lib/SGN/View/Trial.pm

   1 package SGN::View::Trial;
   2 use base 'Exporter';
   3 use List::MoreUtils ':all';
   4 use Data::Dumper;
   5 use strict;
   6 use warnings;
   7
   8 our @EXPORT_OK = qw/
   9     design_layout_view
  10     design_info_view
  11     trial_detail_design_view
  12     design_layout_map_view
  13 /;
  14 our @EXPORT = ();
  15
  16 sub trial_detail_design_view {
  17   my $design_ref = shift;
  18   my %design = %{$design_ref};
  19   my $design_result_html;
  20
  21   $design_result_html .= '<table border="1">';
  22   $design_result_html .= qq{<tr><th>Plot Name</th><th>Accession Name</th><th>Check Name</th><th>Row number</th><th>Col number</th><th>Block Number</th><th>Block Row Number</th><th>Block Col Number</th><th>Rep Number</th></tr>};
  23
  24   foreach my $key (sort { $a <=> $b} keys %design) {
  25       $design_result_html .= "<tr>";
  26       if ($design{$key}->{plot_name}) {
  27           $design_result_html .= "<td>".$design{$key}->{plot_name}."</td>";
  28       } else {
  29           $design_result_html .= "<td></td>";
  30       }
  31       if ($design{key}->{accession_name}) {
  32           $design_result_html .= "<td>".$design{$key}->{accession_name}."</td>";
  33       } else {
  34           $design_result_html .= "<td></td>";
  35       }
  36       if ($design{key}->{check_name}) {
  37           $design_result_html .= "<td>".$design{$key}->{check_name}."</td>";
  38       } else {
  39           $design_result_html .= "<td></td>";
  40       }
  41       if ($design{key}->{row_number}) {
  42           $design_result_html .= "<td>".$design{$key}->{row_number}."</td>";
  43       } else {
  44           $design_result_html .= "<td></td>";
  45       }
  46       if ($design{key}->{col_number}) {
  47           $design_result_html .= "<td>".$design{$key}->{col_number}."</td>";
  48       } else {
  49           $design_result_html .= "<td></td>";
  50       }
  51       if ($design{key}->{block_number}) {
  52           $design_result_html .= "<td>".$design{$key}->{block_number}."</td>";
  53       } else {
  54           $design_result_html .= "<td></td>";
  55       }
  56       if ($design{key}->{block_row_number}) {
  57           $design_result_html .= "<td>".$design{$key}->{block_row_number}."</td>";
  58       } else {
  59           $design_result_html .= "<td></td>";
  60       }
  61       if ($design{key}->{block_col_number}) {
  62           $design_result_html .= "<td>".$design{$key}->{block_col_number}."</td>";
  63       } else {
  64           $design_result_html .= "<td></td>";
  65       }
  66       if ($design{key}->{rep_number}) {
  67           $design_result_html .= "<td>".$design{$key}->{rep_number}."</td>";
  68       } else {
  69           $design_result_html .= "<td></td>";
  70       }
  71       $design_result_html .= "</tr>";
  72   }
  73   $design_result_html .= "</table>";
  74   return  "$design_result_html";
  75
  76 }
  77
  78 sub design_layout_map_view {
  79     my $design_ref = shift;
  80     my $design_type = shift;
  81     my $result;
  82     my %design = %{$design_ref};
  83     my @layout_info;
  84     my @row_numbers = ();
  85     my @col_numbers = ();
  86     my @rep_numbers = ();
  87     my @block_numbers = ();
  88     my @check_names = ();
  89
  90     foreach my $key (sort { $a <=> $b} keys %design) {
  91         my $plot_name = $design{$key}->{plot_name} || '';
  92         my $stock_name = $design{$key}->{stock_name} || '';
  93         my $check_name = $design{$key}->{is_a_control} || '';
  94         my $row_number = $design{$key}->{row_number} || '';
  95         my $col_number = $design{$key}->{col_number} || '';
  96         my $block_number = $design{$key}->{block_number} || '';
  97         my $rep_number = $design{$key}->{rep_number} || '';
  98         my $plot_number = $key;
  99
 100         if ($col_number) {
 101             push @col_numbers, $col_number;
 102         }
 103         if ($row_number) {
 104             push @row_numbers, $row_number;
 105         }elsif (!$row_number){
 106                         if ($block_number && $design_type ne 'splitplot'){
