mason/breeders_toolbox/download.mas

   1 <%args>
   2 $seedlot_maintenance_enabled => 0
   3 </%args>
   4
   5 <& /util/import_javascript.mas, classes => [ 'jqueryui', 'jquery.cookie', 'CXGN.BreederSearch', 'CXGN.List', 'CXGN.BreedersToolbox.HTMLSelect', 'spin_min', 'ladda_min' ] &>
   6
   7 <& /page/page_title.mas, title=>"Download Using Lists" &>
   8
   9 <div class="container-fluid">
  10
  11 <div class="well">
  12 Choose a list for each parameter and click "Download".
  13 </div>
  14
  15 <div class="well well-sm">
  16 <h4>Download Phenotypes Using Lists</h4><p>Select Parameters:</p>
  17 <form id="download_form" action="/breeders/download_action" method="POST" >
  18 <table class="table table-bordered" >
  19   <thead>
  20   <tr>
  21     <th>
  22       Accessions
  23     </th>
  24     <th>
  25       Trials
  26     </th>
  27     <th>
  28       Traits
  29     </th>
  30     <th>
  31         Options
  32     </th>
  33     <th>
  34       Action
  35     </th>
  36   </tr>
  37   </thead>
  38   <tbody>
  39   <tr>
  40     <td>
  41       <div id="accession_list">
  42       </div>
  43     </td>
  44     <td>
  45       <div id="trial_list">
  46       </div>
  47     </td>
  48     <td>
  49       <div id="trait_list">
  50       </div>
  51    </td>
  52     <td>
  53     <b>Format:</b><br/>
  54     <select class="form-control" id="format" name="format">
  55         <option value=".csv">CSV</option>
  56         <option value=".xlsx">XLSX</option>
  57         <option value="html">HTML</option>
  58     </select>
  59     <br/>
  60     <b>Data Level:</b><br/>
  61     <select class="form-control" id="phenotype_datalevel" name="phenotype_datalevel">
  62         <option value="all">All</option>
  63         <option value="plot">Plot</option>
  64         <option value="plant">Plant</option>
  65     </select>
  66     <br/>
  67     <b>Timestamp:</b><br/>
  68     <select class="form-control" id="timestamp" name="timestamp">
  69         <option value="0">No</option>
  70         <option value="1">Yes</option>
  71     </select>
  72     <br/>
  73     <b>Exclude Phenotype Outliers:</b><br/>
  74     <select class="form-control" id="exclude_phenotype_outlier" name="exclude_phenotype_outlier">
  75         <option value="0">No</option>
  76         <option value="1">Yes</option>
  77     </select>
  78     </td>
  79     <td>
  80       <button class="btn btn-primary" type="button" id="phenotype">Download</button>
  81       <input type="hidden" id="phenotype_download_token" name="phenotype_download_token"/>
  82     </td>
  83   </tr>
  84   </tbody>
  85   </table>
  86 </form>
  87 </div>
  88
  89 <div class="well well-sm">
  90 <h4>Inspect Datasets</h4>
  91 <table class="table table-bordered" >
  92   <thead>
  93   <tr>
  94     <th>
  95       Datasets
  96     </th>
  97   </tr>
  98   </thead>
  99   <tbody>
 100   <tr>
 101     <td>
 102       <div id="phenotype_download_dataset_list">
 103       </div>
 104     </td>
 105   </tr>
 106   </tbody>
 107   </table>
 108 </div>
 109
 110 <div class="well well-sm">
 111 <h4>Download Metadata</h4><p>Select Parameters:</p>
 112 <form id="download_metadata_form" action="/breeders/download_action" method="POST" >
 113 <table class="table table-bordered" >
 114   <thead>
 115   <tr>
 116     <th>
 117       Trials
 118     </th>
 119     <th>
 120         Options
 121     </th>
 122     <th>
 123       Action
 124     </th>
 125   </tr>
 126   </thead>
 127   <tbody>
 128   <tr>
 129     <td>
 130       <div id="trial_metadata_list">
 131       </div>
 132     </td>
 133     <td>
 134     <b>Format:</b><br/>
 135     <select class="form-control" id="metadata_format" name="metadata_format">
 136         <option value=".xlsx">XLSX</option>
 137         <option value=".csv">CSV</option>
 138         <option value="html">HTML</option>
 139     </select>
 140     <br/>
 141     <div id="datalevel" style="display:none">
 142       <select class="form-control" id="metadata_datalevel" name="metadata_datalevel">
 143           <option value="metadata">Metadata</option>
 144       </select>
 145     </div>
 146     </td>
 147     <td>
 148       <button class="btn btn-primary" type="button" id="metadata">Download</button>
 149       <input type="hidden" id="metadata_download_token" name="metadata_download_token"/>
 150     </td>
 151   </tr>
 152   </tbody>
 153   </table>
 154 </form>
 155 </div>
 156
 157 <script>
