mason/breeders_toolbox/trial.mas

   1
   2 <%doc>
   3
   4 =head1 NAME
   5
   6 /breeders/trial.mas - a mason component to display a trial detail page
   7
   8 =head1 AUTHOR
   9
  10 Jeremy D. Edwards
  11
  12 =cut
  13
  14 </%doc>
  15
  16 <%args>
  17 $trial_id
  18 $breeding_program
  19 $trial_name
  20 $location_data => undef
  21 $year => undef
  22 $trial_type => undef
  23 $planting_date => undef
  24 $harvest_date => undef
  25 $trial_description => undef
  26 $design_layout_view => undef
  27 $user_can_modify => undef
  28 $hidap_enabled => undef
  29 $folder_name => undef
  30 $folder_id => undef
  31 </%args>
  32
  33 <& /util/import_javascript.mas, classes => [ 'jquery.iframe-post-form', 'CXGN.Trial' , 'jstree/dist/jstree', 'CXGN.BreedersToolbox.HTMLSelect' ] &>
  34
  35 <%perl>
  36   use Data::Dumper;
  37 my $start_time = time();
  38 my $description_empty = 1;
  39 if ($trial_description) {
  40   if ($trial_description ne "") {
  41     $description_empty = 0;
  42   }
  43 }
  44
  45 my $design_subtitle = '[<a href="\\fieldbook\\trial_download\\'.$trial_id.'">Download Field Book</a>]';
  46
  47 my $change_breeding_program_link = qq{[<a id="show_change_breeding_program_link">change</a>] } if $user_can_modify;
  48
  49 print STDERR "Check 7 (mason) : ".(time() - $start_time)."\n";
  50
  51 #print STDERR "BREEDING PROGRAM: ".Dumper($breeding_program);
  52
  53 </%perl>
  54
  55 <br/>
  56
  57 <& /page/page_title.mas, title=>"Trial detail for ".$trial_name &>
  58
  59 <&| /page/info_section.mas, title=>"Trial details",  collapsible => 1, &>
  60
  61
  62 <div class="panel panel-default">
  63 <table class="table table-hover" >
  64
  65 <tr>
  66 <td><b>Breeding Program </b></td>
  67 <td>
  68 <span id="breeding_programs">
  69 % if ($breeding_program) {
  70 % foreach (@$breeding_program) {
  71 %  print "$_->[1] ($_->[2]) <br/>";
  72 % }
  73 % } else {
  74 % print "No Breeding Program";
  75 % }
  76 </span>
  77 </td>
  78 <td>
  79  <% $change_breeding_program_link %>
  80 </td>
  81 </tr>
  82
  83 <tr>
  84 <td><b>Trial Name</b></td>
  85 <td>
  86 <div id="trial_name">
  87 % if ($trial_name) {
  88 %   print "$trial_name";
  89 % } else {
  90 %   print "[No Trial Name]";
  91 % }
  92 </div>
  93 </td>
  94 <td>
  95   [<a id="edit_trial_name">change</a>]
  96 </td>
  97 <& /breeders_toolbox/trial/edit_trial_name.mas, trial_id=>$trial_id, trial_name=>$trial_name, trial_type=>"Trial" &>
  98
  99 </tr>
 100
 101 <tr>
 102 <td><b>Trial Type</b></td>
 103 <td>
 104 <div id="trial_type">
 105 % if ($trial_type) {
 106 %  print "@$trial_type[1]<br/>";
 107 % } else {
 108 % print "[Type not set]";
 109 % }
 110 </div>
 111 </td>
 112 <td>
 113   [<a id="edit_trial_type" >change</a>]
 114 </td>
 115 </tr>
 116
 117 <tr>
 118 <td><b>Year</b></td>
 119 <td>
 120 <div id="trial_year">
 121 % if ($year) {
 122 %  print "$year";
 123 % } else {
 124 %  print "[No Year]";
 125 % }
 126 </div>
 127 </td>
 128 <td>
 129   [<a id="change_year_link">change</a>]
 130 </td>
 131 </tr>
 132
 133 <tr>
 134 <td><b>Trial Location</b></td>
 135 <td>
 136 <div id="trial_location">
 137 % if ($location_data) {
 138 %  print "$location_data->[1]";
 139 % } else {
 140 %  print "[No Location]";
 141 % }
 142 </div>
 143 </td>
 144 <td>
 145   [<a id="change_trial_location_link">change</a>]
 146 </td>
 147 </tr>
 148
 149 <tr>
 150 <td><b>Planting Date</b></td>
 151 <td>
 152 <div id="planting_date">
 153 % if ($planting_date) {
 154 %  print "$planting_date";
 155 % } else {
