lib/CXGN/Trial/TrialDesignStore/AbstractTrial.pm

   1
   2 =head1 NAME
   3
   4 CXGN::Trial::TrialDesignStore::AbstractTrial - a class to provide function in common to all subclasses of trial store objects.
   5
   6 =cut
   7
   8 package CXGN::Trial::TrialDesignStore::AbstractTrial;
   9
  10 use Moose;
  11 use MooseX::FollowPBP;
  12 use Try::Tiny;
  13 use Data::Dumper;
  14 use CXGN::Stock;
  15 use JSON;
  16
  17 =head1 ACCESSORS
  18
  19 =head2 bcs_schema()
  20
  21 Bio::Chado::Schema object, required parameter.
  22
  23 =cut
  24
  25 has 'bcs_schema' => (
  26     is       => 'rw',
  27     isa      => 'DBIx::Class::Schema',
  28     predicate => 'has_chado_schema',
  29     required => 1,
  30 );
  31
  32 =head2 set_trial_id(), get_trial_id()
  33
  34 The trial id, which essentially is a project_id. Required.
  35
  36 =cut
  37
  38 has 'trial_id' => (isa => 'Int', is => 'rw', predicate => 'has_trial_id', required => 1);
  39
  40 =head2 set_trial_name(), get_trial_name()
  41
  42 The name of the trial. Should be unique in the database.
  43
  44 =cut
  45
  46 has 'trial_name' => (isa => 'Str', is => 'rw', predicate => 'has_trial_name', required => 0);
  47
  48 =head2 set_nd_experiment_id(), get_nd_experiment_id(), has_nd_experiment_id()
  49
  50 The nd_experiment_id of the associated design data.
  51
  52 =cut
  53
  54 has 'nd_experiment_id' => (isa => 'Int', is => 'rw', predicate => 'has_nd_experiment_id', required => 0);
  55
  56 =head2 set_nd_geolocation_id(), get_nd_geolocation_id(), has_nd_geolocation_id()
  57
  58 The nd_geolocation_id of this trial (globally, not individiual plots etc). Required.
  59
  60 =cut
  61
  62 has 'nd_geolocation_id' => (isa => 'Int', is => 'rw', predicate => 'has_nd_geolocation_id', required => 1);
  63
  64 =head2 set_design_type(), get_design_type(), has_design_type()
  65
  66 The type of the design. CBSD, etc. Optional.
  67
  68 =cut
  69
  70 has 'design_type' => (isa => 'Maybe[Str]', is => 'rw', predicate => 'has_design_type', required => 0);
  71
  72 =head2 set_design(), get_design(), has_design()
  73
  74 The Perl design data structure.
  75
  76 =cut
  77
  78 has 'design' => (isa => 'HashRef[HashRef]|Undef', is => 'rw', predicate => 'has_design', required => 1);
  79
  80 =head2 set_is_genotyping(), get_is_genotyping()
  81
  82 Whether this is a genotyping experiment. (deprecated; rather, check the object type).
  83
  84 =cut
  85
  86 has 'is_genotyping' => (isa => 'Bool', is => 'rw', required => 0, default => 0);
  87
  88 =head2 set_is_analysis(), get_is_analysis()
  89
  90 Whether the object is an analysis object. Assumes is_genotyping to be false.
  91
  92 =cut
  93
  94 has 'is_analysis' => (isa => 'Bool', is => 'rw', required => 0, default => 0);
  95
  96 =head2 set_is_sampling_trial(), get_is_sampling_trial()
  97
  98 Whether the object is a sampling trial object. Assumes is_sampling_trial to be false.
  99
 100 =cut
 101
 102 has 'is_sampling_trial' => (isa => 'Bool', is => 'rw', required => 0, default => 0);
 103
 104 =head2 set_stock_exist(), get_stock_exist()
 105
 106 If the stocks in the design were checked and whether the check passed. Internal use only.
 107
 108 =cut
 109
 110 has 'stocks_exist' => (isa => 'Bool', is => 'rw', required => 0, default => 0);
 111
 112 =head2 set_new_treatment_has_plant_entries(), get_new_treatment_has_plant_entries()
 113
 114 Whether this treatment has plant entries.
 115
 116 =cut
 117
 118 has 'new_treatment_has_plant_entries' => (isa => 'Maybe[Int]', is => 'rw', required => 0, default => 0);
 119
 120 =head2 set_new_treatment_has_subplot_entries(), get_new_treatment_has_subplot_entries()
 121
 122 Whether this treatment has subplot entries.
 123
 124 =cut
 125
 126 has 'new_treatment_has_subplot_entries' => (isa => 'Maybe[Int]', is => 'rw', required => 0, default => 0);
 127
 128 =head2 set_new_treatment_has_tissue_sample_entries(), get_new_treatment_has_tissue_sample_entries()
 129
 130 Whether this treatment has tissue_sample entries.
 131
 132 =cut
 133
 134 has 'new_treatment_has_tissue_sample_entries' => (isa => 'Maybe[Int]', is => 'rw', required => 0, default => 0);
 135
 136 =head2 set_new_treatment_date, get_new_treatment_date()
 137
 138 A new treatment date.
 139
 140 =cut
 141
 142 has 'new_treatment_date' => (isa => 'Maybe[Str]', is => 'rw', required => 0, default => 0);
 143
 144 =head2 set_new_treatment_year, get_new_treatment_year()
 145
 146 A new treatment year.
 147
 148 =cut
 149
 150
 151 has 'new_treatment_year' => (isa => 'Maybe[Str]', is => 'rw', required => 0, default => 0);
 152
 153 =head2 set_new_treatment_type, get_new_treatment_type()
 154
 155 A new treatment type.
 156
 157 =cut
 158
 159 has 'new_treatment_type' => (isa => 'Maybe[Str]', is => 'rw', required => 0, default => 0);
 160
 161 =head2 set_operator(), get_operator()
 162
 163 An name for an operator performing the action.
 164
 165 =cut
 166
 167 has 'operator' => (isa => 'Str', is => 'rw', required => 1);
 168
 169 =head2 set_owner_id(), get_owner_id()
 170
 171 An owner id
 172
 173 =cut
 174
 175 has 'owner_id' => (isa => 'Int', is => 'rw', required => 0);
 176
 177 =head2 set_source_stock_types(), get_source_stock_types()
