lib/SGN/Controller/AJAX/LabelDesigner.pm

   1 package SGN::Controller::AJAX::LabelDesigner;
   2
   3 use Moose;
   4 use CXGN::Stock;
   5 use CXGN::List::Transform;
   6 use Data::Dumper;
   7 use Try::Tiny;
   8 use JSON;
   9 use Barcode::Code128;
  10 use CXGN::QRcode;
  11 use CXGN::ZPL;
  12 use PDF::API2;
  13 use Sort::Versions;
  14 use Tie::UrlEncoder; our(%urlencode);
  15 use CXGN::Trial::TrialLayout;
  16
  17 BEGIN { extends 'Catalyst::Controller::REST' }
  18
  19 __PACKAGE__->config(
  20     default   => 'application/json',
  21     stash_key => 'rest',
  22     map       => { 'application/json' => 'JSON', 'text/html' => 'JSON' },
  23    );
  24
  25    sub retrieve_longest_fields :Path('/tools/label_designer/retrieve_longest_fields') {
  26         my $self = shift;
  27         my $c = shift;
  28         my $schema = $c->dbic_schema('Bio::Chado::Schema');
  29         my $data_type = $c->req->param("data_type");
  30         my $value = $c->req->param("value");
  31         my %longest_hash;
  32         print STDERR "Data type is $data_type and id is $value\n";
  33        my ($trial_num, $trial_id, $plot_design, $plant_design) = get_plot_data($c, $schema, $data_type, $value);
  34
  35        #if plant ids exist, use plant design
  36        my %plot_design = %{$plot_design};
  37        my @plot_ids = keys %plot_design;
  38        my $plant_ids = $plot_design{$plot_ids[0]}->{'plant_ids'};
  39        my @plant_ids = @{$plant_ids};
  40        my $design;
  41
  42        if (scalar(@plant_ids) > 0) {
  43            $design = $plant_design;
  44        } else {
  45            $design = $plot_design;
  46        }
  47
  48
  49        print STDERR "Num plants 3: " . scalar(keys %{$design});
  50        print STDERR "AFTER SUB: \nTrial_id is $trial_id and design is ". Dumper($design) ."\n";
  51        if ($trial_num > 1) {
  52            $c->stash->{rest} = { error => "The selected list contains plots from more than one trial. This is not supported. Please select a different data source." };
  53            return;
  54        }
  55
  56        my $trial_name = $schema->resultset("Project::Project")->search({ project_id => $trial_id })->first->name();
  57        if (!$trial_name) {
  58            $c->stash->{rest} = { error => "Trial with id $trial_id does not exist. Can't create labels." };
  59            return;
  60        }
  61
  62        my %design = %{$design};
  63        if (!%design) {
  64            $c->stash->{rest} = { error => "Trial $trial_name does not have a valid field design. Can't create labels." };
  65            return;
  66        }
  67        $longest_hash{'trial_name'} = $trial_name;
  68
  69        my $year_cvterm_id = $schema->resultset("Cv::Cvterm")->search({name=> 'project year' })->first->cvterm_id();
  70        my $year = $schema->resultset("Project::Projectprop")->search({ project_id => $trial_id, type_id => $year_cvterm_id } )->first->value();
  71        $longest_hash{'year'} = $year;
  72
  73        my $design_cvterm_id = $schema->resultset("Cv::Cvterm")->search({name=> 'design' })->first->cvterm_id();
  74        my $design_value = $schema->resultset("Project::Projectprop")->search({ project_id => $trial_id, type_id => $design_cvterm_id } )->first->value();
  75        if ($design_value eq "genotyping_plate") { # for genotyping trials, get "Genotyping Facility" and "Genotyping Project Name"
  76            my $genotyping_facility_cvterm_id = $schema->resultset("Cv::Cvterm")->search({name=> 'genotyping_facility' })->first->cvterm_id();
  77            my $geno_project_name_cvterm_id = $schema->resultset("Cv::Cvterm")->search({name=> 'genotyping_project_name' })->first->cvterm_id();
  78            my $genotyping_facility = $schema->resultset("Project::Projectprop")->search({ project_id => $trial_id, type_id => $genotyping_facility_cvterm_id } )->first->value();
  79            my $genotyping_project_name = $schema->resultset("NaturalDiversity::NdExperimentProject")->search({
  80                    project_id => $trial_id
  81                })->search_related('nd_experiment')->search_related('nd_experimentprops',{
