lib/CXGN/Trial/TrialCreate.pm

   1 package CXGN::Trial::TrialCreate;
   2
   3 =head1 NAME
   4
   5 CXGN::Trial::TrialCreate - Module to create an entirely new trial based on a specified design. For field_layout experiments and genotyping_layout experiments.
   6
   7 Will do the following:
   8 1) Create a new project entry in Project table based on trial and description supplied to object. If there is a project with the name already saved, it will return an error and do nothing.
   9 2) Create a single new experiment entry in nd_experiment. If is_genotyping is supplied, this will be type = genotyping_layout. Otherwise, this will be type = field_layout.
  10 3) Will associate the location to the project through the nd_experiment as well as through a projectprop. Location lookup happens based on location name that is provided. Assumes locations already stored in database.
  11 4) Will associate the trial to its breeding program. Lookup is by breeding program name that is provided and assumes bp already exists in database. Will return an error if breeding program name not found.
  12 5) Creates a single nd_experiment_project entry, linking project to nd_experiment.
  13 6) Creates a year and design projectprop. Also a project_type projectprop if provided. For genotyping plates also creates others like, genotyping_facility and plate_format projectprops
  14 7) Calls the CXGN::Trial::TrialDesignStore object to handle storing stocks (tissue_samples, or plots and plants and subplots) and stockprops (rep, block, well, etc)
  15
  16 =head1 USAGE
  17
  18     FOR FIELD PHENOTYPING TRIALS:
  19     my $trial_create = CXGN::Trial::TrialCreate->new({
  20         chado_schema => $c->dbic_schema("Bio::Chado::Schema"),
  21         dbh => $c->dbc->dbh(),
  22                 owner_id => $c->user()->get_object()->get_sp_person_id(),
  23         operator => $c->user()->get_object()->get_username(),
  24         design_type => 'CRD',
  25         design => $design_hash,
  26         program => $breeding_program->name(),
  27         trial_year => $year,
  28         planting_date => $planting_date,
  29         trial_description => $project_description,
  30         trial_location => $location->name(),
  31         trial_name => $trial_name,
  32         trial_type => $trialtype,
  33         field_size => $field_size, #(ha)
  34         plot_width => $plot_width, #(m)
  35         plot_length => $plot_length, #(m)
  36         field_trial_is_planned_to_cross => 'yes', #yes or no
  37         field_trial_is_planned_to_be_genotyped => 'no', #yes or no
  38         field_trial_from_field_trial => ['source_trial_id1', 'source_trial_id2'],
  39         genotyping_trial_from_field_trial => ['genotyping_trial_id1'],
  40         crossing_trial_from_field_trial => ['crossing_trial_id1']
  41     });
  42     try {
  43         $trial_create->save_trial();
  44     } catch {
  45         print STDERR "ERROR SAVING TRIAL!\n";
  46     };
  47
  48     FOR GENOTYPING PLATES:
  49     my $ct = CXGN::Trial::TrialCreate->new( {
  50         chado_schema => $c->dbic_schema("Bio::Chado::Schema"),
  51         dbh => $c->dbc->dbh(),
  52                 owner_id => $c->user()->get_object()->get_sp_person_id(),
  53         operator => $c->user()->get_object()->get_username(),
  54         trial_year => $year,