 178
 179 The source stock types. Needs to be defined in the constructor (BUILD) of the subclass.
 180
 181 =cut
 182
 183 has 'source_stock_types' => (isa => 'ArrayRef', is => 'rw');
 184
 185 =head1 CVTERM accessors
 186
 187 =head2 set_nd_experiment_type_id(), get_nd_experiment_type_id()
 188
 189 The experiment type id for the trial category.
 190 The values are:
 191 xxx for field trials
 192 yyy for genotyping trials
 193 zzz for analyses
 194
 195 =cut
 196
 197 has 'nd_experiment_type_id' => (isa => 'Int', is => 'rw');
 198
 199 =head2 set_stock_relationship_type_id(), get_stock_relationship_type_id()
 200
 201 The stock_relationship_type_id of the elements in the design.
 202
 203 =cut
 204
 205 has 'stock_relationship_type_id' => (isa => 'Int', is => 'rw');
 206
 207 =head2 set_stock_type_id(), get_stock_type_id()
 208
 209 The stock type_id of the elements in the design.
 210
 211 =cut
 212
 213 has 'stock_type_id' => (isa => 'Int', is => 'rw');
 214
 215 =head2 set_valid_properties(), get_valid_properties()
 216
 217 The properties that are valid in the object for validation purposes. Needs to be set in the constructor of the subclass.
 218
 219 =cut
 220
 221 has 'valid_properties' => (isa => 'Maybe[ArrayRef]', is => 'rw');
 222
 223 has 'seedlot_cvterm_id'  => (isa => 'Int', is => 'rw');
 224
 225 has 'accession_cvterm_id'  => (isa => 'Int', is => 'rw');
 226
 227 has 'tissue_sample_cvterm_id'  => (isa => 'Int', is => 'rw');
 228
 229 has 'tissue_sample_of_cvterm_id'  => (isa => 'Int', is => 'rw');
 230
 231 has 'plot_cvterm_id' => (isa => 'Int', is => 'rw');
 232
 233 has 'plot_of_cvterm_id' => (isa => 'Int', is => 'rw');
 234
 235 has 'plant_cvterm_id' => (isa => 'Int', is => 'rw');
 236
 237 has 'subplot_cvterm_id' => (isa => 'Int', is => 'rw');
 238
 239 has 'subplot_of_cvterm_id' => (isa => 'Int', is => 'rw');
 240
 241 has 'plant_of_subplot_cvterm_id' => (isa => 'Int', is => 'rw');
 242
 243 has 'subplot_index_number_cvterm_id' => (isa => 'Int', is => 'rw');
 244
 245 has 'plant_of_cvterm_id' => (isa => 'Int', is => 'rw');
 246
 247 has 'plant_index_number_cvterm_id' => (isa => 'Int', is => 'rw');
 248
 249 has 'replicate_cvterm_id' => (isa => 'Int', is => 'rw');
 250
 251 has 'block_cvterm_id' => (isa => 'Int', is => 'rw');
 252
 253 has 'plot_number_cvterm_id' => (isa => 'Int', is => 'rw');
 254
 255 has 'is_control_cvterm_id' => (isa => 'Int', is => 'rw');
 256
 257 has 'range_cvterm_id' => (isa => 'Int', is => 'rw');
 258
 259 has 'row_number_cvterm_id' => (isa => 'Int', is => 'rw');
 260
 261 has 'col_number_cvterm_id' => (isa => 'Int', is => 'rw');
 262
 263 has 'is_blank_cvterm_id' => (isa => 'Int', is => 'rw');
 264
 265 has 'concentration_cvterm_id' => (isa => 'Int', is => 'rw');
 266
 267 has 'volume_cvterm_id' => (isa => 'Int', is => 'rw');
 268
 269 has 'dna_person_cvterm_id' => (isa => 'Int', is => 'rw');
 270
 271 has 'extraction_cvterm_id' => (isa => 'Int', is => 'rw');
 272
 273 has 'tissue_type_cvterm_id' => (isa => 'Int', is => 'rw');
 274
 275 has 'acquisition_date_cvterm_id' => (isa => 'Int', is => 'rw');
 276
 277 has 'ncbi_taxonomy_id_cvterm_id' => (isa => 'Int', is => 'rw');
 278
 279 has 'notes_cvterm_id' => (isa => 'Int', is => 'rw');
 280
 281 has 'treatment_nd_experiment_type_id' => (isa => 'Int', is => 'rw');
 282
 283 has 'project_design_cvterm_id' => (isa => 'Int', is => 'rw');
 284
 285 has 'management_factor_year_cvterm_id' => (isa => 'Int', is => 'rw');
 286
 287 has 'management_factor_date_cvterm_id' => (isa => 'Int', is => 'rw');
 288
 289 has 'management_factor_type_cvterm_id' => (isa => 'Int', is => 'rw');
 290
 291 has 'trial_treatment_relationship_cvterm_id' => (isa => 'Int', is => 'rw');
 292
 293 has 'has_plants_cvterm' => (isa => 'Int', is => 'rw');
 294
 295 has 'has_subplots_cvterm' => (isa => 'Int', is => 'rw');
 296
 297 has 'has_tissues_cvterm' => (isa => 'Int', is => 'rw');
 298
 299 has 'cross_cvterm_id' => (isa => 'Int', is => 'rw');
 300
 301 has 'family_name_cvterm_id' => (isa => 'Int', is => 'rw');
 302
 303 has 'facility_identifier_cvterm_id' => (isa => 'Int', is => 'rw');
 304
 305 sub BUILD {
 306     my $self = shift;
 307     my $chado_schema = $self->get_bcs_schema();
 308
 309     $self->set_seedlot_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'seedlot', 'stock_type')->cvterm_id());
 310
 311     $self->set_accession_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'accession', 'stock_type')->cvterm_id());
 312
 313     $self->set_tissue_sample_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'tissue_sample', 'stock_type')->cvterm_id());
 314
 315     $self->set_tissue_sample_of_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'tissue_sample_of', 'stock_relationship')->cvterm_id());
 316
 317     $self->set_plot_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'plot', 'stock_type')->cvterm_id());
 318
 319     $self->set_plot_of_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'plot_of', 'stock_relationship')->cvterm_id());
 320
 321     $self->set_plant_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'plant', 'stock_type')->cvterm_id());
 322
 323     $self->set_subplot_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'subplot', 'stock_type')->cvterm_id());
 324
 325     $self->set_subplot_of_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'subplot_of', 'stock_relationship')->cvterm_id());
 326
 327     $self->set_plant_of_subplot_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'plant_of_subplot', 'stock_relationship')->cvterm_id());
 328
 329     $self->set_subplot_index_number_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'subplot_index_number', 'stock_property')->cvterm_id());
 330
 331     $self->set_plant_of_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'plant_of', 'stock_relationship')->cvterm_id());
 332
 333     $self->set_plant_index_number_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'plant_index_number', 'stock_property')->cvterm_id());
 334
 335     $self->set_replicate_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'replicate', 'stock_property')->cvterm_id());
 336
 337     $self->set_block_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'block', 'stock_property')->cvterm_id());
 338
 339     $self->set_plot_number_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'plot number', 'stock_property')->cvterm_id());
 340
 341     $self->set_is_control_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'is a control', 'stock_property')->cvterm_id());
 342
 343     $self->set_range_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'range', 'stock_property')->cvterm_id());
 344
