lib/CXGN/Trial/TrialCreate.pm

   1 package CXGN::Trial::TrialCreate;
   2
   3 =head1 NAME
   4
   5 CXGN::Trial::TrialCreate - Module to create a trial based on a specified design.
   6
   7
   8 =head1 USAGE
   9
  10  my $trial_create = CXGN::Trial::TrialCreate->new({schema => $schema} );
  11
  12
  13 =head1 DESCRIPTION
  14
  15
  16 =head1 AUTHORS
  17
  18  Jeremy D. Edwards (jde22@cornell.edu)
  19
  20 =cut
  21
  22
  23 use Moose;
  24 use MooseX::FollowPBP;
  25 use Moose::Util::TypeConstraints;
  26 use Try::Tiny;
  27 use CXGN::Stock::StockLookup;
  28 use CXGN::Location::LocationLookup;
  29 use CXGN::BreedersToolbox::Projects;
  30 use CXGN::People::Person;
  31 use CXGN::Trial;
  32 use SGN::Model::Cvterm;
  33 use Data::Dumper;
  34
  35 has 'chado_schema' => (
  36                  is       => 'rw',
  37                  isa      => 'DBIx::Class::Schema',
  38                  predicate => 'has_chado_schema',
  39                  required => 1,
  40                 );
  41 has 'phenome_schema' => (
  42                  is       => 'rw',
  43                  isa      => 'DBIx::Class::Schema',
  44                  predicate => 'has_phenome_schema',
  45                  required => 1,
  46                 );
  47 has 'metadata_schema' => (
  48                  is       => 'rw',
  49                  isa      => 'DBIx::Class::Schema',
  50                  predicate => 'has_metadata_schema',
  51                  required => 0,
  52                          );
  53
  54 has 'dbh' => (is  => 'rw',predicate => 'has_dbh', required => 1,);
  55 has 'user_name' => (isa => 'Str', is => 'rw', predicate => 'has_user_name', required => 1,);
  56 #has 'location' => (isa =>'Str', is => 'rw', predicate => 'has_location', required => 1,);
  57 has 'program' => (isa =>'Str', is => 'rw', predicate => 'has_program', required => 1,);
  58 has 'trial_year' => (isa => 'Str', is => 'rw', predicate => 'has_trial_year', required => 1,);
  59 has 'trial_description' => (isa => 'Str', is => 'rw', predicate => 'has_trial_description', required => 1,);
  60 has 'trial_location' => (isa => 'Str', is => 'rw', predicate => 'has_trial_location', required => 1,);
  61 has 'design_type' => (isa => 'Str', is => 'rw', predicate => 'has_design_type', required => 1);
  62 has 'design' => (isa => 'HashRef[HashRef[Str|ArrayRef]]|Undef', is => 'rw', predicate => 'has_design', required => 1);
  63 #has 'breeding_program_id' => (isa => 'Int', is => 'rw', predicate => 'has_breeding_program_id', required => 1);
  64 has 'trial_name' => (isa => 'Str', is => 'rw', predicate => 'has_trial_name', required => 0,);
  65 has 'greenhouse_num_plants' => (isa => 'ArrayRef[Int]|Undef', is => 'rw', predicate => 'has_greenhouse_num_plants', required => 0,);
  66 has 'is_genotyping' => (isa => 'Bool', is => 'rw', required => 0, default => 0, );
  67 has 'genotyping_user_id' => (isa => 'Str', is => 'rw');
  68
  69 has 'genotyping_project_name' => (isa => 'Str', is => 'rw');
  70
  71 # sub get_trial_name {
  72 #   my $self = shift;
  73 #   my $trial_name;
  74 #   if ($self->has_trial_year() && $self->has_trial_location()) {
  75 #     $trial_name = "Trial ".$self->get_trial_location()." ".$self->get_trial_year();
  76 #   }
  77 #   return $trial_name;
  78 # }
  79
  80 sub trial_name_already_exists {
  81   my $self = shift;
  82   my $trial_name = $self->get_trial_name();
  83   my $schema = $self->get_chado_schema();
  84   if($schema->resultset('Project::Project')->find({name => $trial_name})){
  85     return 1;
  86   }
  87   else {
  88     return;
  89   }
  90 }
  91
  92 sub get_breeding_program_id {
  93   my $self = shift;
  94   my $project_lookup =  CXGN::BreedersToolbox::Projects->new(schema => $self->get_chado_schema);
  95   my $breeding_program_ref = $project_lookup->get_breeding_program_by_name($self->get_program());
  96   if (!$breeding_program_ref ) {
  97       print STDERR "UNDEF breeding program " . $self->get_program . "\n\n";
  98       return ;
  99   }
 100   my $breeding_program_id = $breeding_program_ref->project_id();
 101   print STDERR "get_breeding_program _id returning $breeding_program_id";
 102   return $breeding_program_id;
 103 }
 104
 105
 106 sub save_trial {
 107         #print STDERR "Check 4.1: ".localtime();
 108         print STDERR "**trying to save trial \n\n";
 109         my $self = shift;
 110         my $chado_schema = $self->get_chado_schema();
 111
 112         my %design;
 113         if ($self->get_design) {
 114                 %design = %{$self->get_design()};
 115         }
 116
 117         if ($self->trial_name_already_exists()) {
 118                 print STDERR "Can't create trial: Trial name already exists\n";
 119                 die "trial name already exists" ;
 120         }
 121
 122         if (!$self->get_breeding_program_id()) {
 123                 print STDERR "Can't create trial: Breeding program does not exist\n";
 124                 die "No breeding program id";