  55         planting_date => $planting_date,
  56         trial_location => $location->name(),
  57         program => $breeding_program->name(),
  58         trial_description => $description,
  59         design_type => 'genotyping_plate',
  60         design => $design_hash,
  61         trial_name => $trial_name,
  62         is_genotyping => 1,
  63         genotyping_user_id => $user_id,
  64         genotyping_project_name => $project_name,
  65         genotyping_facility_submit => $plate_info->{genotyping_facility_submit},
  66         genotyping_facility => $plate_info->{genotyping_facility},
  67         genotyping_plate_format => $plate_info->{plate_format},
  68         genotyping_plate_sample_type => $plate_info->{sample_type},
  69         genotyping_trial_from_field_trial => ['field_trial_id1'],
  70     });
  71     try {
  72         $ct->save_trial();
  73     } catch {
  74         print STDERR "ERROR SAVING TRIAL!\n";
  75     };
  76
  77 ---------------------------------------------------------------------------------
  78
  79 For field_layout trials, the design should be a HasfRef of HashRefs like:
  80
  81 {
  82    '1001' => {
  83        "plot_name" => "plot1",
  84        "plot_number" => 1001,
  85        "accession_name" => "accession1",
  86        "block_number" => 1,
  87        "row_number" => 2,
  88        "col_number" => 3,
  89        "rep_number" => 1,
  90        "is_a_control" => 1,
  91        "seedlot_name" => "seedlot1",
  92        "num_seed_per_plot" => 12,
  93        "plot_geo_json" => {},
  94        "plant_names" => ["plant1", "plant2"],
  95    }
  96 }
  97
  98 For genotyping_layout trials, the design should be a HashRef of HashRefs like:
  99
 100 {
 101    'A01' => {
 102        "plot_name" => "mytissuesample_A01",
 103        "stock_name" => "accession1",
 104        "plot_number" => "A01",
 105        "row_number" => "A",
 106        "col_number" => "1",
 107        "is_blank" => 0,
 108        "concentration" => "5",
 109        "volume" => "2",
 110        "tissue_type" => "leaf",
 111        "dna_person" => "nmorales",
 112        "extraction" => "ctab",
 113        "acquisition_date" => "2018/02/16",
 114        "notes" => "test notes",
 115    }
 116 }
 117
 118 =head1 DESCRIPTION
 119
 120
 121 =head1 AUTHORS
 122
 123  Jeremy D. Edwards (jde22@cornell.edu)
 124
 125 =cut
 126
 127
 128 use Moose;
 129 use MooseX::FollowPBP;
 130 use Moose::Util::TypeConstraints;
 131 use Try::Tiny;
 132 use CXGN::Stock::StockLookup;
 133 use CXGN::Location::LocationLookup;
 134 use CXGN::People::Person;
 135 use CXGN::Trial;
 136 use SGN::Model::Cvterm;
 137 use CXGN::Trial::TrialDesignStore;
 138 use Data::Dumper;
 139
 140 has 'chado_schema' => (
 141                  is       => 'rw',
 142                  isa      => 'DBIx::Class::Schema',
 143                  predicate => 'has_chado_schema',
 144                  required => 1,
 145                 );
 146
 147 has 'dbh' => (is  => 'rw',predicate => 'has_dbh', required => 1,);
 148 #has 'user_name' => (isa => 'Str', is => 'rw', predicate => 'has_user_name', required => 1,);
 149 has 'trial_id' => (isa => 'Maybe[Int]', is => 'rw', predicate => 'has_trial_id');
 150 has 'program' => (isa =>'Str', is => 'rw', predicate => 'has_program', required => 1,);