 345     $self->set_row_number_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'row_number', 'stock_property')->cvterm_id());
 346
 347     $self->set_col_number_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'col_number', 'stock_property')->cvterm_id());
 348
 349     $self->set_is_blank_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'is_blank', 'stock_property')->cvterm_id());
 350
 351     $self->set_concentration_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'concentration', 'stock_property')->cvterm_id());
 352
 353     $self->set_volume_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'volume', 'stock_property')->cvterm_id());
 354
 355     $self->set_dna_person_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'dna_person', 'stock_property')->cvterm_id());
 356
 357     $self->set_extraction_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'extraction', 'stock_property')->cvterm_id());
 358
 359     $self->set_tissue_type_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'tissue_type', 'stock_property')->cvterm_id());
 360
 361     $self->set_acquisition_date_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'acquisition date', 'stock_property')->cvterm_id());
 362
 363     $self->set_ncbi_taxonomy_id_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'ncbi_taxonomy_id', 'stock_property')->cvterm_id());
 364
 365     $self->set_notes_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'notes', 'stock_property')->cvterm_id());
 366
 367     $self->set_treatment_nd_experiment_type_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'treatment_experiment', 'experiment_type')->cvterm_id());
 368
 369     $self->set_project_design_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'design', 'project_property')->cvterm_id());
 370
 371     $self->set_management_factor_year_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'project year', 'project_property')->cvterm_id());
 372
 373     $self->set_management_factor_date_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'management_factor_date', 'project_property')->cvterm_id());
 374
 375     $self->set_management_factor_type_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'management_factor_type', 'project_property')->cvterm_id());
 376
 377     $self->set_trial_treatment_relationship_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'trial_treatment_relationship', 'project_relationship')->cvterm_id());
 378
 379     $self->set_has_plants_cvterm(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'project_has_plant_entries', 'project_property')->cvterm_id());
 380
 381     $self->set_has_subplots_cvterm(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'project_has_subplot_entries', 'project_property')->cvterm_id());
 382
 383     $self->set_has_tissues_cvterm(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'project_has_tissue_sample_entries', 'project_property')->cvterm_id());
 384
 385     $self->set_cross_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'cross', 'stock_type')->cvterm_id());
 386
 387     $self->set_family_name_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'family_name', 'stock_type')->cvterm_id());
 388
 389     $self->set_facility_identifier_cvterm_id(SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'facility_identifier', 'stock_property')->cvterm_id());
 390
 391 }
 392
 393 sub validate_design {
 394     print STDERR "Implement validate_design in subclass\n";
 395 }
 396
 397 sub store {
 398     print STDERR "Saving design ".localtime()."\n";
 399     my $self = shift;
 400     my $chado_schema = $self->get_bcs_schema;
 401     my $design_type = $self->get_design_type;
 402     my %design = %{$self->get_design};
 403     my $trial_id = $self->get_trial_id;
 404     my $nd_geolocation_id = $self->get_nd_geolocation_id;
 405
 406
 407     my $nd_experiment_type_id = $self->get_nd_experiment_type_id();
 408     my $stock_type_id = $self->get_stock_type_id();
 409     my $stock_rel_type_id = $self->get_stock_relationship_type_id();
 410     my $additional_info_type_id = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'stock_additional_info', 'stock_property')->cvterm_id();
 411
 412     my @source_stock_types = @{$self->get_source_stock_types()};
 413
 414     print STDERR "!!!!!! stock rel type id = $stock_rel_type_id, stock type_id = $stock_type_id\n";
 415
 416     #$chado_schema->storage->debug(1);
 417     my $nd_experiment_id;
 418     if ($self->has_nd_experiment_id){
 419         $nd_experiment_id = $self->get_nd_experiment_id();
 420     } else {
 421         my $nd_experiment_project;
 422         my $nd_experiment_project_rs = $chado_schema->resultset('NaturalDiversity::NdExperimentProject')->search(
 423             {
 424                 'me.project_id'=>$trial_id,
 425                 'nd_experiment.type_id'=>$self->get_nd_experiment_type_id,
 426                 'nd_experiment.nd_geolocation_id'=>$self->get_nd_geolocation_id
 427             },
 428             { join => 'nd_experiment'}
 429         );
 430
 431         if ($nd_experiment_project_rs->count < 1) {
 432             my $nd_experiment = $chado_schema->resultset('NaturalDiversity::NdExperiment')
 433             ->create({
 434                 nd_geolocation_id => $self->get_nd_geolocation_id,
 435                 type_id => $nd_experiment_type_id,
 436             });
 437             $nd_experiment_project = $nd_experiment->find_or_create_related('nd_experiment_projects', {project_id => $self->get_trial_id} );
 438         } elsif ($nd_experiment_project_rs->count > 1) {
 439             print STDERR "ERROR: More than one nd_experiment of type=$nd_experiment_type_id for project=$trial_id\n";
 440             $nd_experiment_project = $nd_experiment_project_rs->first;
 441         } elsif ($nd_experiment_project_rs->count == 1) {
 442             print STDERR "OKAY: NdExperimentProject type=$nd_experiment_type_id for project$trial_id\n";
 443             $nd_experiment_project = $nd_experiment_project_rs->first;
 444         }
 445         if ($nd_experiment_project){
 446             $nd_experiment_id = $nd_experiment_project->nd_experiment_id();
 447         }
 448     }
 449
 450     my %seen_accessions_hash;
 451     my %seen_seedlots_hash;
 452     foreach my $key (keys %design) {
 453         if ($design{$key}->{stock_name}) {
 454             my $stock_name = $design{$key}->{stock_name};
 455             $seen_accessions_hash{$stock_name}++;
 456         }
 457         if ($design{$key}->{seedlot_name}) {
 458             my $stock_name = $design{$key}->{seedlot_name};
 459             $seen_seedlots_hash{$stock_name}++;