  82                    'nd_experimentprops.type_id' => $geno_project_name_cvterm_id
  83                })->first->value();
  84
  85            $longest_hash{'genotyping_project_name'} = $genotyping_project_name;
  86            $longest_hash{'genotyping_facility'} = $genotyping_facility;
  87        }
  88
  89        #get all fields in this trials design
  90        my $random_plot = $design{(keys %design)[rand keys %design]};
  91        my %reps;
  92        my @keys = keys %{$random_plot};
  93        foreach my $field (@keys) {
  94
  95            # if rep_number, find unique options and return them
  96            if ($field eq 'rep_number') {
  97                print STDERR "Searching for unique rep numbers.\n";
  98             #    foreach my $key (keys %design) {
  99                $reps{$_->{'rep_number'}}++ foreach values %design;
 100                print STDERR "Reps: ".Dumper(%reps);
 101            }
 102
 103
 104            print STDERR " Searching for longest $field\n";
 105            #for each field order values by descending length, then save the first one
 106            foreach my $key ( sort { length($design{$b}{$field}) <=> length($design{$a}{$field}) or versioncmp($a, $b) } keys %design) {
 107                 print STDERR "Longest $field is: ".$design{$key}{$field}."\n";
 108                 my $longest = $design{$key}{$field};
 109                 unless (ref($longest) || length($longest) < 1) { # skip if not scalar or undefined
 110                     $longest_hash{$field} = $longest;
 111                 } elsif (ref($longest) eq 'ARRAY') { # if array (ex. plants), sort array by length and take longest
 112                     print STDERR "Processing array " . Dumper($longest) . "\n";
 113                     # my @array = @{$longest};
 114                     my @sorted = sort { length $a <=> length $b } @{$longest};
 115                     if (length($sorted[0]) > 0) {
 116                         $longest_hash{$field} = $sorted[0];
 117                     }
 118                 } elsif (ref($longest) eq 'HASH') {
 119                     print STDERR "Not handling hashes yet\n";
 120                 }
 121                 last;
 122             }
 123         }
 124
 125         # save longest pedigree string
 126         my $pedigree_strings = get_all_pedigrees($schema, \%design);
 127         my %pedigree_strings = %{$pedigree_strings};
 128
 129         foreach my $key ( sort { length($pedigree_strings{$b}) <=> length($pedigree_strings{$a}) } keys %pedigree_strings) {
 130             $longest_hash{'pedigree_string'} = $pedigree_strings{$key};
 131             last;
 132         }
 133
 134         #print STDERR "Dumped data is: ".Dumper(%longest_hash);
 135         $c->stash->{rest} = {
 136             fields => \%longest_hash,
 137             reps => \%reps,
 138         };
 139    }
 140
 141    sub label_designer_download : Path('/tools/label_designer/download') : ActionClass('REST') { }
 142
 143    sub label_designer_download_GET : Args(0) {
 144         my $self = shift;
 145         my $c = shift;
 146         $c->forward('label_designer_download_POST');
 147     }
 148
 149   sub label_designer_download_POST : Args(0) {
 150        my $self = shift;
 151        my $c = shift;
 152        my $schema = $c->dbic_schema('Bio::Chado::Schema');
 153        my $download_type = $c->req->param("download_type");
 154     #    my $trial_id = $c->req->param("trial_id");
 155        my $data_type = $c->req->param("data_type");
 156        my $value = $c->req->param("value");
 157        my $design_json = $c->req->param("design_json");
 158        my $conversion_factor = 2.83; # for converting from 8 dots per mmm to 2.83 per mm (72 per inch)
 159
 160        # decode json
 161        my $json = new JSON;
 162        my $design_params = $json->allow_nonref->utf8->relaxed->escape_slash->loose->allow_singlequote->allow_barekey->decode($design_json);
 163
 164        my ($trial_num, $trial_id, $plot_design, $plant_design) = get_plot_data($c, $schema, $data_type, $value);
 165
 166        #if plant ids or names are used in design params, use plant design
 167
 168        my $design = $plot_design;