 151 has 'trial_year' => (isa => 'Maybe[Str]', is => 'rw', predicate => 'has_trial_year', required => 0,);
 152 has 'trial_description' => (isa => 'Maybe[Str]', is => 'rw', predicate => 'has_trial_description', required => 0,);
 153 has 'trial_location' => (isa => 'Maybe[Str]', is => 'rw', predicate => 'has_trial_location', required => 0,);
 154 has 'design_type' => (isa => 'Maybe[Str]', is => 'rw', predicate => 'has_design_type', required => 0);
 155 has 'design' => (isa => 'HashRef[HashRef]|Undef', is => 'rw', predicate => 'has_design', required => 0);
 156 has 'trial_name' => (isa => 'Str', is => 'rw', predicate => 'has_trial_name', required => 1);
 157 has 'trial_type' => (isa => 'Str', is => 'rw', predicate => 'has_trial_type', required => 0);
 158 has 'trial_type_value' => (isa => 'Str', is => 'rw', predicate => 'has_trial_type_value', required => 0);
 159 has 'trial_has_plant_entries' => (isa => 'Int', is => 'rw', predicate => 'has_trial_has_plant_entries', required => 0);
 160 has 'trial_has_subplot_entries' => (isa => 'Int', is => 'rw', predicate => 'has_trial_has_subplot_entries', required => 0);
 161 has 'field_size' => (isa => 'Num', is => 'rw', predicate => 'has_field_size', required => 0);
 162 has 'plot_width' => (isa => 'Num', is => 'rw', predicate => 'has_plot_width', required => 0);
 163 has 'plot_length' => (isa => 'Num', is => 'rw', predicate => 'has_plot_length', required => 0);
 164 has 'planting_date' => (isa => 'Str', is => 'rw', predicate => 'has_planting_date', required => 0);
 165 has 'transplanting_date' => (isa => 'Str', is => 'rw', predicate => 'has_transplanting_date', required => 0);
 166 has 'harvest_date' => (isa => 'Str', is => 'rw', predicate => 'has_harvest_date', required => 0);
 167 has 'operator' => (isa => 'Str', is => 'rw', predicate => 'has_operator', required => 1);
 168 has 'trial_stock_type' => (isa => 'Str', is => 'rw', predicate => 'has_trial_stock_type', required => 0, default => 'accession');
 169 has 'additional_info' => (isa => 'Maybe[HashRef]', is => 'rw', required => 0);
 170
 171 # Trial linkage when saving a field trial
 172 #
 173 has 'field_trial_is_planned_to_cross' => (isa => 'Str', is => 'rw', predicate => 'has_field_trial_is_planned_to_cross', required => 0);
 174 has 'field_trial_is_planned_to_be_genotyped' => (isa => 'Str', is => 'rw', predicate => 'has_field_trial_is_planned_to_be_genotyped', required => 0);
 175 has 'field_trial_from_field_trial' => (isa => 'ArrayRef', is => 'rw', predicate => 'has_field_trial_from_field_trial', required => 0);
 176 has 'crossing_trial_from_field_trial' => (isa => 'ArrayRef', is => 'rw', predicate => 'has_crossing_trial_from_field_trial', required => 0);
 177
 178 # Trial linkage when saving either a field trial or genotyping plate
 179 #
 180 has 'genotyping_trial_from_field_trial' => (isa => 'ArrayRef', is => 'rw', predicate => 'has_genotyping_trial_from_field_trial', required => 0);
 181
 182 # Properties for genotyping plates
 183 #
 184 has 'is_genotyping' => (isa => 'Bool', is => 'rw', required => 0, default => 0, );
 185 has 'genotyping_user_id' => (isa => 'Str', is => 'rw');
 186 has 'genotyping_project_id' => (isa => 'Int', is => 'rw');
 187 has 'genotyping_facility_submitted' => (isa => 'Str', is => 'rw');
 188 has 'genotyping_facility' => (isa => 'Str', is => 'rw');
 189 has 'genotyping_plate_format' => (isa => 'Str', is => 'rw');