 107                                 $row_number = $block_number;
 108                                 push @row_numbers, $row_number;
 109                         }elsif ($rep_number && !$block_number && $design_type ne 'splitplot'){
 110                                 $row_number = $rep_number;
 111                                 push @row_numbers, $row_number;
 112                         }elsif ($design_type eq 'splitplot'){
 113                 $row_number = $rep_number;
 114                                 push @row_numbers, $row_number;
 115             }
 116                 }
 117         if ($rep_number) {
 118             push @rep_numbers, $rep_number;
 119         }
 120         if ($block_number) {
 121             push @block_numbers, $block_number;
 122         }
 123         if ($check_name){
 124             push @check_names, $stock_name;
 125         }
 126
 127         push @layout_info, {
 128             plot_number => $plot_number,
 129             row_number => $row_number,
 130             col_number => $col_number,
 131             block_number=> $block_number,
 132             rep_number =>  $rep_number,
 133             plot_name => $plot_name,
 134             accession_name => $stock_name,
 135         };
 136     }
 137
 138     @layout_info = sort { $a->{plot_number} <=> $b->{plot_number}} @layout_info;
 139     my $false_coord;
 140         if (scalar(@col_numbers) < 1){
 141         @col_numbers = ();
 142         $false_coord = 'false_coord';
 143                 my @row_instances = uniq @row_numbers;
 144                 my %unique_row_counts;
 145                 $unique_row_counts{$_}++ for @row_numbers;
 146         my @col_number2;
 147         for my $key (keys %unique_row_counts){
 148             push @col_number2, (1..$unique_row_counts{$key});
 149         }
 150         for (my $i=0; $i < scalar(@layout_info); $i++){
 151                         $layout_info[$i]->{'col_number'} = $col_number2[$i];
 152             push @col_numbers, $col_number2[$i];
 153         }
 154         }
 155
 156     my $plot_popUp;
 157         foreach my $hash (@layout_info){
 158                 $plot_popUp = $hash->{'plot_name'}."\nplot_No:".$hash->{'plot_number'}."\nblock_No:".$hash->{'block_number'}."\nrep_No:".$hash->{'rep_number'}."\nstock:".$hash->{'accession_name'};
 159         push @$result,  {plotname => $hash->{'plot_name'}, stock => $hash->{'accession_name'}, plotn => $hash->{'plot_number'}, blkn=>$hash->{'block_number'}, rep=>$hash->{'rep_number'}, row=>$hash->{'row_number'}, col=>$hash->{'col_number'}, plot_msg=>$plot_popUp} ;
 160     }
 161
 162     my @sorted_block = sort@block_numbers;
 163         my @uniq_block = uniq(@sorted_block);
 164     @check_names = uniq(@check_names);
 165     #print STDERR Dumper(\@check_names);
 166         my ($min_rep, $max_rep) = minmax @rep_numbers;
 167         my ($min_block, $max_block) = minmax @block_numbers;
 168         my ($min_col, $max_col) = minmax @col_numbers;
 169         my ($min_row, $max_row) = minmax @row_numbers;
 170         my (@unique_col,@unique_row);
 171         for my $x (1..$max_col){
 172                 push @unique_col, $x;
 173         }
 174         for my $y (1..$max_row){
 175                 push @unique_row, $y;
 176         }
 177
 178     my %return = (
 179                 coord_row =>  \@row_numbers,
 180                 coord_col =>  \@col_numbers,
 181                 max_row => $max_row,
 182                 max_col => $max_col,
 183                 max_rep => $max_rep,
 184                 max_block => $max_block,
 185                 controls => \@check_names,
 186                 unique_col => \@unique_col,
 187                 unique_row => \@unique_row,
 188                 false_coord => $false_coord,
 189                 result => $result,
 190         );
 191
 192     return  \%return;
 193 }
 194
 195 #For printing the table view of the generated design, splitplot design is different from the others:
 196 # The splitplot generates plots, subplots, and plant entries, so the table should reflect that.