 460         }
 461     }
 462     my @seen_accessions = keys %seen_accessions_hash;
 463     my @seen_seedlots = keys %seen_seedlots_hash;
 464
 465     my $seedlot_rs = $chado_schema->resultset('Stock::Stock')->search({
 466         'is_obsolete' => { '!=' => 't' },
 467         'type_id' => $self->get_seedlot_cvterm_id,
 468         'uniquename' => {-in=>\@seen_seedlots}
 469     });
 470     my %seedlot_data;
 471     while (my $s = $seedlot_rs->next()) {
 472         $seedlot_data{$s->uniquename} = $s->stock_id;
 473     }
 474
 475     my $rs = $chado_schema->resultset('Stock::Stock')->search({
 476         'is_obsolete' => { '!=' => 't' },
 477         'type_id' => {-in=>\@source_stock_types},
 478         'uniquename' => {-in=>\@seen_accessions}
 479     });
 480     my %stock_data;
 481     while (my $s = $rs->next()) {
 482         $stock_data{$s->uniquename} = [$s->stock_id, $s->organism_id, $s->type_id];
 483     }
 484
 485     my $stock_id_checked;
 486     my $stock_name_checked;
 487     my $organism_id_checked;
 488     my $stock_type_checked;
 489     my $timestamp = localtime();
 490
 491     my $coderef = sub {
 492
 493         #print STDERR Dumper \%design;
 494         my %new_stock_ids_hash;
 495         my $stock_rs = $chado_schema->resultset("Stock::Stock");
 496
 497         foreach my $key (keys %design) {
 498
 499             if ($key eq 'treatments'){
 500                 next;
 501             }
 502
 503             my $plot_name;
 504             if ($design{$key}->{plot_name}) {
 505                 $plot_name = $design{$key}->{plot_name};
 506             }
 507             my $plot_number;
 508             if ($design{$key}->{plot_number}) {
 509                 $plot_number = $design{$key}->{plot_number};
 510             } else {
 511                 $plot_number = $key;
 512             }
 513             my $plant_names;
 514             if ($design{$key}->{plant_names}) {
 515                 $plant_names = $design{$key}->{plant_names};
 516             }
 517             my $subplot_names;
 518             if ($design{$key}->{subplots_names}) {
 519                 $subplot_names = $design{$key}->{subplots_names};
 520             }
 521             my $subplots_plant_names;
 522             if ($design{$key}->{subplots_plant_names}) {
 523                 $subplots_plant_names = $design{$key}->{subplots_plant_names};
 524             }
 525             my $stock_name;
 526             if ($design{$key}->{stock_name}) {
 527                 $stock_name = $design{$key}->{stock_name};
 528             }
 529             my $seedlot_name;
 530             my $seedlot_stock_id;
 531             if ($design{$key}->{seedlot_name}) {
 532                 $seedlot_name = $design{$key}->{seedlot_name};
 533                 $seedlot_stock_id = $seedlot_data{$seedlot_name};
 534             }
 535             my $num_seed_per_plot;
 536             if($design{$key}->{num_seed_per_plot}){
 537                 $num_seed_per_plot = $design{$key}->{num_seed_per_plot};
 538             }
 539             my $weight_gram_seed_per_plot;
 540             if($design{$key}->{weight_gram_seed_per_plot}){
 541                 $weight_gram_seed_per_plot = $design{$key}->{weight_gram_seed_per_plot};
 542             }
 543             my $block_number;
 544             if ($design{$key}->{block_number}) { #set block number to 1 if no blocks are specified
 545                 $block_number = $design{$key}->{block_number};
 546             } else {
 547                 $block_number = 1;
 548             }
 549             my $rep_number;
 550             if ($design{$key}->{rep_number}) { #set rep number to 1 if no reps are specified
 551                 $rep_number = $design{$key}->{rep_number};
 552             } else {
 553                 $rep_number = 1;
 554             }
 555             my $is_a_control;
 556             if ($design{$key}->{is_a_control}) {
 557                 $is_a_control = $design{$key}->{is_a_control};
 558             }
 559             my $row_number;
 560             if ($design{$key}->{row_number}) {
 561                 $row_number = $design{$key}->{row_number};
 562             }
 563             my $col_number;
 564             if ($design{$key}->{col_number}) {
 565                 $col_number = $design{$key}->{col_number};
 566             }
 567             my $range_number;
 568             if ($design{$key}->{range_number}) {
 569                 $range_number = $design{$key}->{range_number};
 570             }
 571             my $well_is_blank;
 572             if ($design{$key}->{is_blank}) {
 573                 $well_is_blank = $design{$key}->{is_blank};
 574             }
 575             my $well_concentration;
 576             if ($design{$key}->{concentration}) {
 577                 $well_concentration = $design{$key}->{concentration};
 578             }
 579             my $well_volume;
 580             if ($design{$key}->{volume}) {
 581                 $well_volume = $design{$key}->{volume};
 582             }
 583             my $well_dna_person;
 584             if ($design{$key}->{dna_person}) {
 585                 $well_dna_person = $design{$key}->{dna_person};
 586             }
 587             my $well_extraction;
 588             if ($design{$key}->{extraction}) {
 589                 $well_extraction = $design{$key}->{extraction};
 590             }
 591             my $well_tissue_type;
 592             if ($design{$key}->{tissue_type}) {
 593                 $well_tissue_type = $design{$key}->{tissue_type};
 594             }
 595             my $acquisition_date;
 596             if ($design{$key}->{acquisition_date}) {
 597                 $acquisition_date = $design{$key}->{acquisition_date};
 598             }
 599             my $notes;
 600             if ($design{$key}->{notes}) {
 601                 $notes = $design{$key}->{notes};
 602             }
 603             my $ncbi_taxonomy_id;
 604             if ($design{$key}->{ncbi_taxonomy_id}) {
 605                 $ncbi_taxonomy_id = $design{$key}->{ncbi_taxonomy_id};
 606             }
 607             my $additional_info = $design{$key}->{additional_info} ? encode_json $design{$key}->{additional_info} : undef;
 608
 609             my $facility_identifier;
 610             if ($design{$key}->{facility_identifier}) {
 611                 $facility_identifier = $design{$key}->{facility_identifier};
 612             }
 613
 614             #check if stock_name exists in database by checking if stock_name is key in %stock_data. if it is not, then check if it exists as a synonym in the database.