 156 %  print "[No Planting Date]";
 157 % }
 158 </div>
 159 </td>
 160 <td>
 161     [<a id="change_planting_date_link">change</a>]
 162 </td>
 163 </tr>
 164
 165 <tr>
 166 <td><b>Harvest Date</b></td>
 167 <td>
 168 <div id="harvest_date">
 169 % if ($harvest_date) {
 170 %  print "$harvest_date";
 171 % } else {
 172 %  print "[No Harvest Date]";
 173 % }
 174 </div>
 175 </td>
 176 <td>
 177     [<a id="change_harvest_date_link">change</a>]
 178 </td>
 179 </tr>
 180
 181 <tr><td><b>Description</b></td>
 182 <td>
 183 <div id="trial_description">
 184 % if ($trial_description) {
 185 %  print "$trial_description";
 186 % } else {
 187 %  print "[No Description]";
 188 % }
 189 </div>
 190 </td>
 191 <td>
 192   [<a id="edit_trial_description">edit</a>]
 193 </td>
 194 </tr>
 195 </table>
 196 </div>
 197
 198 </&>
 199
 200 <div id="edit_trial_description_dialog">
 201    Please enter the description for this trial:<br/>
 202    <textarea id="trial_description_input" cols="50" rows="10"></textarea>
 203 </div>
 204
 205 <div id="edit_trial_type_dialog">
 206   Please choose the type of this trial:<br />
 207   <select id="trial_type_select"></select>
 208 </div>
 209
 210 <div id="change_trial_location_dialog">
 211   Please choose the location fro this trial:<br />
 212   <div id="trial_location_select_div" /></div>
 213 </div>
 214
 215 <div id="change_planting_date_dialog">
 216   Please enter a planting date:<br />
 217   <input id="planting_date_picker"></input>
 218 </select>
 219
 220 </div>
 221
 222 <div id="change_harvest_date_dialog">
 223   Please enter a harvest date [MM/DD/YYYY]:<br />
 224   <input id="harvest_date_picker"></input>
 225 </div>
 226
 227 % my $folder_collapsed = 1;
 228 % if ($folder_id) {
 229 % $folder_collapsed = 0;
 230 % }
 231
 232 <&| /page/info_section.mas, title=>"Folder", collaspible=>1, collapsed=>$folder_collapsed,
 233   subtitle => '[<a id="new_folder_dialog_link">New Folder</a>] | [<a id="open_folder_dialog_link">Change</a>]' &>
 234
 235   <& /breeders_toolbox/folder/folder_set.mas, breeding_program_id => $breeding_program->[0]->[0], breeding_program_name =>$breeding_program->[0]->[1], trial_id => $trial_id, trial_name =>$trial_name &>
 236   <& /breeders_toolbox/folder/folder_new.mas, breeding_program_id => $breeding_program->[0]->[0], breeding_program_name =>$breeding_program->[0]->[1] &>
 237
 238   <span id="trial_folder_div"><a href="/folder/<% $folder_id %>"><% $folder_name %></a></span>
 239
 240 </&>
 241
 242
 243 % if ($hidap_enabled) {
 244
 245 <&| /page/info_section.mas, id => "hidap_trial", title=>"HIDAP Trial Analysis", collapsible=>1, collapsed => 0 &>
 246
 247 <div class="row">
 248   <div class="col-sm-4">
 249     <a href="http://hidap.sgn.cornell.edu/hd/?tabAnalysis=Map&fbaInput=<% $trial_id %>" target="_blank">
 250       <div class="well">
 251         <div class="row">
 252           <div class="col-sm-9">
 253             Phenotype Plot Map
 254           </div>
 255           <div class="col-sm-3">
 256             <span class="glyphicon glyphicon-th"></span>
 257           </div>
 258         </div>
 259       </div>
 260     </a>
 261   </div>
 262   <div class="col-sm-4">
 263     <a href="http://hidap.sgn.cornell.edu/hd/?tabAnalysis=Correlation&fbaInput=<% $trial_id %>" target="_blank">
 264       <div class="well">
 265         <div class="row">
 266           <div class="col-sm-9">
 267             Phenotype Correlation
 268           </div>
 269           <div class="col-sm-3">