 169        my $label_params = $design_params->{'label_elements'};
 170        foreach my $element (@$label_params) {
 171            my %element = %{$element};
 172            my $filled_value = $element{'value'};
 173            print STDERR "Filled value is $filled_value\n";
 174            if ($filled_value eq '{plant_id}' || $filled_value eq '{plant_name}') {
 175                $design = $plant_design;
 176            }
 177        }
 178
 179        if ($trial_num > 1) {
 180            $c->stash->{rest} = { error => "The selected list contains plots from more than one trial. This is not supported. Please select a different data source." };
 181            return;
 182        }
 183
 184         my $trial_name = $schema->resultset("Project::Project")->search({ project_id => $trial_id })->first->name();
 185         if (!$trial_name) {
 186             $c->stash->{rest} = { error => "Trial with id $trial_id does not exist. Can't create labels." };
 187             return;
 188         }
 189        my %design = %{$design};
 190        if (!$design) {
 191            $c->stash->{rest} = { error => "Trial $trial_name does not have a valid field design. Can't create labels." };
 192            return;
 193        }
 194
 195        my $design_cvterm_id = $schema->resultset("Cv::Cvterm")->search({name=> 'design' })->first->cvterm_id();
 196        my $design_value = $schema->resultset("Project::Projectprop")->search({ project_id => $trial_id, type_id => $design_cvterm_id } )->first->value();
 197
 198        my ($genotyping_facility, $genotyping_project_name);
 199        if ($design_value eq "genotyping_plate") { # for genotyping trials, get "Genotyping Facility" and "Genotyping Project Name"
 200            my $genotyping_facility_cvterm_id = $schema->resultset("Cv::Cvterm")->search({name=> 'genotyping_facility' })->first->cvterm_id();
 201            my $geno_project_name_cvterm_id = $schema->resultset("Cv::Cvterm")->search({name=> 'genotyping_project_name' })->first->cvterm_id();
 202            $genotyping_facility = $schema->resultset("Project::Projectprop")->search({ project_id => $trial_id, type_id => $genotyping_facility_cvterm_id } )->first->value();
 203            $genotyping_project_name = $schema->resultset("NaturalDiversity::NdExperimentProject")->search({
 204                    project_id => $trial_id
 205                })->search_related('nd_experiment')->search_related('nd_experimentprops',{
 206                    'nd_experimentprops.type_id' => $geno_project_name_cvterm_id
 207                })->first->value();
 208        }
 209
 210        my $year_cvterm_id = $schema->resultset("Cv::Cvterm")->search({name=> 'project year' })->first->cvterm_id();
 211        my $year = $schema->resultset("Project::Projectprop")->search({ project_id => $trial_id, type_id => $year_cvterm_id } )->first->value();
 212
 213        # if needed retrieve pedigrees in bulk
 214        my $pedigree_strings;
 215        foreach my $element (@$label_params) {
 216            if ($element->{'value'} eq '{pedigree_string}') {
 217                $pedigree_strings = get_all_pedigrees($schema, $design);
 218            }
 219        }
 220
 221        # Create a blank PDF file
 222        my $dir = $c->tempfiles_subdir('labels');
 223        my $file_prefix = $trial_name;
 224        $file_prefix =~ s/[^a-zA-Z0-9-_]//g;
 225
 226        my ($FH, $filename) = $c->tempfile(TEMPLATE=>"labels/$file_prefix-XXXXX", SUFFIX=>".$download_type");
 227
 228        # initialize loop variables
 229        my $col_num = 1;
 230        my $row_num = 1;
 231        my $key_number = 0;
 232        my $sort_order = $design_params->{'sort_order'};
 233
 234        if ($download_type eq 'pdf') {
 235            # Create pdf
 236            print STDERR "Creating the PDF . . .\n";
 237            my $pdf  = PDF::API2->new(-file => $FH);
 238            my $page = $pdf->page();
 239            my $text = $page->text();
 240            my $gfx = $page->gfx();
 241            $page->mediabox($design_params->{'page_width'}, $design_params->{'page_height'});
 242
 243            # loop through plot data in design hash