 615             if ($stock_data{$stock_name}) {
 616                 $stock_id_checked = $stock_data{$stock_name}[0];
 617                 $organism_id_checked = $stock_data{$stock_name}[1];
 618                 $stock_type_checked = $stock_data{$stock_name}[2];
 619                 $stock_name_checked = $stock_name;
 620             } else {
 621                 my $parent_stock;
 622                 my $stock_lookup = CXGN::Stock::StockLookup->new(schema => $chado_schema);
 623                 $stock_lookup->set_stock_name($stock_name);
 624                 $parent_stock = $stock_lookup->get_stock($self->get_accession_cvterm_id());
 625                 if (!$parent_stock) {
 626                     die ("Error while saving trial layout: no accession found matching $stock_name");
 627                 }
 628
 629                 $stock_id_checked = $parent_stock->stock_id();
 630                 $stock_name_checked = $parent_stock->uniquename;
 631                 $stock_type_checked = $parent_stock->type_id;
 632                 $organism_id_checked = $parent_stock->organism_id();
 633             }
 634
 635             #create the plot, if plot given
 636             my $new_plot_id;
 637             if ($plot_name) {
 638                 my @plot_stock_props = (
 639                     { type_id => $self->get_replicate_cvterm_id, value => $rep_number },
 640                     { type_id => $self->get_block_cvterm_id, value => $block_number },
 641                     { type_id => $self->get_plot_number_cvterm_id, value => $plot_number }
 642                 );
 643                 if ($is_a_control) {
 644                     push @plot_stock_props, { type_id => $self->get_is_control_cvterm_id, value => $is_a_control };
 645                 }
 646                 if ($range_number) {
 647                     push @plot_stock_props, { type_id => $self->get_range_cvterm_id, value => $range_number };
 648                 }
 649                 if ($row_number) {
 650                     push @plot_stock_props, { type_id => $self->get_row_number_cvterm_id, value => $row_number };
 651                 }
 652                 if ($col_number) {
 653                     push @plot_stock_props, { type_id => $self->get_col_number_cvterm_id, value => $col_number };
 654                 }
 655                 if ($well_is_blank) {
 656                     push @plot_stock_props, { type_id => $self->get_is_blank_cvterm_id, value => $well_is_blank };
 657                 }
 658                 if ($well_concentration) {
 659                     push @plot_stock_props, { type_id => $self->get_concentration_cvterm_id, value => $well_concentration };
 660                 }
 661                 if ($well_volume) {
 662                     push @plot_stock_props, { type_id => $self->get_volume_cvterm_id, value => $well_volume };
 663                 }
 664                 if ($well_extraction) {
 665                     push @plot_stock_props, { type_id => $self->get_extraction_cvterm_id, value => $well_extraction };
 666                 }
 667                 if ($well_tissue_type) {
 668                     push @plot_stock_props, { type_id => $self->get_tissue_type_cvterm_id, value => $well_tissue_type };
 669                 }
 670                 if ($well_dna_person) {
 671                     push @plot_stock_props, { type_id => $self->get_dna_person_cvterm_id, value => $well_dna_person };
 672                 }
 673                 if ($acquisition_date) {
 674                     push @plot_stock_props, { type_id => $self->get_acquisition_date_cvterm_id, value => $acquisition_date };
 675                 }
 676                 if ($notes) {
 677                     push @plot_stock_props, { type_id => $self->get_notes_cvterm_id, value => $notes };
 678                 }
 679                 if ($ncbi_taxonomy_id) {
 680                     push @plot_stock_props, { type_id => $self->get_ncbi_taxonomy_id_cvterm_id, value => $ncbi_taxonomy_id };
 681                 }
 682                 if ($additional_info) {
 683                     push @plot_stock_props, { type_id => $additional_info_type_id, value => $additional_info };
 684                 }
 685                 if ($facility_identifier) {
 686                     push @plot_stock_props, { type_id => $self->get_facility_identifier_cvterm_id, value => $facility_identifier };
 687                 }
 688
 689                 my @plot_subjects;
 690                 my @plot_objects;
 691
 692                 my $parent_stock;
 693                 push @plot_subjects, { type_id => $stock_rel_type_id, object_id => $stock_id_checked };
 694
 695                 # For genotyping plate, if the well tissue_sample is sourced from a plot, then we store relationships between the tissue_sample and the plot, and the tissue sample and the plot's accession if it exists.
 696                 if ($stock_type_checked == $self->get_plot_cvterm_id){
 697                     my $parent_plot_accession_rs = $chado_schema->resultset("Stock::StockRelationship")->search({
 698                         'me.subject_id'=>$stock_id_checked,
 699                         'me.type_id'=>$self->get_plot_of_cvterm_id,
 700                         'object.type_id'=>$self->get_accession_cvterm_id
 701                     }, {join => 'object'});
 702                     if ($parent_plot_accession_rs->count > 1){
 703                         die "Plot $stock_id_checked is linked to more than one accession!\n"
 704                     }
 705                     if ($parent_plot_accession_rs->count == 1){
 706                         push @plot_subjects, { type_id => $stock_rel_type_id, object_id => $parent_plot_accession_rs->first->object_id };
 707                     }
 708                 }
 709                 # For genotyping plate, if the well tissue_sample is sourced from a plant, then we store relationships between the tissue_sample and the plant, and the tissue_sample and the plant's plot if it exists, and the tissue sample and the plant's accession if it exists.