 197
 198 sub design_layout_view {
 199     my $design_ref = shift;
 200     my $design_info_ref = shift;
 201     my $design_type = shift;
 202     my $trial_stock_type = shift;
 203     my %design = %{$design_ref};
 204     my %design_info = %{$design_info_ref};
 205     my $design_result_html;
 206
 207     $design_result_html .= '<table class="table table-bordered table-hover">';
 208
 209     if ($trial_stock_type eq 'family_name') {
 210         if ($design_type eq 'greenhouse') {
 211             $design_result_html .= qq{<tr><th>Plant Name</th><th>Plot Name</th><th>Family Name</th><th>Check Name</th><th>Plot Number</th><th>Row number</th><th>Col number</th><th>Block Number</th><th>Block Row Number</th><th>Block Col Number</th><th>Rep Number</th><th>Seedlot Name</th><th>Num Seeds Per Plot</th></tr>};
 212         } elsif ($design_type eq 'splitplot') {
 213             $design_result_html .= qq{<tr><th>Plant Name</th><th>Subplot Name</th><th>Plot Name</th><th>Family Name</th><th>Check Name</th><th>Plot Number</th><th>Row number</th><th>Col number</th><th>Block Number</th><th>Block Row Number</th><th>Block Col Number</th><th>Rep Number</th><th>Seedlot Name</th><th>Num Seeds Per Plot</th></tr>};
 214         } else {
 215             $design_result_html .= qq{<tr><th>Plot Name</th><th>Family Name</th><th>Check Name</th><th>Plot Number</th><th>Row number</th><th>Col number</th><th>Block Number</th><th>Block Row Number</th><th>Block Col Number</th><th>Rep Number</th><th>Seedlot Name</th><th>Num Seeds Per Plot</th></tr>};
 216         }
 217     } elsif ($trial_stock_type eq 'cross') {
 218         if ($design_type eq 'greenhouse') {
 219             $design_result_html .= qq{<tr><th>Plant Name</th><th>Plot Name</th><th>Cross Unique ID</th><th>Check Name</th><th>Plot Number</th><th>Row number</th><th>Col number</th><th>Block Number</th><th>Block Row Number</th><th>Block Col Number</th><th>Rep Number</th><th>Seedlot Name</th><th>Num Seeds Per Plot</th></tr>};
 220         } elsif ($design_type eq 'splitplot') {
 221             $design_result_html .= qq{<tr><th>Plant Name</th><th>Subplot Name</th><th>Plot Name</th><th>Cross Unique ID</th><th>Check Name</th><th>Plot Number</th><th>Row number</th><th>Col number</th><th>Block Number</th><th>Block Row Number</th><th>Block Col Number</th><th>Rep Number</th><th>Seedlot Name</th><th>Num Seeds Per Plot</th></tr>};
 222         } else {
 223             $design_result_html .= qq{<tr><th>Plot Name</th><th>Cross Unique ID</th><th>Check Name</th><th>Plot Number</th><th>Row number</th><th>Col number</th><th>Block Number</th><th>Block Row Number</th><th>Block Col Number</th><th>Rep Number</th><th>Seedlot Name</th><th>Num Seeds Per Plot</th></tr>};
 224         }
 225     } else {
 226         if ($design_type eq 'greenhouse') {
 227             $design_result_html .= qq{<tr><th>Plant Name</th><th>Plot Name</th><th>Accession Name</th><th>Check Name</th><th>Plot Number</th><th>Row number</th><th>Col number</th><th>Block Number</th><th>Block Row Number</th><th>Block Col Number</th><th>Rep Number</th><th>Seedlot Name</th><th>Num Seeds Per Plot</th></tr>};
 228         } elsif ($design_type eq 'splitplot') {
 229             $design_result_html .= qq{<tr><th>Plant Name</th><th>Subplot Name</th><th>Plot Name</th><th>Accession Name</th><th>Check Name</th><th>Plot Number</th><th>Row number</th><th>Col number</th><th>Block Number</th><th>Block Row Number</th><th>Block Col Number</th><th>Rep Number</th><th>Seedlot Name</th><th>Num Seeds Per Plot</th></tr>};
 230         } else {
 231             $design_result_html .= qq{<tr><th>Plot Name</th><th>Accession Name</th><th>Check Name</th><th>Plot Number</th><th>Row number</th><th>Col number</th><th>Block Number</th><th>Block Row Number</th><th>Block Col Number</th><th>Rep Number</th><th>Seedlot Name</th><th>Num Seeds Per Plot</th></tr>};
 232         }
 233     }
 234
 235     foreach my $key (sort { $a <=> $b} keys %design) {
 236         if ($key eq 'treatments'){
 237             next;
 238         }
 239         my $plot_name = $design{$key}->{plot_name} || '';