 244            foreach my $key ( sort { versioncmp( $design{$a}{$sort_order} , $design{$b}{$sort_order} ) or  $a <=> $b } keys %design) {
 245
 246                 #print STDERR "Design key is $key\n";
 247                 my %design_info = %{$design{$key}};
 248                 $design_info{'trial_name'} = $trial_name;
 249                 $design_info{'year'} = $year;
 250                 $design_info{'genotyping_facility'} = $genotyping_facility;
 251                 $design_info{'genotyping_project_name'} = $genotyping_project_name;
 252                 $design_info{'pedigree_string'} = $pedigree_strings->{$design_info{'accession_name'}};
 253                 #print STDERR "Design info: " . Dumper(%design_info);
 254
 255                 if ( $design_params->{'plot_filter'} eq 'all' || $design_params->{'plot_filter'} eq $design_info{'rep_number'}) { # filter by rep if needed
 256
 257                     for (my $i=0; $i < $design_params->{'copies_per_plot'}; $i++) {
 258                         #print STDERR "Working on label num $i\n";
 259                         my $label_x = $design_params->{'left_margin'} + ($design_params->{'label_width'} + $design_params->{'horizontal_gap'}) * ($col_num-1);
 260                         my $label_y = $design_params->{'page_height'} - $design_params->{'top_margin'} - ($design_params->{'label_height'} + $design_params->{'vertical_gap'}) * ($row_num-1);
 261
 262                        foreach my $element (@$label_params) {
 263                            #print STDERR "Element Dumper\n" . Dumper($element);
 264                            my %element = %{$element};
 265                            my $elementx = $label_x + ( $element{'x'} / $conversion_factor );
 266                            my $elementy = $label_y - ( $element{'y'} / $conversion_factor );
 267
 268                            my $filled_value = $element{'value'};
 269                            $filled_value =~ s/\{(.*?)\}/process_field($1,$key_number,\%design_info)/ge;
 270                            #print STDERR "Element ".$element{'type'}."_".$element{'size'}." filled value is ".$filled_value." and coords are $elementx and $elementy\n";
 271                            #print STDERR "Writing to the PDF . . .\n";
 272                            if ( $element{'type'} eq "Code128" || $element{'type'} eq "QRCode" ) {
 273
 274                                 if ( $element{'type'} eq "Code128" ) {
 275
 276                                    my $barcode_object = Barcode::Code128->new();
 277
 278                                    my ($png_location, $png_uri) = $c->tempfile( TEMPLATE => [ 'barcode', 'bc-XXXXX'], SUFFIX=>'.png');
 279                                    open(PNG, ">", $png_location) or die "Can't write $png_location: $!\n";
 280                                    binmode(PNG);
 281
 282                                    $barcode_object->option("scale", $element{'size'}, "font_align", "center", "padding", 5, "show_text", 0);
 283                                    $barcode_object->barcode($filled_value);
 284                                    my $barcode = $barcode_object->gd_image();
 285                                    print PNG $barcode->png();
 286                                    close(PNG);
 287
 288                                     my $image = $pdf->image_png($png_location);
 289                                     my $height = $element{'height'} / $conversion_factor ; # scale to 72 pts per inch
 290                                     my $width = $element{'width'} / $conversion_factor ; # scale to 72 pts per inch
 291                                     my $elementy = $elementy - ($height/2); # adjust for img position sarting at bottom
 292                                     my $elementx = $elementx - ($width/2);
 293                                     #print STDERR 'adding Code 128 params $image, $elementx, $elementy, $width, $height with: '."$image, $elementx, $elementy, $width, $height\n";
 294                                     $gfx->image($image, $elementx, $elementy, $width, $height);
 295
 296
 297                               } else { #QRCode
 298