 125                 #return ( error => "no breeding program id" );
 126         }
 127
 128         #print STDERR "Check 4.2: ".localtime();
 129
 130         #lookup user by name
 131         my $user_name = $self->get_user_name();
 132         my $dbh = $self->get_dbh();
 133         my $owner_sp_person_id;
 134         $owner_sp_person_id = CXGN::People::Person->get_person_by_username($dbh, $user_name); #add person id as an option.
 135         if (!$owner_sp_person_id) {
 136                 print STDERR "Can't create trial: User/owner not found\n";
 137                 die "no owner $user_name" ;
 138         }
 139
 140         #print STDERR "Check 4.3: ".localtime();
 141
 142         my $geolocation;
 143         my $geolocation_lookup = CXGN::Location::LocationLookup->new(schema => $chado_schema);
 144         $geolocation_lookup->set_location_name($self->get_trial_location());
 145         $geolocation = $geolocation_lookup->get_geolocation();
 146         if (!$geolocation) {
 147                 print STDERR "Can't create trial: Location not found\n";
 148                 die "no geolocation" ;
 149         }
 150
 151         #print STDERR "Check 4.4: ".localtime();
 152
 153         my $field_layout_cvterm = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'field_layout', 'experiment_type');
 154         my $accession_cvterm = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'accession', 'stock_type');
 155         my $plot_cvterm = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'plot', 'stock_type');
 156         my $plant_cvterm = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'plant', 'stock_type');
 157         my $plot_of = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'plot_of', 'stock_relationship');
 158         my $plant_of = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'plant_of', 'stock_relationship');
 159         my $sample_cvterm = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'tissue_sample', 'stock_type');
 160         my $sample_of = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'tissue_sample_of', 'stock_relationship');
 161         my $genotyping_layout_cvterm = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'genotyping_layout', 'experiment_type');
 162         my $plant_index_number_cvterm = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'plant_index_number', 'stock_property')->cvterm_id();
 163
 164         my $project = $chado_schema->resultset('Project::Project')
 165         ->create({
 166                 name => $self->get_trial_name(),
 167                 description => $self->get_trial_description(),
 168         });
 169
 170         my $field_layout_experiment = $chado_schema->resultset('NaturalDiversity::NdExperiment')
 171         ->create({
 172                 nd_geolocation_id => $geolocation->nd_geolocation_id(),
 173                 type_id => $field_layout_cvterm->cvterm_id(),
 174         });
 175
 176         my $genotyping_layout_experiment = $chado_schema->resultset('NaturalDiversity::NdExperiment')
 177         ->create({
 178                 nd_geolocation_id => $geolocation->nd_geolocation_id(),
 179                 type_id => $genotyping_layout_cvterm->cvterm_id(),
 180         });
 181
 182         #print STDERR "Check 4.5: ".localtime();
 183
 184         #modify cvterms used to create the trial when it is a genotyping trial
 185         if ($self->get_is_genotyping()){
 186                 $field_layout_cvterm = $genotyping_layout_cvterm;
 187                 $field_layout_experiment = $genotyping_layout_experiment;
 188                 $plot_cvterm = $sample_cvterm;
 189                 $plot_of = $sample_of;
 190
 191                 #print STDERR "Storing user_id and project_name provided by the IGD spreadksheet for later recovery in the spreadsheet download... ".(join ",", ($self->get_genotyping_user_id(), $self->get_genotyping_project_name()))."\n";
 192
 193                 $genotyping_layout_experiment->create_nd_experimentprops(
 194                 {
 195                         'genotyping_user_id' => $self->get_genotyping_user_id(),
 196                         'genotyping_project_name' => $self->get_genotyping_project_name(),
 197                 },
 198                 { autocreate => 1});
 199         }
 200
 201         #print STDERR "Check 4.6: ".localtime();
 202
 203         my $t = CXGN::Trial->new( { bcs_schema => $chado_schema, trial_id => $project->project_id() } );
 204         $t->set_location($geolocation->nd_geolocation_id()); # set location also as a project prop
 205
 206         my $design_type = $self->get_design_type();
 207         if ($design_type eq 'greenhouse') {
 208                 my $has_plants_cvterm = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'project_has_plant_entries', 'project_property')->cvterm_id();
 209                 my $rs = $chado_schema->resultset("Project::Projectprop")->find_or_create({