 190 has 'genotyping_plate_sample_type' => (isa => 'Str', is => 'rw');
 191
 192 # properties for analyses
 193 #
 194 has 'is_analysis' => (isa => 'Bool', is => 'rw', required => 0, default => 0, );
 195 has 'analysis_model_protocol_id' => (isa => 'Int|Undef', is => 'rw', required => 0 );
 196
 197 # Trial linkage when saving either a sampling trial
 198 #
 199 has 'sampling_trial_from_field_trial' => (isa => 'ArrayRef', is => 'rw', predicate => 'has_sampling_trial_from_field_trial', required => 0);
 200
 201 # Properties for sampling trials
 202 #
 203 has 'is_sampling_trial' => (isa => 'Bool', is => 'rw', required => 0, default => 0, );
 204 has 'sampling_trial_facility' => (isa => 'Str', is => 'rw');
 205 has 'sampling_trial_sample_type' => (isa => 'Str', is => 'rw');
 206
 207 has 'owner_id' => (isa => 'Int' , is => 'rw');
 208
 209 sub trial_name_already_exists {
 210     my $self = shift;
 211
 212     if ($self->get_is_analysis()) { return; }
 213     my $trial_name = $self->get_trial_name();
 214     my $schema = $self->get_chado_schema();
 215     if($schema->resultset('Project::Project')->find({name => $trial_name})){
 216         return 1;
 217     }
 218     else {
 219         return;
 220     }
 221 }
 222
 223 sub get_breeding_program_id {
 224   my $self = shift;
 225   my $breeding_program_ref = $self->get_chado_schema->resultset('Project::Project')->find({name=>$self->get_program});
 226   if (!$breeding_program_ref ) {
 227       print STDERR "UNDEF breeding program " . $self->get_program . "\n\n";
 228       return ;
 229   }
 230   my $breeding_program_id = $breeding_program_ref->project_id();
 231   #print STDERR "get_breeding_program _id returning $breeding_program_id";
 232   return $breeding_program_id;
 233 }
 234
 235
 236 sub save_trial {
 237     print STDERR "Check 4.1: ".localtime();
 238     my $self = shift;
 239     my $chado_schema = $self->get_chado_schema();
 240     my %design = %{$self->get_design()};
 241     my $trial_name = $self->get_trial_name();
 242     $trial_name =~ s/^\s+|\s+$//g; #trim whitespace from both ends
 243
 244     # if a trial id is provided, the project row has already been
 245     # created by other means, so use that trial_id
 246
 247     if (! $self->has_trial_id()) {
 248
 249         if (!$trial_name) {
 250                 print STDERR "Trial not saved: Can't create trial without a trial name\n";
 251                 return { error => "Trial not saved: Can't create trial without a trial name" };
 252         }
 253
 254     if ($self->trial_name_already_exists()) {
 255                 print STDERR "Can't create trial: Trial name already exists\n";
 256                 return { error => "Trial not saved: Trial name already exists" };
 257         }
 258
 259         if (!$self->get_breeding_program_id()) {
 260                 print STDERR "Can't create trial: Breeding program does not exist\n";
 261                 return { error => "Trial not saved: breeding program does not exist" };
 262         }
 263
 264         #lookup user by name
 265         #my $user_name = $self->get_user_name();
 266         #my $dbh = $self->get_dbh();
 267         #my $owner_sp_person_id;
 268         #$owner_sp_person_id = CXGN::People::Person->get_person_by_username($dbh, $user_name); #add person id as an option.
