->{dbpass}, $f->config->{cluster_shared_tempdir}."/test_temp_nd_experiment_id_delete");
 852 ok(!$del_ret);
 853 print STDERR Dumper $del_ret;
 854
 855 ok($trial->phenotype_count() ==0, "phenotype data deleted");
 856
 857 is($trial->total_phenotypes(), $total_phenotypes - $trial_phenotype_count, "check total phenotypes");
 858
 859 # check trial layout deletion
 860 #
 861 my $error = $trial->delete_field_layout();
 862
 863 ok(! $error, "no error upon layout deletion");
 864
 865 my $after_design_deletion_count = $stock_count_rs->count();
 866
 867 is( $after_design_deletion_count, $initial_stock_count, "check that stock counts before layout creation and after deletion match");
 868
 869 # test name accessors
 870 #
 871 is($trial->get_name(), "anothertrial");
 872 $trial->set_name("anothertrial modified");
 873 is($trial->get_name(), "anothertrial modified");
 874
 875 # test description accessors
 876 #
 877 my $desc = $trial->get_description();
 878
 879 ok($desc == "test_trial", "another test trial...");
 880
 881 $trial->set_description("blablabla");
 882
 883 is($trial->get_description(), "blablabla", "description setter test");
 884
 885 # test harvest_date accessors
 886 #
 887 $trial->set_harvest_date('2016/01/01 12:20:10');
 888 my $harvest_date = $trial->get_harvest_date();
 889 #print STDERR Dumper $harvest_date;
 890 is($harvest_date, '2016-January-01 12:20:10', "set harvest_date test");
 891 $trial->remove_harvest_date('2016/01/01 12:20:10');
 892 $harvest_date = $trial->get_harvest_date();
 893 ok(!$harvest_date, "test remove harvest_date");
 894
 895 # test planting_date accessors
 896 #
 897 $trial->set_planting_date('2016/01/01 12:20:10');
 898 my $planting_date = $trial->get_planting_date();
 899 #print STDERR Dumper $planting_date;
 900 is($planting_date, '2016-January-01 12:20:10', "set harvest_date test");
 901 $trial->remove_planting_date('2016/01/01 12:20:10');
 902 $planting_date = $trial->get_planting_date();
 903 ok(!$planting_date, "test remove planting_date");
 904
 905 # test transplanting_date accessors
 906 $trial->set_transplanting_date('2016/01/02 12:21:11');
 907 my $transplanting_date = $trial->get_transplanting_date();
 908 #print STDERR Dumper $transplanting_date;
 909 is($transplanting_date, '2016-January-02 12:21:11', "set transplanting_date test");
 910 $trial->set_transplanting_date('2016/01/03 12:21:11');
 911 $transplanting_date = $trial->get_transplanting_date();
 912 is($transplanting_date, '2016-January-03 12:21:11', "update/set transplanting_date test");
 913 $trial->remove_transplanting_date('2016/01/03 12:21:11');
 914 $transplanting_date = $trial->get_transplanting_date();
 915 ok(!$transplanting_date, "test remove transplanting_date");
 916
 917 # test transplantnig date accessors visibility
 918 $trial->set_transplanting_date('2023/06/15 12:21:14');
 919 my $transplanting_date = $trial->get_transplanting_date();
 920 is($transplanting_date, '2023-June-15 12:21:14', "set transplanting_date test");
 921 $trial->set_transplanting_date('2023/06/16 12:21:14');
 922 $transplanting_date = $trial->get_transplanting_date();
 923 is($transplanting_date, '2023-June-16 12:21:14', "update/set transplanting_date test");
 924 $trial->remove_transplanting_date('2023/06/16 12:21:14');
 925 $transplanting_date = $trial->get_transplanting_date();
 926 ok(!$transplanting_date, "remove transplanting_date test");
 927
 928 #test transplanting_date accessors
 929 $trial->set_transplanting_date('2017/02/03 12:21:12');
 930 my $transplanting_date = $trial->get_transplanting_date();
 931 #print STDERR Dumper $transplanting_date;
 932 is($transplanting_date, '2017-February-03 12:21:12', "set transplanting_date test");
 933 $trial->set_transplanting_date('2017/02/04 12:21:13');
 934 $transplanting_date = $trial->get_transplanting_date();
 935 is($transplanting_date, '2017-February-04 12:21:13', "update/set transplanting_date test");
 936 $trial->remove_transplanting_date('2017/02/04 12:21:13');
 937 $transplanting_date = $trial->get_transplanting_date();
 938 ok(!$transplanting_date, "test remove transplanting_date");
 939
 940 # test year accessors
 941 #
 942 is($trial->get_year(), 2014, "get year test");
 943
 944 $trial->set_year(2013);
 945 is($trial->get_year(), 2013, "set year test");
 946
 947 # test planting date accessors
 948 #
 949 #$trial-> set_planting_date ('2016/01/02 12:21:12');
 950 #my $planting_date = $trial -> get_planting_date();
 951 #print STDERR Dumper $planting_date;
 952 #is($planting_date, '2016-January-02 12:21:12', "set planting_date test");
 953 #$trial-> set_planting_date('2016/01/04 12:21:12');
 954 #$planting_date = $trial-> get_planting_date();
 955 #is($planting_date, '2016-January-04 12:21:12', "update/set planting_date test");
 956 #$trial-> remove_planting_date ('2016/01/04 12:21:12');
 957 #$planting_date = $trial-> get_planting_date();
 958 #ok(!$planting_date, "test remove planting_date");
 959
 960 # test breeding program accessors
 961 #
 962 is($trial->get_breeding_program(), 'test', "get breeding program test");
 963
 964 $trial->set_breeding_program($breeding_program_row->project_id());
 965 is($trial->get_breeding_program(), 'test', "set breeding program test");
 966
 967 # test location accessors
 968 #
 969 is_deeply($trial->get_location(), [ 23, 'test_location' ], "get location");
 970
 971 $trial->set_location(23);
 972 is_deeply($trial->get_location(), [ 23, 'test_location' ], "set location");
 973
 974 # test project type accessors
 975 #
 976 is($trial->get_project_type()->[1], "Advanced Yield Trial", "get type test");
 977
 978 my $error = $trial->set_project_type("77106");
 979
 980 is($trial->get_project_type()->[1], "Clonal Evaluation", "set type test");
 981
 982 print STDERR "DELETING PROJECT ENTRY... ";
 983 $trial->delete_project_entry();
 984 print STDERR "Done.\n";
 985
 986 my $deleted_trial;
 987 eval {
 988      $deleted_trial = CXGN::Trial->new( { bcs_schema => $f->bcs_schema, trial_id=>$trial_id });
 989 };
 990
 991 if ($@) { print "An error occurred: $@\n"; }
 992 ok($@, "deleted trial id (".$@.")");
 993
 994
 995 done_testing();