 710                 if ($stock_type_checked == $self->get_plant_cvterm_id){
 711                     my $parent_plant_accession_rs = $chado_schema->resultset("Stock::StockRelationship")->search({
 712                         'me.subject_id'=>$stock_id_checked,
 713                         'me.type_id'=>$self->get_plant_of_cvterm_id,
 714                         'object.type_id'=>$self->get_accession_cvterm_id
 715                     }, {join => "object"});
 716                     if ($parent_plant_accession_rs->count > 1){
 717                         die "Plant $stock_id_checked is linked to more than one accession!\n"
 718                     }
 719                     if ($parent_plant_accession_rs->count == 1){
 720                         push @plot_subjects, { type_id => $stock_rel_type_id, object_id => $parent_plant_accession_rs->first->object_id };
 721                     }
 722                     my $parent_plot_of_plant_rs = $chado_schema->resultset("Stock::StockRelationship")->search({
 723                         'me.subject_id'=>$stock_id_checked,
 724                         'me.type_id'=>$self->get_plant_of_cvterm_id,
 725                         'object.type_id'=>$self->get_plot_cvterm_id
 726                     }, {join => "object"});
 727                     if ($parent_plot_of_plant_rs->count > 1){
 728                         die "Plant $stock_id_checked is linked to more than one plot!\n"
 729                     }
 730                     if ($parent_plot_of_plant_rs->count == 1){
 731                         push @plot_subjects, { type_id => $stock_rel_type_id, object_id => $parent_plot_of_plant_rs->first->object_id };
 732                     }
 733                 }
 734                 # For genotyping plate, if the well tissue_sample is sourced from another tissue_sample, then we store relationships between the new tissue_sample and the source tissue_sample, and the new tissue_sample and the tissue_sample's plant if it exists, and the new tissue_sample and the tissue_sample's plot if it exists, and the new tissue sample and the tissue_sample's accession if it exists.
 735                 if ($stock_type_checked == $self->get_tissue_sample_cvterm_id){
 736                     my $parent_tissue_sample_accession_rs = $chado_schema->resultset("Stock::StockRelationship")->search({
 737                         'me.subject_id'=>$stock_id_checked,
 738                         'me.type_id'=>$self->get_tissue_sample_of_cvterm_id,
 739                         'object.type_id'=>$self->get_accession_cvterm_id
 740                     }, {join => "object"});
 741                     if ($parent_tissue_sample_accession_rs->count > 1){
 742                         die "Tissue_sample $stock_id_checked is linked to more than one accession!\n"
 743                     }
 744                     if ($parent_tissue_sample_accession_rs->count == 1){
 745                         push @plot_subjects, { type_id => $stock_rel_type_id, object_id => $parent_tissue_sample_accession_rs->first->object_id };
 746                     }
 747                     my $parent_plot_of_tissue_sample_rs = $chado_schema->resultset("Stock::StockRelationship")->search({
 748                         'me.subject_id'=>$stock_id_checked,
 749                         'me.type_id'=>$self->get_tissue_sample_of_cvterm_id,
 750                         'object.type_id'=>$self->get_plot_cvterm_id
 751                     }, {join => "object"});
 752                     if ($parent_plot_of_tissue_sample_rs->count > 1){
 753                         die "Tissue_sample $stock_id_checked is linked to more than one plot!\n"
 754                     }
 755                     if ($parent_plot_of_tissue_sample_rs->count == 1){
 756                         push @plot_subjects, { type_id => $stock_rel_type_id, object_id => $parent_plot_of_tissue_sample_rs->first->object_id };
 757                     }
 758                     my $parent_plant_of_tissue_sample_rs = $chado_schema->resultset("Stock::StockRelationship")->search({
 759                         'me.subject_id'=>$stock_id_checked,
 760                         'me.type_id'=>$self->get_tissue_sample_of_cvterm_id,
 761                         'object.type_id'=>$self->get_plant_cvterm_id
 762                     }, {join => "object"});
 763                     if ($parent_plant_of_tissue_sample_rs->count > 1){
 764                         die "Tissue_sample $stock_id_checked is linked to more than one plant!\n"
 765                     }
 766                     if ($parent_plant_of_tissue_sample_rs->count == 1){
 767                         push @plot_subjects, { type_id => $stock_rel_type_id, object_id => $parent_plant_of_tissue_sample_rs->first->object_id };
 768                     }
 769                 }
 770
 771                 my @plot_nd_experiment_stocks = (
 772                     { nd_experiment_id => $nd_experiment_id, type_id => $self->get_nd_experiment_type_id }
 773                 );
 774
 775                 #print STDERR "STOCK TYPE ID NOW: $stock_type_id\n";
 776                 my $plot_params = {
 777                     organism_id => $organism_id_checked,
 778                     name       => $plot_name,
 779                     uniquename => $plot_name,
 780                     type_id => $stock_type_id,
 781                     stockprops => \@plot_stock_props,
 782                     stock_relationship_subjects => \@plot_subjects,
 783                     stock_relationship_objects => \@plot_objects,
 784                     nd_experiment_stocks => \@plot_nd_experiment_stocks,
 785                 };
 786                 my $plot;
 787                 if (! defined $plant_names || scalar $plant_names eq 0) {
 788                     $plot = $stock_rs->create($plot_params);
 789                 } else {
 790                     $plot = $stock_rs->find_or_create($plot_params);
 791                 }
 792                 $new_plot_id = $plot->stock_id();
 793                 $new_stock_ids_hash{$plot_name} = $new_plot_id;
 794
 795                 my %design = %{$self->get_design()};
 796                 my $sp_person_id = $self->get_owner_id;
 797                 my $username = $self->get_operator;
 798                 my $stock = CXGN::Stock->new({schema=>$chado_schema,stock_id=>$new_plot_id});
 799                 $stock->associate_owner($sp_person_id,$sp_person_id,$username,"");
 800
 801                 if ($seedlot_stock_id && $seedlot_name){
 802                     my $transaction = CXGN::Stock::Seedlot::Transaction->new(schema => $chado_schema);
 803                     $transaction->from_stock([$seedlot_stock_id, $seedlot_name]);
 804                     $transaction->to_stock([$plot->stock_id(), $plot->uniquename()]);
 805                     if ($num_seed_per_plot){
 806                         $transaction->amount($num_seed_per_plot);
 807                     }
 808                     if ($weight_gram_seed_per_plot){
 809                         $transaction->weight_gram($weight_gram_seed_per_plot);
 810                     }
 811                     $transaction->timestamp($timestamp);
 812                     my $description = "Created Trial: ".$self->get_trial_name." Plot: ".$plot->uniquename;
 813                     $transaction->description($description);
 814                     $transaction->operator($self->get_operator);
 815                     my $transaction_id = $transaction->store();
 816                     my $sl = CXGN::Stock::Seedlot->new(schema=>$chado_schema, seedlot_id=>$seedlot_stock_id);
 817                     $sl->set_current_count_property();
 818                     $sl->set_current_weight_property();
 819                 }
 820             }
 821
 822             #Create plant entry if given. Currently this is for the greenhouse trial creation and splitplot trial creation.