 269         #if (!$owner_sp_person_id) {
 270         #       print STDERR "Can't create trial: User/owner not found\n";
 271         #       die "no owner $user_name" ;
 272         #}
 273     }
 274         my $geolocation;
 275         my $geolocation_lookup = CXGN::Location::LocationLookup->new(schema => $chado_schema);
 276         $geolocation_lookup->set_location_name($self->get_trial_location());
 277         $geolocation = $geolocation_lookup->get_geolocation();
 278         if (!$geolocation) {
 279                 print STDERR "Can't create trial: Location not found: ".$self->get_trial_location()."\n";
 280                 return { error => "Trial not saved: location not found" };
 281         }
 282
 283     my $project_year_cvterm = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'project year', 'project_property');
 284     my $project_planting_date_cvterm = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'project_planting_date', 'project_property');
 285     my $project_design_cvterm = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'design', 'project_property');
 286     my $field_size_cvterm = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'field_size', 'project_property');
 287     my $plot_width_cvterm = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'plot_width', 'project_property');
 288     my $plot_length_cvterm = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'plot_length', 'project_property');
 289     my $field_trial_is_planned_to_be_genotyped_cvterm = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'field_trial_is_planned_to_be_genotyped', 'project_property');
 290     my $field_trial_is_planned_to_cross_cvterm = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'field_trial_is_planned_to_cross', 'project_property');
 291     my $has_plant_entries_cvterm = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'project_has_plant_entries', 'project_property');
 292     my $has_subplot_entries_cvterm = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'project_has_subplot_entries', 'project_property');
 293     my $genotyping_facility_cvterm = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'genotyping_facility', 'project_property');
 294     my $genotyping_facility_submitted_cvterm = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'genotyping_facility_submitted', 'project_property');
 295     my $genotyping_plate_format_cvterm = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'genotyping_plate_format', 'project_property');
 296     my $genotyping_plate_sample_type_cvterm = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'genotyping_plate_sample_type', 'project_property');
 297     my $genotyping_user_cvterm = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'genotyping_user_id', 'nd_experiment_property');
 298     my $genotyping_project_name_cvterm = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'genotyping_project_name', 'nd_experiment_property');
 299     my $trial_stock_type_cvterm = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'trial_stock_type', 'project_property');
 300     my $sampling_facility_cvterm = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'sampling_facility', 'project_property');
 301     my $sampling_trial_sample_type_cvterm = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'sampling_trial_sample_type', 'project_property');
 302
 303     my $project;
 304     if ($self->has_trial_id()) {
 305         $project = $chado_schema->resultset('Project::Project')->find( { project_id => $self->get_trial_id() });
 306         if (! $project) {  die "The specified project id ".$self->get_trial_id()." does not exit in the database\n"; }
 307     }
 308     else {
 309         $project = $chado_schema->resultset('Project::Project')
 310         ->create({
 311             name => $trial_name,
 312             description => $self->get_trial_description(),
 313         });
 314     }
 315
 316     my $t = CXGN::Trial->new({
 317         bcs_schema => $chado_schema,
 318         trial_id => $project->project_id()
 319     });
 320
 321     $t->set_trial_owner($self->get_owner_id);
 322     #print STDERR "TRIAL TYPE = ".ref($t)."!!!!\n";
 323     my $nd_experiment_type_id;
 324     if ($self->get_is_genotyping()) {
 325         print STDERR "Generating a genotyping trial...\n";
 326         $nd_experiment_type_id = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'genotyping_layout', 'experiment_type')->cvterm_id();
 327     }
 328     elsif ($self->get_is_analysis()) {
 329         print STDERR "Generating an analysis trial...\n";