 270             <span class="glyphicon glyphicon-stats"></span>
 271           </div>
 272         </div>
 273       </div>
 274     </a>
 275   </div>
 276   <div class="col-sm-4">
 277     <a href="http://hidap.sgn.cornell.edu/hd/?tabAnalysis=Report&fbaInput=<% $trial_id %>" target="_blank">
 278       <div class="well">
 279         <div class="row">
 280           <div class="col-sm-9">
 281             Analysis Report
 282           </div>
 283           <div class="col-sm-3">
 284             <span class="glyphicon glyphicon-book"></span>
 285           </div>
 286         </div>
 287       </div>
 288     </a>
 289   </div>
 290 </div>
 291
 292 </&>
 293
 294 % }
 295
 296
 297 <&| /page/info_section.mas, id => "physical_layout", title=>"Physical Trial Layout", collapsible=>1, collapsed => 1, subtitle=>'[<a id="upload_trial_coords_link">Upload trial coordinates</a>]' &>
 298
 299
 300   <& /breeders_toolbox/trial/trial_coords.mas, trial_id => $trial_id &>
 301
 302 </&>
 303
 304 <& /breeders_toolbox/trial/trial_coords_spreadsheet_upload_format_info.mas &>
 305
 306 <div id="upload_trial_coord_error_display" class="ui-widget">
 307   <table>
 308     <tbody></tbody>
 309   </table>
 310 </div>
 311
 312 <div id="trial_coord_upload_success_dialog_message" class="ui-widget">
 313   The trial coord upload finished.
 314 </div>
 315
 316 <div id="upload_trial_coord_dialog" title="Upload trial coordinates">
 317
 318   <&| /page/explanation.mas, title=>'Template information' &>
 319     <p>
 320       <b>File format information</b>
 321       <br>
 322       <a id="trial_coordinates_upload_spreadsheet_format_info">Spreadsheet format</a>
 323     </p>
 324   </&>
 325
 326   <form method="post" enctype="multipart/form-data" encoding="multipart/form-data" id="upload_trial_coordinates_form" name="upload_trial_coordinates_form">
 327
 328     <label for="trial_coordinates_uploaded_file" style="display: inline-block; width: 100px;">Upload trial coordinates file:</label>
 329     <input type="file" name="trial_coordinates_uploaded_file" id="trial_coordinates_uploaded_file" encoding="multipart/form-data" />
 330
 331     </form>
 332
 333 </div>
 334
 335 <!--<style>
 336   div.left {
 337     float: left;
 338     clear: both;
 339   }
 340 .ui-autocomplete {
 341   max-height: 100px;
 342   overflow-y: auto;
 343   /* prevent horizontal scrollbar */
 344   overflow-x: hidden;
 345 }
 346
 347 </style> -->
 348
 349
 350 <&| /page/info_section.mas, id => "trial_design_section", title=>"Design", collapsible=>1, collapsed=>0, subtitle=>"Download layout [<a id=\"download_layout_xls_link\" href=\"/breeders/trial/$trial_id/download/layout?format=xls\">xls</a>] [<a id=\"download_layout_csv_link\" href=\"/breeders/trial/$trial_id/download/layout?format=csv\">csv</a>]"  &>
 351
 352 <& /breeders_toolbox/trial/design.mas, trial_id => $trial_id &>
 353
 354 <&| /page/info_section.mas, id => "trial_accessions", title=>"Accessions", is_subsection => 1, collapsible=>1, collapsed=>1 &>
 355
 356 <& /breeders_toolbox/trial/trial_accessions.mas, trial_id => $trial_id &>
 357
 358 </&>
 359
 360 <&| /page/info_section.mas, id => "trial_controls", title=>"Controls",  is_subsection => 1, collapsible=>1, collapsed=>1 &>
 361
 362 <& /breeders_toolbox/trial/trial_controls.mas, trial_id => $trial_id &>
 363
 364 </&>
 365
 366 <&| /page/info_section.mas, id => "trial_plots", title=>"Plots",  is_subsection => 1, collapsible=>1, collapsed=>1 &>
 367
 368 <& /breeders_toolbox/trial/trial_plots.mas, trial_id => $trial_id &>
 369
 370 </&>
 371