 823             if ($plant_names) {
 824                 my $plant_index_number = 1;
 825                 foreach my $plant_name (@$plant_names) {
 826
 827                     my @plant_stock_props = (
 828                         { type_id => $self->get_plant_index_number_cvterm_id, value => $plant_index_number },
 829                         { type_id => $self->get_replicate_cvterm_id, value => $rep_number },
 830                         { type_id => $self->get_block_cvterm_id, value => $block_number },
 831                         { type_id => $self->get_plot_number_cvterm_id, value => $plot_number }
 832                     );
 833                     if ($is_a_control) {
 834                         push @plant_stock_props, { type_id => $self->get_is_control_cvterm_id, value => $is_a_control };
 835                     }
 836                     if ($range_number) {
 837                         push @plant_stock_props, { type_id => $self->get_range_cvterm_id, value => $range_number };
 838                     }
 839                     if ($row_number) {
 840                         push @plant_stock_props, { type_id => $self->get_row_number_cvterm_id, value => $row_number };
 841                     }
 842                     if ($col_number) {
 843                         push @plant_stock_props, { type_id => $self->get_col_number_cvterm_id, value => $col_number };
 844                     }
 845                     if ($additional_info) {
 846                         push @plant_stock_props, { type_id => $additional_info_type_id, value => $additional_info };
 847                     }
 848
 849                     my @plant_objects = (
 850                         { type_id => $self->get_plant_of_cvterm_id, subject_id => $new_plot_id }
 851                     );
 852                     my @plant_subjects = (
 853                         { type_id => $self->get_plant_of_cvterm_id, object_id => $stock_id_checked }
 854                     );
 855                     my @plant_nd_experiment_stocks = (
 856                         { type_id => $self->get_nd_experiment_type_id, nd_experiment_id => $nd_experiment_id }
 857                     );
 858
 859
 860                     my $plant = $stock_rs->create({
 861                         organism_id => $organism_id_checked,
 862                         name       => $plant_name,
 863                         uniquename => $plant_name,
 864                         type_id => $self->get_plant_cvterm_id,
 865                         stockprops => \@plant_stock_props,
 866                         stock_relationship_subjects => \@plant_subjects,
 867                         stock_relationship_objects => \@plant_objects,
 868                         nd_experiment_stocks => \@plant_nd_experiment_stocks,
 869                     });
 870                     $new_stock_ids_hash{$plant_name} = $plant->stock_id();
 871                     $plant_index_number++;
 872                 }
 873
 874                 # Set the study to have plant entries
 875                 if (scalar @$plant_names > 0) {
 876                     my $study = $chado_schema->resultset('Project::Project')->find( { project_id => $self->get_trial_id() });
 877                     $study->create_projectprops({ 'project_has_plant_entries' => 1 });
 878                 }
 879             }
 880             #Create subplot entry if given. Currently this is for the splitplot trial creation.
 881             if ($subplot_names) {
 882                 my $subplot_index_number = 1;
 883                 foreach my $subplot_name (@$subplot_names) {
 884                     my @subplot_stockprops = (
 885                         { type_id => $self->get_subplot_index_number_cvterm_id, value => $subplot_index_number },
 886                         { type_id => $self->get_replicate_cvterm_id, value => $rep_number },
 887                         { type_id => $self->get_block_cvterm_id, value => $block_number },
 888                         { type_id => $self->get_plot_number_cvterm_id, value => $plot_number }
 889                     );
 890                     if ($is_a_control) {
 891                         push @subplot_stockprops, { type_id => $self->get_is_control_cvterm_id, value => $is_a_control };
 892                     }
 893                     if ($range_number) {
 894                         push @subplot_stockprops, { type_id => $self->get_range_cvterm_id, value => $range_number };
 895                     }
 896                     if ($row_number) {
 897                         push @subplot_stockprops, { type_id => $self->get_row_number_cvterm_id, value => $row_number };
 898                     }
 899                     if ($col_number) {
 900                         push @subplot_stockprops, { type_id => $self->get_col_number_cvterm_id, value => $col_number };
 901                     }
 902
 903                     my @subplot_objects = (
 904                         { type_id => $self->get_subplot_of_cvterm_id, subject_id => $new_plot_id }
 905                     );
 906                     my @subplot_subjects = (
 907                         { type_id => $self->get_subplot_of_cvterm_id, object_id => $stock_id_checked }
 908                     );
 909                     my @subplot_nd_experiment_stocks = (
 910                         { type_id => $self->get_nd_experiment_type_id, nd_experiment_id => $nd_experiment_id }
 911                     );
 912
 913                     if ($subplots_plant_names){
 914                         my $subplot_plants = $subplots_plant_names->{$subplot_name};
 915                         foreach (@$subplot_plants) {
 916                             my $plant_stock_id = $new_stock_ids_hash{$_};
 917                             push @subplot_objects, { type_id => $self->get_plant_of_subplot_cvterm_id, subject_id => $plant_stock_id };
 918                         }
 919                     }
 920
 921                     my $subplot = $stock_rs->create({
 922                         organism_id => $organism_id_checked,
 923                         name       => $subplot_name,
 924                         uniquename => $subplot_name,
 925                         type_id => $self->get_subplot_cvterm_id,
 926                         stockprops => \@subplot_stockprops,
 927                         stock_relationship_subjects => \@subplot_subjects,
 928                         stock_relationship_objects => \@subplot_objects,
 929                         nd_experiment_stocks => \@subplot_nd_experiment_stocks,