 299                                   my ($jpeg_location, $jpeg_uri) = $c->tempfile( TEMPLATE => [ 'barcode', 'bc-XXXXX'], SUFFIX=>'.jpg');
 300                                   my $barcode_generator = CXGN::QRcode->new(
 301                                       text => $filled_value,
 302                                       size => $element{'size'},
 303                                       margin => 0,
 304                                       version => 0,
 305                                       level => 'M'
 306                                   );
 307                                   my $barcode_file = $barcode_generator->get_barcode_file($jpeg_location);
 308
 309                                    my $image = $pdf->image_jpeg($jpeg_location);
 310                                    my $height = $element{'height'} / $conversion_factor ; # scale to 72 pts per inch
 311                                    my $width = $element{'width'} / $conversion_factor ; # scale to 72 pts per inch
 312                                    my $elementy = $elementy - ($height/2); # adjust for img position sarting at bottom
 313                                    my $elementx = $elementx - ($width/2);
 314                                    $gfx->image($image, $elementx, $elementy, $width, $height);
 315
 316                               }
 317                            }
 318                            else { #Text
 319
 320                                 my $font = $pdf->corefont($element{'font'}); # Add a built-in font to the PDF
 321                                 # Add text to the page
 322                                 my $adjusted_size = $element{'size'} / $conversion_factor; # scale to 72 pts per inch
 323                                 $text->font($font, $adjusted_size);
 324                                 my $height = $element{'height'} / $conversion_factor ; # scale to 72 pts per inch
 325                                 my $elementy = $elementy - ($height/4); # adjust for img position starting at bottom
 326                                 $text->translate($elementx, $elementy);
 327                                 $text->text_center($filled_value);
 328                            }
 329                        }
 330
 331                         if ($col_num < $design_params->{'number_of_columns'}) { #next column
 332                             $col_num++;
 333                         } else { #new row, reset col num
 334                             $col_num = 1;
 335                             $row_num++;
 336                         }
 337
 338                         if ($row_num > $design_params->{'number_of_rows'}) { #create new page and reset row and col num
 339                             $pdf->finishobjects($page, $gfx, $text); #flush the page to save memory on big PDFs
 340                             $page = $pdf->page();
 341                             $text = $page->text();
 342                             $gfx = $page->gfx();
 343                             $page->mediabox($design_params->{'page_width'}, $design_params->{'page_height'});
 344                             $row_num = 1;
 345                         }
 346                     }
 347                 }
 348              $key_number++;
 349              }
 350
 351            print STDERR "Saving the PDF . . .\n";
 352            $pdf->save();
 353
 354        } elsif ($download_type eq 'zpl') {
 355
 356            print STDERR "Generating zpl . . .\n";
 357            my $zpl_obj = CXGN::ZPL->new(
 358                print_width => $design_params->{'label_width'} * $conversion_factor,
 359                label_length => $design_params->{'label_height'} * $conversion_factor
 360            );
 361            $zpl_obj->start_sequence();
 362            $zpl_obj->label_format();
 363            foreach my $element (@$label_params) {
 364                my $x = $element->{'x'} - ($element->{'width'}/2);
 365                my $y = $element->{'y'} - ($element->{'height'}/2);
 366                $zpl_obj->new_element($element->{'type'}, $x, $y, $element->{'size'}, $element->{'value'});
 367            }
 368            $zpl_obj->end_sequence();
 369            my $zpl_template = $zpl_obj->render();