 210                         type_id => $has_plants_cvterm,
 211                         value => 'varies',
 212                         project_id => $project->project_id(),
 213                 });
 214         }
 215
 216         #link to the project
 217         $field_layout_experiment->find_or_create_related('nd_experiment_projects',{project_id => $project->project_id()});
 218
 219         #print STDERR "Check 4.7: ".localtime();
 220
 221         $project->create_projectprops( { 'project year' => $self->get_trial_year(),'design' => $self->get_design_type()}, {autocreate=>1});
 222
 223         my $rs = $chado_schema->resultset('Stock::Stock')->search(
 224                 { 'me.is_obsolete' => { '!=' => 't' }, 'me.type_id' => $accession_cvterm->cvterm_id },
 225                 { join => [ 'stock_relationship_objects', 'nd_experiment_stocks' ],
 226                 '+select'=> ['me.stock_id', 'me.uniquename', 'me.organism_id', 'stock_relationship_objects.type_id', 'stock_relationship_objects.subject_id', 'nd_experiment_stocks.nd_experiment_id', 'nd_experiment_stocks.type_id'],
 227                 '+as'=> ['stock_id', 'uniquename', 'organism_id', 'stock_relationship_type_id', 'stock_relationship_subject_id', 'stock_experiment_id', 'stock_experiment_type_id']
 228                 }
 229         );
 230
 231         my %stock_data;
 232         my %stock_relationship_data;
 233         my %stock_experiment_data;
 234         while (my $s = $rs->next()) {
 235                 $stock_data{$s->get_column('uniquename')} = [$s->get_column('stock_id'), $s->get_column('organism_id') ];
 236                 if ($s->get_column('stock_relationship_type_id') && $s->get_column('stock_relationship_subject_id') ) {
 237                         $stock_relationship_data{$s->get_column('stock_id'), $s->get_column('stock_relationship_type_id'), $s->get_column('stock_relationship_subject_id') } = 1;
 238                 }
 239                 if ($s->get_column('stock_experiment_id') && $s->get_column('stock_experiment_type_id') ) {
 240                         $stock_experiment_data{$s->get_column('stock_id'), $s->get_column('stock_experiment_id'), $s->get_column('stock_experiment_type_id')} = 1;
 241                 }
 242         }
 243
 244         my $stock_id_checked;
 245         my $organism_id_checked;
 246
 247         #print STDERR Dumper \%design;
 248         foreach my $key (sort { $a cmp $b} keys %design) {
 249
 250                 #print STDERR "Check 01: ".localtime();
 251
 252                 my $plot_name;
 253                 if ($design{$key}->{plot_name}) {
 254                         $plot_name = $design{$key}->{plot_name};
 255                 }
 256                 my $plot_number;
 257                 if ($design{$key}->{plot_number}) {
 258                         $plot_number = $design{$key}->{plot_number};
 259                 }
 260                 my $plant_names;
 261                 if ($design{$key}->{plant_names}) {
 262                         $plant_names = $design{$key}->{plant_names};
 263                 }
 264                 my $stock_name;
 265                 if ($design{$key}->{stock_name}) {
 266                         $stock_name = $design{$key}->{stock_name};
 267                 }
 268                 my $block_number;
 269                 if ($design{$key}->{block_number}) { #set block number to 1 if no blocks are specified
 270                         $block_number = $design{$key}->{block_number};
 271                 } else {
 272                         $block_number = 1;
 273                 }
 274                 my $rep_number;
 275                 if ($design{$key}->{rep_number}) { #set rep number to 1 if no reps are specified
 276                         $rep_number = $design{$key}->{rep_number};
 277                 } else {
 278                         $rep_number = 1;
 279                 }
 280                 my $well;
 281                 if ($design{$key}->{well}) {
 282                         $well = $design{$key}->{well};
 283                 }
 284                 my $plate;
 285                 if ($design{$key}->{plate}) {
 286                         $plate = $design{$key}->{plate};
 287                 }
 288                 my $is_a_control;
 289                 if ($design{$key}->{is_a_control}) {
 290                         $is_a_control = $design{$key}->{is_a_control};
 291                 }
 292                 my $row_number;
 293                 if ($design{$key}->{row_number}) {
 294                         $row_number = $design{$key}->{row_number};
 295                 }
 296                 my $col_number;
 297                 if ($design{$key}->{col_number}) {
 298                         $col_number = $design{$key}->{col_number};
 299                 }
 300
 301
 302
 303                 #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.
 304                 if ($stock_data{$stock_name}) {