 372 </&>
 373
 374 <br />
 375
 376 %# <&| /page/info_section.mas, title=>"Traits assayed", subtitle=>"Download trial data [<a id=\"download_phenotypes_xls_link\" href=\"/breeders/trial/$trial/download/phenotype?format=xls\">xls</a>] [<a id=\"download_phenotypes_csv_link\" href=\"/breeders/trial/$trial_id/download/phenotype?format=csv\">csv</a>] " &>
 377 %# foreach my $trait (@phenotype_data) {
 378 %# my $trait_id = $trait->[1];
 379 %# my $trait_name = ucfirst($trait->[0]);
 380 %# print "$trait_name" . ' [ ' . "<a href=\"/breeders_toolbox/trial/$trial_id/trait/$trait_id\">view statistics</a>" . ' ] ' . "<br />";
 381 %# }
 382
 383 %# </&>
 384
 385 <&| /page/info_section.mas, id=> "trial_detail_traits_assayed", title => "Traits assayed", collapsible=>1, collapsed=>1, hide_if_empty=>1, subtitle => "Download trial data [<a id=\"download_phenotypes_xls_link\" href=\"/breeders/trial/$trial_id/download/phenotype?format=xls\">xls</a>] [<a id=\"download_phenotypes_csv_link\" href=\"/breeders/trial/$trial_id/download/phenotype?format=csv\">csv</a>] " &>
 386
 387 <& /breeders_toolbox/trial/phenotype_summary.mas, trial_id => $trial_id &>
 388
 389 </&>
 390
 391
 392 <&| /page/info_section.mas,
 393    title       => 'Trial JBrowse',
 394    collapsible => 1,
 395 &>
 396
 397         <& /breeders_toolbox/trial_jbrowse_instance.mas, trial_id => $trial_id &>
 398
 399 </&>
 400
 401 <&| /page/info_section.mas, title=>"Files", collapsible=>1, collapsed=>0 &>
 402   <&| /page/info_section.mas, title=>"Data Collection Files", is_subsection => 1, collapsible=>1, collapsed=>0, &>
 403     <&| /page/info_section.mas, title=>"Phenotyping Spreadsheets", is_subsection => 1, collapsible=>1, collapsed=>0, subtitle=>'[<a id="create_spreadsheet_link">Create Spreadsheet</a>]' &>
 404     </&>
 405     <&| /page/info_section.mas, title=>"Android Field Book Layout", is_subsection => 1, collapsible=>1, collapsed=>0, subtitle=>'[<a id="create_fieldbook_link">Create Field Book</a>]' &>
 406     </&>
 407     <&| /page/info_section.mas, title=>"Data Collector Spreadsheet", is_subsection => 1, collapsible=>1, collapsed=>0, subtitle=> '[<a id="create_DataCollector_link">Create DataCollector Spreadsheet</a>]' &>
 408     </&>
 409   </&>
 410   <&| /page/info_section.mas, title=>"Uploaded Phenotyping Files", is_subsection => 1, collapsible=>1, collapsed=>0, &>
 411     <&| /page/info_section.mas, title=>"Phenotyping Spreadsheets", is_subsection => 1, collapsible=>1, collapsed=>0, subtitle=>'[<a id="upload_spreadsheet_phenotypes_link">Upload</a>]'&>
 412     </&>
 413     <&| /page/info_section.mas, title=>"Android Field Book Exported", is_subsection => 1, collapsible=>1, collapsed=>0, subtitle=>'[<a id="upload_fieldbook_phenotypes_link">Upload</a>]'&>
 414     </&>
 415     <&| /page/info_section.mas, title=>"Data Collector Spreadsheet", is_subsection => 1, collapsible=>1, collapsed=>0, subtitle=>'[<a id="upload_datacollector_phenotypes_link">Upload</a>]'&>
 416     </&>
 417   </&>
 418 </&>
 419
 420 <& /breeders_toolbox/upload_phenotype_spreadsheet.mas &>
 421 <& /fieldbook/upload_phenotype_fieldbook.mas &>
 422 <& /breeders_toolbox/upload_phenotype_datacollector.mas &>
 423
 424 % my $data_agreement_link = "Add/edit data agreement";
 425 % if ($user_can_modify) { $data_agreement_link = '[<a id="add_data_agreement">Add/edit data agreement</a>]'; }
 426 <&| /page/info_section.mas, title=>"Data Agreement", is_subsection => 0, collapsible=>1, collapsed=>0,  subtitle=> $data_agreement_link  &>
 427