 370            foreach my $key ( sort { versioncmp( $design{$a}{$sort_order} , $design{$b}{$sort_order} ) or  $a <=> $b } keys %design) {
 371             #    print STDERR "Design key is $key\n";
 372                my %design_info = %{$design{$key}};
 373                $design_info{'trial_name'} = $trial_name;
 374                $design_info{'year'} = $year;
 375                $design_info{'pedigree_string'} = $pedigree_strings->{$design_info{'accession_name'}};
 376
 377                my $zpl = $zpl_template;
 378                $zpl =~ s/\{(.*?)\}/process_field($1,$key_number,\%design_info)/ge;
 379               for (my $i=0; $i < $design_params->{'copies_per_plot'}; $i++) {
 380                   print $FH $zpl;
 381                }
 382             $key_number++;
 383             }
 384        }
 385
 386        close($FH);
 387        print STDERR "Returning with filename . . .\n";
 388        $c->stash->{rest} = {
 389            filename => $urlencode{$filename},
 390            filepath => $c->config->{basepath}."/".$filename
 391        };
 392
 393    }
 394
 395    sub process_field {
 396        my $field = shift;
 397        my $key_number = shift;
 398        my $design_info = shift;
 399        my %design_info = %{$design_info};
 400        #print STDERR "Field is $field\n";
 401        if ($field =~ m/Number:/) {
 402            our ($placeholder, $start_num, $increment) = split ':', $field;
 403            my $length = length($start_num);
 404            #print STDERR "Increment is $increment\nKey Number is $key_number\n";
 405            my $custom_num =  $start_num + ($increment * $key_number);
 406            return sprintf("%0${length}d", $custom_num);
 407        } else {
 408            return $design_info{$field};
 409        }
 410    }
 411
 412 sub process_field {
 413     my $field = shift;
 414     my $key_number = shift;
 415     my $design_info = shift;
 416     my %design_info = %{$design_info};
 417     #print STDERR "Field is $field\n";
 418     if ($field =~ m/Number:/) {
 419         our ($placeholder, $start_num, $increment) = split ':', $field;
 420         my $length = length($start_num);
 421         #print STDERR "Increment is $increment\nKey Number is $key_number\n";
 422         my $custom_num =  $start_num + ($increment * $key_number);
 423         return sprintf("%0${length}d", $custom_num);
 424     } else {
 425         return $design_info{$field};
 426     }
 427 }
 428
 429 sub get_all_pedigrees {
 430     my $schema = shift;
 431     my $design = shift;
 432     my %design = %{$design};
 433
 434     # collect all unique accession ids for pedigree retrieval
 435     my %accession_id_hash;
 436     foreach my $key (keys %design) {
 437         $accession_id_hash{$design{$key}{'accession_id'}} = $design{$key}{'accession_name'};
 438     }
 439     my @accession_ids = keys %accession_id_hash;
 440
 441     # retrieve pedigree info using batch download (fastest method), then extract pedigree strings from download rows.
 442     my $stock = CXGN::Stock->new ( schema => $schema);
 443     my $pedigree_rows = $stock->get_pedigree_rows(\@accession_ids, 'parents_only');
 444     my %pedigree_strings;
 445     foreach my $row (@$pedigree_rows) {
 446         my ($progeny, $female_parent, $male_parent, $cross_type) = split "\t", $row;
 447         my $string = join ('/', $female_parent ? $female_parent : 'NA', $male_parent ? $male_parent : 'NA');
 448         $pedigree_strings{$progeny} = $string;
 449     }
 450     return \%pedigree_strings;
 451 }
 452
 453 sub get_plot_data {
 454     my $c = shift;
 455     my $schema = shift;
 456     my $data_type = shift;
 457     my $value = shift;
 458     my $num_trials = 1;
 459     my ($trial_id, $plot_design, $plant_design);
 460
 461     # print STDERR "Data type is $data_type and value is $value\n";
 462
 463     if ($data_type =~ m/Plant List/) {
 464     }
 465     elsif ($data_type =~ m/Plot List/) {
 466         # get items from list, get trial id from plot id. Or, get plot data one by one
 467         my $plot_data = SGN::Controller::AJAX::List->retrieve_list($c, $value);