 930                     });
 931                     $new_stock_ids_hash{$subplot_name} = $subplot->stock_id();
 932                     $subplot_index_number++;
 933
 934                 }
 935             }
 936         }
 937
 938         if (exists($design{'treatments'})){
 939             print STDERR "Saving treatments\n";
 940             my %treatments_hash = %{$design{'treatments'}};
 941
 942             foreach my $treatment_name (sort keys %treatments_hash) {
 943                 my $stock_names;
 944                 my $management_factor_type;
 945                 my $management_factor_year;
 946                 my $management_factor_date;
 947                 my $management_factor_description = '';
 948 #                my %info_hashes = %{$treatments_hash{$treatment_name}};
 949                 my $info_value = $treatments_hash{$treatment_name};
 950                 my $info_type = ref($info_value);
 951                 if ($info_type eq 'HASH'){
 952                     my %info_hashes = %$info_value;
 953                     $stock_names = $info_hashes{'new_treatment_stocks'};
 954                     $management_factor_type = $info_hashes{'new_treatment_type'};
 955                     $management_factor_year = $info_hashes{'new_treatment_year'};
 956                     $management_factor_date = $info_hashes{'new_treatment_date'};
 957                     $management_factor_description = $info_hashes{'new_treatment_description'} || 'No description';
 958                 } else {
 959                     $stock_names = $treatments_hash{$treatment_name};
 960                 }
 961 #                print STDERR "STOCK NAMES =".Dumper($stock_names)."\n";
 962                 my @treatment_nd_experiment_stocks;
 963                 foreach (@$stock_names){
 964                     my $stock_id;
 965                     if (exists($new_stock_ids_hash{$_})){
 966                         $stock_id = $new_stock_ids_hash{$_};
 967                     } else {
 968                         $stock_id = $chado_schema->resultset("Stock::Stock")->find({uniquename=>$_})->stock_id();
 969                     }
 970                     push @treatment_nd_experiment_stocks, { type_id => $self->get_treatment_nd_experiment_type_id, stock_id => $stock_id };
 971                 }
 972
 973                 my $nd_experiment = $chado_schema->resultset('NaturalDiversity::NdExperiment')->create({
 974                     nd_geolocation_id => $nd_geolocation_id,
 975                     type_id => $self->get_treatment_nd_experiment_type_id,
 976                     nd_experiment_stocks => \@treatment_nd_experiment_stocks
 977                 });
 978
 979                 my @treatment_project_props = (
 980                     { type_id => $self->get_project_design_cvterm_id, value => 'treatment' }
 981                 );
 982
 983                 if ($self->get_new_treatment_has_plant_entries){
 984                     push @treatment_project_props, { type_id => $self->get_has_plants_cvterm, value => $self->get_new_treatment_has_plant_entries };
 985                 }
 986                 if ($self->get_new_treatment_has_subplot_entries){
 987                     push @treatment_project_props, { type_id => $self->get_has_subplots_cvterm, value => $self->get_new_treatment_has_subplot_entries };
 988                 }
 989                 if ($self->get_new_treatment_has_tissue_sample_entries){
 990                     push @treatment_project_props, { type_id => $self->get_has_tissues_cvterm, value => $self->get_new_treatment_has_tissue_sample_entries };
 991                 }
 992                 if (defined $management_factor_type){
 993                     push @treatment_project_props, { type_id => $self->get_management_factor_type_cvterm_id, value => $management_factor_type };
 994                 }
 995                 if (defined $management_factor_year){
 996                     push @treatment_project_props, { type_id => $self->get_management_factor_year_cvterm_id, value => $management_factor_year };
 997                 } else {
 998                     my $t = CXGN::Trial->new({
 999                         bcs_schema => $chado_schema,
1000                         trial_id => $self->get_trial_id
1001                     });
1002                     push @treatment_project_props, { type_id => $self->get_management_factor_year_cvterm_id, value => $t->get_year() };
1003                 }
1004
1005
1006                 if (defined $management_factor_date){
1007                     push @treatment_project_props, { type_id => $self->get_management_factor_date_cvterm_id, value => $management_factor_date };
1008                 }
1009
1010                 my @treatment_nd_experiment_project = (
1011                     { nd_experiment_id => $nd_experiment->nd_experiment_id }
1012                 );
1013
1014                 my @treatment_relationships = (
1015                     { type_id => $self->get_trial_treatment_relationship_cvterm_id, object_project_id => $self->get_trial_id }
1016                 );
1017
1018                 #Create a project for each treatment_name
1019                 my $project_treatment_name = $self->get_trial_name()."_".$treatment_name;
1020                 my $treatment_project = $chado_schema->resultset('Project::Project')->create({
1021                     name => $project_treatment_name,
1022                     description => $management_factor_description,
1023                     projectprops => \@treatment_project_props,
1024                     project_relationship_subject_projects => \@treatment_relationships,
1025                     nd_experiment_projects => \@treatment_nd_experiment_project
1026                 });
1027
1028                 if ($self->get_new_treatment_date()) {
1029                     my $management_factor_t = CXGN::Trial->new({
1030                         bcs_schema => $chado_schema,
1031                         trial_id => $treatment_project->project_id()
1032                     });
1033                     $management_factor_t->set_management_factor_date($self->get_new_treatment_date() );
1034                 }
1035             }
1036         }
1037
1038         print STDERR "Design Stored ".localtime."\n";
1039     };
1040
1041     my $transaction_error;
1042
1043     try {
1044         $chado_schema->txn_do($coderef);
1045     }
1046     catch {
1047         print STDERR "Transaction Error: $_\n";
1048         $transaction_error =  $_;
1049     };
1050     return $transaction_error;
1051 }
1052
1053
1054
1055 1;