 330         $nd_experiment_type_id = SGN::Model::Cvterm->get_cvterm_row($chado_schema, , 'analysis_experiment', 'experiment_type')->cvterm_id();
 331     }
 332     elsif ($self->get_is_sampling_trial()) {
 333         print STDERR "Generating a sampling trial...\n";
 334         $nd_experiment_type_id = SGN::Model::Cvterm->get_cvterm_row($chado_schema, , 'sampling_layout', 'experiment_type')->cvterm_id();
 335     }
 336     else {
 337         print STDERR "Generating a phenotyping trial...\n";
 338         $nd_experiment_type_id = SGN::Model::Cvterm->get_cvterm_row($chado_schema, , 'field_layout', 'experiment_type')->cvterm_id();
 339     }
 340     my $nd_experiment = $chado_schema->resultset('NaturalDiversity::NdExperiment')
 341     ->create({
 342         nd_geolocation_id => $geolocation->nd_geolocation_id(),
 343         type_id => $nd_experiment_type_id,
 344     });
 345
 346
 347     if ($self->get_is_genotyping()) {
 348         #print STDERR "Storing user_id and project_name provided by the IGD spreadksheet for later recovery in the spreadsheet download... ".(join ",", ($self->get_genotyping_user_id(), $self->get_genotyping_project_name()))."\n";
 349         $nd_experiment->create_nd_experimentprops({
 350             $genotyping_user_cvterm->name() => $self->get_genotyping_user_id(),
 351 #            $genotyping_project_name_cvterm->name() => $self->get_genotyping_project_name(),
 352         });
 353
 354         $project->create_projectprops({
 355             $genotyping_facility_cvterm->name() => $self->get_genotyping_facility(),
 356             $genotyping_facility_submitted_cvterm->name() => $self->get_genotyping_facility_submitted(),
 357             $genotyping_plate_format_cvterm->name() => $self->get_genotyping_plate_format(),
 358             $genotyping_plate_sample_type_cvterm->name() => $self->get_genotyping_plate_sample_type()
 359         });
 360
 361                 my $genotyping_project_relationship_cvterm = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'genotyping_project_and_plate_relationship', 'project_relationship');
 362                 my $relationship_row = $chado_schema->resultset("Project::ProjectRelationship")->create ({
 363                         object_project_id => $self->get_genotyping_project_id(),
 364                         subject_project_id => $project->project_id(),
 365                         type_id => $genotyping_project_relationship_cvterm->cvterm_id()
 366                 });
 367                 $relationship_row->insert();
 368
 369         my $source_field_trial_ids = $t->set_source_field_trials_for_genotyping_trial($self->get_genotyping_trial_from_field_trial);
 370     }
 371     elsif ($self->get_is_analysis()) {
 372         if ($self->get_analysis_model_protocol_id) {
 373             #link to the saved analysis model
 374             $nd_experiment->find_or_create_related('nd_experiment_protocols', {nd_protocol_id => $self->get_analysis_model_protocol_id() });
 375         }
 376     }
 377     elsif ($self->get_is_sampling_trial()) {
 378         $project->create_projectprops({
 379             $sampling_facility_cvterm->name() => $self->get_sampling_trial_facility(),
 380             $sampling_trial_sample_type_cvterm->name() => $self->get_sampling_trial_sample_type()
 381         });
 382
 383         my $source_field_trial_ids = $t->set_source_field_trials_for_sampling_trial($self->get_sampling_trial_from_field_trial);
 384     }
 385     else {
 386         my $source_field_trial_ids = $t->set_field_trials_source_field_trials($self->get_field_trial_from_field_trial);
 387         my $genotyping_trial_ids = $t->set_genotyping_trials_from_field_trial($self->get_genotyping_trial_from_field_trial);
 388         my $crossing_trial_ids = $t->set_crossing_trials_from_field_trial($self->get_crossing_trial_from_field_trial);
 389     }
 390
 391     $t->set_location($geolocation->nd_geolocation_id()); # set location also as a project prop
 392     $t->set_breeding_program($self->get_breeding_program_id);
 393     if ($self->get_trial_type){
 394         $t->set_project_type($self->get_trial_type);
 395     }
 396     if ($self->get_planting_date()){ # here is local getter
 397         $t->set_planting_date($self->get_planting_date); # here is Project.pm unusual setter with writing to db instead of object
 398     }
 399     if ($self->get_harvest_date()){ # here is local getter
 400         $t->set_harvest_date($self->get_harvest_date); # here is Project.pm unusual setter with writing to db instead of object
 401     }