 468         my @plot_list = map { $_->[1] } @$plot_data;
 469         my $t = CXGN::List::Transform->new();
 470         my $acc_t = $t->can_transform("plots", "plot_ids");
 471         my $plot_id_hash = $t->transform($schema, $acc_t, \@plot_list);
 472         my @plot_ids = @{$plot_id_hash->{transform}};
 473         my $trial_rs = $schema->resultset("NaturalDiversity::NdExperimentStock")->search({
 474             stock_id => { -in => \@plot_ids }
 475         })->search_related('nd_experiment')->search_related('nd_experiment_projects');
 476         my %trials = ();
 477         while (my $row = $trial_rs->next()) {
 478             print STDERR "Looking at id ".$row->project_id()."\n";
 479             my $id = $row->project_id();
 480             $trials{$id} = 1;
 481         }
 482         $num_trials = scalar keys %trials;
 483         print STDERR "Count is $num_trials\n";
 484         $trial_id = $trial_rs->first->project_id();
 485         my $full_design = CXGN::Trial::TrialLayout->new({schema => $schema, trial_id => $trial_id, experiment_type=>'field_layout' })->get_design();
 486         print STDERR "Full Design is: ".Dumper($full_design);
 487         # reduce design hash, removing plots that aren't in list
 488         my %full_design = %{$full_design};
 489
 490         foreach my $i (0 .. $#plot_ids) {
 491             foreach my $key (keys %full_design) {
 492                 if ($full_design{$key}->{'plot_id'} eq $plot_ids[$i]) {
 493                     print STDERR "Plot name is ".$full_design{$key}->{'plot_name'}."\n";
 494                     $plot_design->{$key} = $full_design{$key};
 495                     $plot_design->{$key}->{'list_order'} = $i;
 496                 }
 497             }
 498         }
 499
 500     }
 501     elsif ($data_type =~ m/Genotyping Trial/) {
 502         $trial_id = $value;
 503         $plot_design = CXGN::Trial::TrialLayout->new({schema => $schema, trial_id => $trial_id, experiment_type=>'field_layout' })->get_design();
 504     }
 505     elsif ($data_type =~ m/Field Trials/) {
 506         $trial_id = $value;
 507         $plot_design = CXGN::Trial::TrialLayout->new({schema => $schema, trial_id => $trial_id, experiment_type=>'field_layout' })->get_design();
 508         my %plot_design = %{$plot_design};
 509         my @plot_ids = keys %plot_design;
 510         my $plant_ids = $plot_design{$plot_ids[0]}->{'plant_ids'};
 511         my @plant_ids = @{$plant_ids};
 512         #check if there are plant ids
 513         my %plant_design;
 514         if (scalar(@plant_ids) > 0) {
 515             foreach my $plot_id (keys %plot_design) {
 516                 #print STDERR "Working on key $plot_id and value: " . Dumper($design{$plot_id});
 517                 my $plant_ids = $plot_design{$plot_id}->{'plant_ids'};
 518                 my @plant_ids = @{$plant_ids};
 519                 my $plant_names = $plot_design{$plot_id}->{'plant_names'};
 520                 my @plant_names = @{$plant_names};
 521                 for (my $i=0; $i < scalar(@plant_ids); $i++) {
 522                     my $plant_id = $plant_ids[$i];
 523                     my $plant_name = $plant_names[$i];
 524                     #print STDERR "plant id is $plant_id and name is $plant_name\n";
 525                     foreach my $property (keys %{$plot_design{$plot_id}}) { $plant_design{$plant_id}->{$property} = $plot_design{$plot_id}->{$property}; }
 526                     $plant_design{$plant_id}->{'plant_id'} = $plant_id;
 527                     $plant_design{$plant_id}->{'plant_name'} = $plant_name;
 528                     #print STDERR "Added key " . $plant_id . " and value: " . Dumper($plant_design{$plant_id});
 529                 }
 530             }
 531             $plant_design = \%plant_design;
 532         }
 533     }
 534     # elsif ($data_type =~ m/Field Trial Plots/) {
 535     #     $trial_id = $value;
 536     #     $design = CXGN::Trial::TrialLayout->new({schema => $schema, trial_id => $trial_id, experiment_type=>'field_layout' })->get_design();
 537     # }
 538     return ($num_trials, $trial_id, $plot_design, $plant_design);
 539 }
 540
 541
 542 #########
 543 1;
 544 #########