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
 196 sub design_layout_view {
 197     my $design_ref = shift;
 198     my $design_info_ref = shift;
 199     my $design_level = shift;
 200     my %design = %{$design_ref};
 201     my %design_info = %{$design_info_ref};
 202     my $design_result_html;
 203
 204     $design_result_html .= '<table class="table table-bordered table-hover">';
 205
 206     if ($design_level eq 'plants') {
 207         $design_result_html .= qq{<tr><th>Plant Name</th><th>Plot Name</th><th>Accession Name</th><th>Check Name</th><th>Plot Number</th><th>Row number</th><th>Col number</th><th>Block Number</th><th>Block Row Number</th><th>Block Col Number</th><th>Rep Number</th><th>Seedlot Name</th><th>Num Seeds Per Plot</th></tr>};
 208     } elsif ($design_level eq 'subplots') {
 209         $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>};
 210     } else {
 211         $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>};
 212     }
 213
 214     foreach my $key (sort { $a <=> $b} keys %design) {
 215         if ($key eq 'treatments'){
 216             next;
 217         }
 218         my $plot_name = $design{$key}->{plot_name} || '';
 219         my $stock_name = $design{$key}->{stock_name} || '';
 220         my $seedlot_name = $design{$key}->{seedlot_name} || '';
 221         my $num_seed_per_plot = $design{$key}->{num_seed_per_plot} || '';
 222         my $check_name = $design{$key}->{is_a_control} || '';
 223         my $row_number = $design{$key}->{row_number} || '';
 224         my $col_number = $design{$key}->{col_number} || '';
 225         my $block_number = $design{$key}->{block_number} || '';
 226         my $block_row_number = $design{$key}->{block_row_number} || '';
 227         my $block_col_number = $design{$key}->{block_col_number} || '';
 228         my $rep_number = $design{$key}->{rep_number} || '';
 229         my $plot_number = $key;
 230
 231         if ($design{$key}->{subplots_plant_names}) {
 232             foreach my $subplot_name (sort keys %{$design{$key}->{subplots_plant_names}}) {
 233                 my $plant_names = $design{$key}->{subplots_plant_names}->{$subplot_name};
 234                 foreach my $plant_name (@$plant_names){
 235                     $design_result_html .= "<tr><td>".$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>".$num_seed_per_plot."</td></tr>";
 236                 }
 237             }
 238         } elsif ($design{$key}->{plant_names}) {
 239             foreach my $plant_name (@{$design{$key}->{plant_names}}) {
 240                 $design_result_html .= "<tr><td>".$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>";
 241             }
 242         } else {
 243             $design_result_html .= "<tr><td>".$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>";
 244         }
 245     }
 246
 247     $design_result_html .= "</table>";
 248     return  "$design_result_html";
 249 }
 250
 251 sub design_info_view {
 252   my $design_ref = shift;
 253   my $design_info_ref = shift;
 254   my %design = %{$design_ref};
 255   my %design_info = %{$design_info_ref};
 256   my %block_hash;
 257   my %rep_hash;
 258   my $design_info_html;
 259   my $design_description;
 260
 261
 262   $design_info_html .= "<dl>";
 263
 264   if ($design_info{'design_type'}) {
 265     $design_description = $design_info{'design_type'};
 266     if ($design_info{'design_type'} eq "CRD") {
 267       $design_description = "Completely Randomized Design";
 268     }
 269     if ($design_info{'design_type'} eq "RCBD") {
 270       $design_description = "Randomized Complete Block Design";
 271     }
 272     if ($design_info{'design_type'} eq "Alpha") {
 273       $design_description = "Alpha Lattice Incomplete Block Design";
 274     }
 275     if ($design_info{'design_type'} eq "Augmented") {
 276       $design_description = "Augmented Incomplete Block Design";
 277     }
 278     if ($design_info{'design_type'} eq "MAD") {
 279       $design_description = "Modified Augmented Design";
 280     }
 281     if ($design_info{'design_type'} eq "greenhouse") {
 282       $design_description = "Greenhouse Design";
 283     }
 284 #    if ($design_info{'design_type'} eq "MADII") {
 285 #      $design_description = "Modified Augmented Design II";
 286 #    }
 287 #    if ($design_info{'design_type'} eq "MADIII") {
 288 #      $design_description = "Modified Augmented Design III";
 289 #    }
 290 #    if ($design_info{'design_type'} eq "MADIV") {
 291 #      $design_description = "Modified Augmented Design IV";
 292 #    }
 293     $design_info_html .= "<dt>Design type</dt><dd>".$design_description."</dd>";
 294   }
 295   if ($design_info{'number_of_locations'}) {
 296     $design_info_html .= "<dt>Number of locations</dt><dd>".$design_info{'number_of_locations'}."</dd>";
 297   }
 298   if ($design_info{'number_of_stocks'}) {
 299     $design_info_html .= "<dt>Number of accessions</dt><dd>".$design_info{'number_of_stocks'}."</dd>";
 300   }
 301   if ($design_info{'number_of_checks'}) {
 302     $design_info_html .= "<dt>Number of checks</dt><dd>".$design_info{'number_of_checks'}."</dd>";
 303   }
 304   if ($design_info{'number_of_controls'}) {
 305     $design_info_html .= "<dt>Number of controls</dt><dd>".$design_info{'number_of_controls'}."</dd>";
 306   }
 307
 308   my $treatment_info_string = "";
 309   foreach my $key (sort { $a <=> $b} keys %design) {
 310     my $current_block_number = $design{$key}->{block_number};
 311     my $current_rep_number;
 312     if ($current_block_number) {
 313         if ($block_hash{$current_block_number}) {
 314           $block_hash{$current_block_number} += 1;
 315         } else {
 316           $block_hash{$current_block_number} = 1;
 317         }
 318     }
 319     if ($design{$key}->{rep_number}) {
 320       $current_rep_number = $design{$key}->{rep_number};
 321       if ($rep_hash{$current_rep_number}) {
 322         $rep_hash{$current_rep_number} += 1;
 323       } else {
 324         $rep_hash{$current_rep_number} = 1;
 325       }
 326     }
 327
 328     if($key eq 'treatments'){
 329         while(my($k,$v) = each %{$design{$key}}){
 330             my $treatment_units = join ',', @{$v};
 331             $treatment_info_string .= "<b>$k:</b> $treatment_units<br/>";
 332         }
 333     }
 334   }
 335
 336   if (%block_hash) {
 337     $design_info_html .= "<dt>Number of blocks</dt><dd>".scalar(keys %block_hash)."</dd>";
 338     $design_info_html .= "<dt>Number of accessions per block</dt><dd>";
 339     foreach my $key (sort { $a <=> $b} keys %block_hash) {
 340       $design_info_html .= "Block ".$key.": ".$block_hash{$key}." accessions <br>";
 341     }
 342     $design_info_html .= "</dt>";
 343   }
 344
 345
 346   if (%rep_hash) {
 347     $design_info_html .= "<dt>Number of reps</dt><dd>".scalar(keys %rep_hash)."</dd>";
 348   }
 349
 350   $design_info_html .= "<dt>Treatments:</dt><dd><div id='trial_design_confirm_treatments' >$treatment_info_string</div></dd>";
 351
 352   $design_info_html .= "</dl>";
 353
 354   return $design_info_html;
 355
 356 }
 357
 358
 359 ######
 360 1;
 361 ######