 428 <& /breeders_toolbox/data_agreement.mas, trial_id => $trial_id &>
 429
 430 </&>
 431
 432 <&| /page/info_section.mas, title=>'Delete trial data', subtitle=>'<font color="red" role="">Deletion cannot be undone</font>', collapsed=>1, collapsible=>1 &>
 433   <& /breeders_toolbox/trial/trial_deletion.mas, trial_id => $trial_id  &>
 434
 435 </&>
 436
 437 % print STDERR "Check 9 (mason) : ".(time() - $start_time)."\n";
 438
 439 <!-- Phenotypic correlation analysis -->
 440 <& /solgs/population/correlation.mas,
 441    trial_id => $trial_id
 442 &>
 443
 444   <!-- Population structure analysis -- PCA -->
 445 <& /solgs/model/pca.mas,
 446    trial_id => $trial_id
 447  &>
 448
 449 % print STDERR "Check 10 (mason) : ".(time() - $start_time)."\n";
 450
 451 <div id="trialIDDiv" class="trialIDDivClass" style="display:none;">
 452 % print $trial_id;
 453 </div>
 454
 455 <div id="tablet_field_layout_saved_dialog_message" title="Field book layout file" style="display:none;">
 456   <p>
 457     <span class="ui-icon ui-icon-circle-check" style="float: left; margin: 0 7px 50px 0;"></span>
 458     The field book layout file was saved successfully
 459   </p>
 460   <p>
 461     <a id="tablet_layout_download_link">Download File</a>
 462   </p>
 463 </div>
 464
 465 <div id="create_spreadsheet_dialog" title="Create Phenotyping Spreadsheet" style="display:none;">
 466   <div id="trait_list" name="trait_list">
 467     <label id="trait_list_label" for="trait_list_list_select" style="display: inline-block; width: 200px;">List of traits:
 468     </label>
 469   </div>
 470 </div>
 471
 472 <div id="create_DataCollector_dialog" title="Create Data Collector Spreadsheet" style="display:none;">
 473   <div id="trait_list_dc" name="trait_list">
 474     <label id="trait_list_label_dc" for="trait_list_list_select" style="display: inline-block; width: 200px;">List of traits:
 475     </label>
 476   </div>
 477 </div>
 478
 479 <div id="data_collector_saved_dialog_message" title="Data collector spreadsheet" style="display:none;">
 480   <p>
 481     <span class="ui-icon ui-icon-circle-check" style="float: left; margin: 0 7px 50px 0;"></span>
 482     The data collector spreadsheet file was saved successfully
 483   </p>
 484   <p>
 485     <a id="data_collector_download_link">Download File</a>
 486   </p>
 487 </div>
 488
 489 <div id="change_breeding_program_dialog">
 490   Please select a breeding program for this trial:<br />
 491   <div id="change_breeding_program_select_div">
 492   </div>
 493 </div>
 494
 495 <div id="change_trial_year_dialog">
 496   Please select a year for this trial:<br />
 497   <div id="change_year_select_div">
 498   </div>
 499 </div>
 500
 501 <div id="trial_design_view_layout" title="Trial design layout">
 502 % print $design_layout_view;
 503 </div>
 504
 505
 506 <script defer="defer">
 507
 508 jQuery(document).ready(function () {
 509
 510   trial_detail_page_setup_dialogs();
 511
 512   jQuery('#delete_breeding_program_trial_association_link').click(
 513      function() {
 514         var trial_id = get_trial_id();
 515
 516         var yes = confirm("Do you really want to remove this trial from the breeding program?");
 517         if (yes) {
 518             jQuery.ajax( {
 519                 url: '/breeders/program/remove/<% $breeding_program->[0]->[0] %>/'+trial_id,
 520                 data: { },
 521                 async: false,
 522                 success: function(response) {
 523                 }
 524             });
 525         }
 526     });
 527
 528 });
 529
 530 </script>