 240         my $stock_name = $design{$key}->{stock_name} || '';
 241         my $seedlot_name = $design{$key}->{seedlot_name} || '';
 242         my $num_seed_per_plot = $design{$key}->{num_seed_per_plot} || '';
 243         my $check_name = $design{$key}->{is_a_control} || '';
 244         my $row_number = $design{$key}->{row_number} || '';
 245         my $col_number = $design{$key}->{col_number} || '';
 246         my $block_number = $design{$key}->{block_number} || '';
 247         my $block_row_number = $design{$key}->{block_row_number} || '';
 248         my $block_col_number = $design{$key}->{block_col_number} || '';
 249         my $rep_number = $design{$key}->{rep_number} || '';
 250         my $plot_number = $key;
 251
 252         if ($design{$key}->{subplots_plant_names}) {
 253             foreach my $subplot_name (sort keys %{$design{$key}->{subplots_plant_names}}) {
 254                 my $plant_names = $design{$key}->{subplots_plant_names}->{$subplot_name};
 255                 foreach my $plant_name (@$plant_names){
 256                     $design_result_html .= "<tr><td>".$plant_name."</td><td>".$subplot_name."</td><td>".$plot_name."</td><td>".$stock_name."</td><td>".$check_name."</td><td>".$plot_number."</td><td>".$row_number."</td><td>".$col_number."</td><td>".$block_number."</td><td>".$block_row_number."</td><td>".$block_col_number."</td><td>".$rep_number."</td><td>".$seedlot_name."</td><td>".$num_seed_per_plot."</td></tr>";
 257                 }
 258             }
 259         } elsif ($design{$key}->{plant_names}) {
 260             foreach my $plant_name (@{$design{$key}->{plant_names}}) {
 261                 $design_result_html .= "<tr><td>".$plant_name."</td><td>".$plot_name."</td><td>".$stock_name."</td><td>".$check_name."</td><td>".$plot_number."</td><td>".$row_number."</td><td>".$col_number."</td><td>".$block_number."</td><td>".$block_row_number."</td><td>".$block_col_number."</td><td>".$rep_number."</td><td>".$seedlot_name."</td><td>".$num_seed_per_plot."</td></tr>";
 262             }
 263         } else {
 264             $design_result_html .= "<tr><td>".$plot_name."</td><td>".$stock_name."</td><td>".$check_name."</td><td>".$plot_number."</td><td>".$row_number."</td><td>".$col_number."</td><td>".$block_number."</td><td>".$block_row_number."</td><td>".$block_col_number."</td><td>".$rep_number."</td><td>".$seedlot_name."</td><td>".$num_seed_per_plot."</td></tr>";
 265         }
 266     }
 267
 268     $design_result_html .= "</table>";
 269     return  "$design_result_html";
 270 }
 271
 272 sub design_info_view {
 273     my $design_ref = shift;
 274     my $design_info_ref = shift;
 275     my $trial_stock_type = shift;
 276     my %design = %{$design_ref};
 277     my %design_info = %{$design_info_ref};
 278     my %block_hash;
 279     my %rep_hash;
 280     my $design_info_html;
 281     my $design_description;
 282
 283
 284     $design_info_html .= "<dl>";
 285
 286     if ($design_info{'design_type'}) {
 287         $design_description = $design_info{'design_type'};
 288         if ($design_info{'design_type'} eq "CRD") {
 289             $design_description = "Completely Randomized Design";
 290         }
 291         if ($design_info{'design_type'} eq "RCBD") {
 292             $design_description = "Randomized Complete Block Design";
 293         }
 294         if ($design_info{'design_type'} eq "Alpha") {
 295             $design_description = "Alpha Lattice Incomplete Block Design";
 296         }
 297         if ($design_info{'design_type'} eq "Augmented") {
 298             $design_description = "Augmented Incomplete Block Design";
 299         }
 300         if ($design_info{'design_type'} eq "MAD") {
 301             $design_description = "Modified Augmented Design";
 302         }
 303         if ($design_info{'design_type'} eq "greenhouse") {
 304             $design_description = "Greenhouse Design";
 305         }
 306 #    if ($design_info{'design_type'} eq "MADII") {
 307 #      $design_description = "Modified Augmented Design II";
 308 #    }
 309 #    if ($design_info{'design_type'} eq "MADIII") {