 305                         $stock_id_checked = $stock_data{$stock_name}[0];
 306                         $organism_id_checked = $stock_data{$stock_name}[1];
 307                 } else {
 308                         my $parent_stock;
 309                         my $stock_lookup = CXGN::Stock::StockLookup->new(schema => $chado_schema);
 310                         $stock_lookup->set_stock_name($stock_name);
 311                         $parent_stock = $stock_lookup->get_stock();
 312
 313                         if (!$parent_stock) {
 314                                 die ("Error while saving trial layout: no stocks found matching $stock_name");
 315                         }
 316
 317                         $stock_id_checked = $parent_stock->stock_id();
 318                         $organism_id_checked = $parent_stock->organism_id();
 319                 }
 320
 321                 #print STDERR "Check 02: ".localtime();
 322
 323                 #create the plot, if plot given
 324                 my $plot;
 325                 if ($plot_name) {
 326                         $plot = $chado_schema->resultset("Stock::Stock")
 327                         ->find_or_create({
 328                                 organism_id => $organism_id_checked,
 329                                 name       => $plot_name,
 330                                 uniquename => $plot_name,
 331                                 type_id => $plot_cvterm->cvterm_id,
 332                         });
 333                         if ($rep_number) {
 334                                 $plot->create_stockprops({'replicate' => $rep_number}, {autocreate => 1} );
 335                         }
 336                         if ($block_number) {
 337                                 $plot->create_stockprops({'block' => $block_number}, {autocreate => 1} );
 338                         }
 339                         if ($plot_number) {
 340                                 $plot->create_stockprops({'plot number' => $plot_number}, {autocreate => 1});
 341                         }
 342                         else {
 343                                 $plot->create_stockprops({'plot number' => $key}, {autocreate => 1});
 344                         }
 345
 346                         if ($is_a_control) {
 347                                 $plot->create_stockprops({'is a control' => $is_a_control}, {autocreate => 1} );
 348                         }
 349                         if ($design{$key}->{'range_number'}) {
 350                                 $plot->create_stockprops({'range' => $key}, {autocreate => 1});
 351                         }
 352                         if ($well) {
 353                                 $plot->create_stockprops({'well' => $well}, {autocreate => 1});
 354                         }
 355                         if ($plate) {
 356                                 $plot->create_stockprops({'plate' => $plate}, {autocreate => 1});
 357                         }
 358                         if ($row_number) {
 359                                 $plot->create_stockprops({'row_number' => $row_number}, {autocreate => 1} );
 360                         }
 361                         if ($col_number) {
 362                                 $plot->create_stockprops({'col_number' => $col_number}, {autocreate => 1} );
 363                         }
 364
 365                         # print STDERR "Check 03: ".localtime();
 366
 367                         #create the stock_relationship of the accession with the plot, if it does not exist already
 368                         if (!$stock_relationship_data{$stock_id_checked, $plot_of->cvterm_id(), $plot->stock_id()} ) {
 369                                 my $parent_stock = $chado_schema->resultset("Stock::StockRelationship")->create({
 370                                         object_id => $stock_id_checked,
 371                                         type_id => $plot_of->cvterm_id(),
 372                                         subject_id => $plot->stock_id()
 373                                 });
 374                         }
 375
 376                         #link the experiment to the plot, if it is not already
 377                         if (!$stock_experiment_data{$plot->stock_id(), $field_layout_experiment->nd_experiment_id(), $field_layout_cvterm->cvterm_id()} ) {
 378                                 my $stock_experiment_link = $chado_schema->resultset("NaturalDiversity::NdExperimentStock")->create({
 379                                         nd_experiment_id => $field_layout_experiment->nd_experiment_id(),
 380                                         type_id => $field_layout_cvterm->cvterm_id(),
 381                                         stock_id => $plot->stock_id(),
 382                                 });
 383                         }
 384                 }
 385
 386                 #Create plant entry if given. Currently this is for the greenhouse trial creation.