 402     if ($self->get_transplanting_date()){ # here is local getter
 403         $t->set_transplanting_date($self->get_transplanting_date); # here is Project.pm unusual setter with writing to db instead of object
 404     }
 405
 406     #link to the project
 407     $nd_experiment->find_or_create_related('nd_experiment_projects',{project_id => $project->project_id()});
 408
 409     $project->create_projectprops({
 410         $project_year_cvterm->name() => $self->get_trial_year(),
 411         $project_design_cvterm->name() => $self->get_design_type()
 412     });
 413     if ($self->has_field_size && $self->get_field_size){
 414         $project->create_projectprops({
 415             $field_size_cvterm->name() => $self->get_field_size
 416         });
 417     }
 418     if ($self->has_plot_width && $self->get_plot_width){
 419         $project->create_projectprops({
 420             $plot_width_cvterm->name() => $self->get_plot_width
 421         });
 422     }
 423     if ($self->has_plot_length && $self->get_plot_length){
 424         $project->create_projectprops({
 425             $plot_length_cvterm->name() => $self->get_plot_length
 426         });
 427     }
 428     if ($self->has_trial_has_plant_entries && $self->get_trial_has_plant_entries){
 429         $project->create_projectprops({
 430             $has_plant_entries_cvterm->name() => $self->get_trial_has_plant_entries
 431         });
 432     }
 433     if ($self->has_trial_has_subplot_entries && $self->get_trial_has_subplot_entries){
 434         $project->create_projectprops({
 435             $has_subplot_entries_cvterm->name() => $self->get_trial_has_subplot_entries
 436         });
 437     }
 438     if ($self->has_field_trial_is_planned_to_cross && $self->get_field_trial_is_planned_to_cross){
 439         $project->create_projectprops({
 440             $field_trial_is_planned_to_cross_cvterm->name() => $self->get_field_trial_is_planned_to_cross
 441         });
 442     }
 443     if ($self->has_field_trial_is_planned_to_be_genotyped && $self->get_field_trial_is_planned_to_be_genotyped){
 444         $project->create_projectprops({
 445             $field_trial_is_planned_to_be_genotyped_cvterm->name() => $self->get_field_trial_is_planned_to_be_genotyped
 446         });
 447     }
 448
 449     if (!$self->get_is_genotyping) {
 450         if ($self->has_trial_stock_type && $self->get_trial_stock_type){
 451             $project->create_projectprops({
 452                 $trial_stock_type_cvterm->name() => $self->get_trial_stock_type()
 453             });
 454         }
 455     }
 456
 457     my $design_type = $self->get_design_type();
 458     if ($design_type eq 'greenhouse') {
 459         my $has_plants_cvterm = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'project_has_plant_entries', 'project_property');
 460         $project->create_projectprops({ $has_plants_cvterm->name() => 'varies' });
 461     }
 462
 463     print STDERR "NOW CALLING TRIAl DESIGN STORE...\n";
 464     my $trial_design_store = CXGN::Trial::TrialDesignStore->new({
 465         bcs_schema => $chado_schema,
 466         trial_id => $project->project_id(),
 467         trial_name => $trial_name,
 468         nd_geolocation_id => $geolocation->nd_geolocation_id(),
 469         nd_experiment_id => $nd_experiment->nd_experiment_id(),
 470         design_type => $design_type,
 471         design => \%design,
 472         is_genotyping => $self->get_is_genotyping(),
 473         is_analysis => $self->get_is_analysis(),
 474         is_sampling_trial => $self->get_is_sampling_trial(),
 475         new_treatment_has_plant_entries => $self->get_trial_has_plant_entries,
 476         new_treatment_has_subplot_entries => $self->get_trial_has_subplot_entries,
 477         operator => $self->get_operator,
 478         trial_stock_type => $self->get_trial_stock_type(),
 479     });
 480     my $error;
 481     my $validate_design_error = $trial_design_store->validate_design();
 482     if ($validate_design_error) {
 483         print STDERR "ERROR: $validate_design_error\n";
 484         return { error => "Error validating trial design: $validate_design_error." };
 485     } else {
 486         try {
 487             $error = $trial_design_store->store();
 488         } catch {
 489             print STDERR "ERROR store: $_\n";
 490             $error = $_;
 491         };
 492     }
 493     if ($error) {
 494         return { error => $error };
 495     }
 496     return { trial_id => $project->project_id };
 497 }
 498
 499
 500
 501
 502
 503 #######
 504 1;
 505 #######