 310 #      $design_description = "Modified Augmented Design III";
 311 #    }
 312 #    if ($design_info{'design_type'} eq "MADIV") {
 313 #      $design_description = "Modified Augmented Design IV";
 314 #    }
 315         $design_info_html .= "<dt>Design type</dt><dd>".$design_description."</dd>";
 316     }
 317     if ($design_info{'number_of_locations'}) {
 318         $design_info_html .= "<dt>Number of locations</dt><dd>".$design_info{'number_of_locations'}."</dd>";
 319     }
 320     if ($design_info{'number_of_stocks'}) {
 321         if ($trial_stock_type eq 'family_name') {
 322             $design_info_html .= "<dt>Number of family names</dt><dd>".$design_info{'number_of_stocks'}."</dd>";
 323         } elsif ($trial_stock_type eq 'cross') {
 324             $design_info_html .= "<dt>Number of cross unique ids</dt><dd>".$design_info{'number_of_stocks'}."</dd>";
 325         } else {
 326             $design_info_html .= "<dt>Number of accessions</dt><dd>".$design_info{'number_of_stocks'}."</dd>";
 327         }
 328     }
 329     if ($design_info{'number_of_checks'}) {
 330         $design_info_html .= "<dt>Number of checks</dt><dd>".$design_info{'number_of_checks'}."</dd>";
 331     }
 332     if ($design_info{'number_of_controls'}) {
 333         $design_info_html .= "<dt>Number of controls</dt><dd>".$design_info{'number_of_controls'}."</dd>";
 334     }
 335
 336     my $treatment_info_string = "";
 337     foreach my $key (sort { $a <=> $b} keys %design) {
 338         my $current_block_number = $design{$key}->{block_number};
 339         my $current_rep_number;
 340         if ($current_block_number) {
 341             if ($block_hash{$current_block_number}) {
 342                 $block_hash{$current_block_number} += 1;
 343             } else {
 344                 $block_hash{$current_block_number} = 1;
 345             }
 346         }
 347         if ($design{$key}->{rep_number}) {
 348             $current_rep_number = $design{$key}->{rep_number};
 349             if ($rep_hash{$current_rep_number}) {
 350                 $rep_hash{$current_rep_number} += 1;
 351             } else {
 352                 $rep_hash{$current_rep_number} = 1;
 353             }
 354         }
 355
 356         if($key eq 'treatments'){
 357             while(my($k,$v) = each %{$design{$key}}){
 358                 my $treatment_units = join ',', @{$v};
 359                 $treatment_info_string .= "<b>$k:</b> $treatment_units<br/>";
 360             }
 361         }
 362     }
 363
 364     if (%block_hash) {
 365         $design_info_html .= "<dt>Number of blocks</dt><dd>".scalar(keys %block_hash)."</dd>";
 366         if ($trial_stock_type eq 'family_name') {
 367             $design_info_html .= "<dt>Number of family names per block</dt><dd>";
 368             foreach my $key (sort { $a <=> $b} keys %block_hash) {
 369                 $design_info_html .= "Block ".$key.": ".$block_hash{$key}." family names <br>";
 370             }
 371         } elsif ($trial_stock_type eq 'cross') {
 372             $design_info_html .= "<dt>Number of cross unique ids per block</dt><dd>";
 373             foreach my $key (sort { $a <=> $b} keys %block_hash) {
 374                 $design_info_html .= "Block ".$key.": ".$block_hash{$key}." cross unique ids <br>";
 375             }
 376         } else {
 377             $design_info_html .= "<dt>Number of accessions per block</dt><dd>";
 378             foreach my $key (sort { $a <=> $b} keys %block_hash) {
 379                 $design_info_html .= "Block ".$key.": ".$block_hash{$key}." accessions <br>";
 380             }
 381         }
 382         $design_info_html .= "</dt>";
 383     }
 384
 385
 386     if (%rep_hash) {
 387         $design_info_html .= "<dt>Number of reps</dt><dd>".scalar(keys %rep_hash)."</dd>";
 388     }
 389
 390     $design_info_html .= "<dt>Treatments:</dt><dd><div id='trial_design_confirm_treatments' >$treatment_info_string</div></dd>";
 391
 392     $design_info_html .= "</dl>";
 393
 394     return $design_info_html;
 395
 396 }
 397
 398
 399 ######
 400 1;
 401 ######