 387                 #print STDERR "Check 04: ".localtime();
 388                 if ($plant_names) {
 389                         foreach my $plant_name (@$plant_names) {
 390                                 my $plant = $chado_schema->resultset("Stock::Stock")
 391                                 ->find_or_create({
 392                                         organism_id => $organism_id_checked,
 393                                         name       => $plant_name,
 394                                         uniquename => $plant_name,
 395                                         type_id => $plant_cvterm->cvterm_id,
 396                                 });
 397
 398                                 my $plantprop = $chado_schema->resultset("Stock::Stockprop")->find_or_create( {
 399                                         stock_id => $plant->stock_id(),
 400                                         type_id => $plant_index_number_cvterm,
 401                                         value => 1,
 402                                 });
 403
 404                                 $plant->create_stockprops({'plot number' => $plot_number}, {autocreate => 1});
 405                                 $plant->create_stockprops({'replicate' => $rep_number}, {autocreate => 1} );
 406                                 $plant->create_stockprops({'block' => $block_number}, {autocreate => 1} );
 407
 408                                 #the plant has a relationship to the plot
 409                                 if (!$stock_relationship_data{$plant->stock_id(), $plant_of->cvterm_id(), $plot->stock_id()} ) {
 410                                         my $stock_relationship = $chado_schema->resultset("Stock::StockRelationship")->create({
 411                                                 subject_id => $plot->stock_id,
 412                                                 object_id => $plant->stock_id(),
 413                                                 type_id => $plant_of->cvterm_id(),
 414                                         });
 415                                 }
 416
 417                                 #create the stock_relationship of the accession with the plant, if it does not exist already
 418                                 if (!$stock_relationship_data{$stock_id_checked, $plant_of->cvterm_id(), $plant->stock_id()} ) {
 419                                         my $parent_stock = $chado_schema->resultset("Stock::StockRelationship")->create({
 420                                                 object_id => $stock_id_checked,
 421                                                 type_id => $plant_of->cvterm_id(),
 422                                                 subject_id => $plant->stock_id()
 423                                         });
 424                                 }
 425
 426                                 #link the experiment to the plant, if it is not already
 427                                 if (!$stock_experiment_data{$plant->stock_id(), $field_layout_experiment->nd_experiment_id(), $field_layout_cvterm->cvterm_id()} ) {
 428                                         my $stock_experiment_link = $chado_schema->resultset("NaturalDiversity::NdExperimentStock")->create({
 429                                                 nd_experiment_id => $field_layout_experiment->nd_experiment_id(),
 430                                                 type_id => $field_layout_cvterm->cvterm_id(),
 431                                                 stock_id => $plant->stock_id(),
 432                                         });
 433                                 }
 434                         }
 435                 }
 436         }
 437
 438         #print STDERR "Check 4.8: ".localtime();
 439
 440         $t->set_breeding_program($self->get_breeding_program_id);
 441
 442         #print STDERR "Check 4.9: ".localtime();
 443
 444         return ( trial_id => $project->project_id );
 445
 446 }
 447
 448
 449
 450
 451
 452 #######
 453 1;
 454 #######