 158 $(document).ready(function() {
 159
 160     var lo = new CXGN.List();
 161
 162     $('#accession_list').html(lo.listSelect('accession_list', [ 'accessions' ], 'select', undefined, undefined));
 163     $('#trial_list').html(lo.listSelect('trial_list', [ 'trials' ], 'select', undefined, undefined ));
 164     $('#trait_list').html(lo.listSelect('trait_list', [ 'traits' ], 'select', undefined, undefined  ));
 165     $('#trial_metadata_list').html(lo.listSelect('trial_metadata_list', ['trials'], 'select', undefined, undefined));
 166
 167     get_select_box('datasets', 'phenotype_download_dataset_list');
 168
 169     $('#metadata').click(function() {
 170       var trial_list_id = $('#trial_metadata_list_list_select').val();
 171       var trial_validation = 1;
 172       if (trial_list_id) { trial_validation = lo.validate(trial_list_id, 'trials', true).then(
 173          function(r) {
 174             if (r.missing.length != 0) {
 175                alert("The following lists did not pass validation: "+r.missing.join(", ")+". Please correct the list(s) and try again");
 176             }
 177             else {
 178
 179
 180 //      var ladda = Ladda.create(this);
 181 //      ladda.start();
 182 //      var token = new Date().getTime(); //use the current timestamp as the token name and value
 183 //      manage_dl_with_cookie(token, ladda);
 184 //      jQuery('#metadata_download_token').val(token);
 185                jQuery('#download_metadata_form').submit();
 186             }
 187         });
 188       } });
 189
 190     $('#phenotype').click(function() {
 191
 192       var accession_list_id = $('#accession_list_list_select').val();
 193       var trial_list_id = $('#trial_list_list_select').val();
 194       var trait_list_id = $('#trait_list_list_select').val();
 195
 196       var lists = new Array();
 197       var types = new Array();
 198
 199       if (accession_list_id) {
 200          lists.push(accession_list_id);
 201          types.push('accessions');
 202          //alert("ACC LIST ID = "+accession_list_id);
 203       }
 204       if (trial_list_id) {
 205           lists.push(trial_list_id);
 206           types.push('trials');
 207       }
 208
 209       if (trait_list_id) {
 210           lists.push(trait_list_id);
 211           types.push('traits');
 212       }
 213
 214       jQuery('#working_modal').modal('show');
 215
 216       validateLists(lists, types).then(function(r) {
 217          console.log('validation results: '+JSON.stringify(r));
 218          var names_str = '';
 219          for (var n=0; n < r.invalid_lists.length; n++) {
 220             names_str += r.invalid_lists[n][1];
 221          }
 222          if(names_str.length > 0) {
 223             alert('Some lists ('+names_str+') are not valid, please check.');
 224             jQuery('#working_modal').modal('hide');
 225          }
 226          else {
 227             download_phenotypes(this);
 228             jQuery('#working_modal').modal('hide');
 229
 230          }},
 231
 232          function(e) { alert(e);     jQuery('#working_modal').modal('hide');
 233 }
 234          );
 235
 236       });
 237
 238
 239
 240
 241 //alert("The following lists did not pass validation: "+problem_lists.join(", ")+". Please correct the list(s) and try again");
 242 //       return;
 243 //
 244
 245
 246 });
 247
 248
 249 function download_phenotypes() {
 250     //alert("NOW DOWNLOADING!");
 251     //var ladda = Ladda.create(data);
 252      // ladda.start();
 253       var token = new Date().getTime(); //use the current timestamp as the token name and value
 254      // manage_dl_with_cookie(token, ladda);
 255       jQuery('#phenotype_download_token').val(token);
 256       jQuery('#download_form').submit();
 257
 258
 259 }
 260
 261 </script>
 262
 263
 264
 265 <!-- DOWNLOAD ACCESSION PROPERTIES -->
 266
 267 <div class="well well-sm">
 268   <form id="download_accession_properties" action="/breeders/download_accession_properties_action" method="POST">
 269     <table class="table"  cellpadding="10">
 270       <thead>
 271         <tr><td colspan="2"><h4>Download Accession Properties</h4><p>Select parameters:</p></tr>
 272         <tr>
 273           <th>Accessions</th>
 274           <th>Format</th>
 275           <th>Action</th>
 276         </tr>
 277       </thead>
 278       <tbody>
 279       <tr>
 280         <td>
 281           <div id="accession_list5"></div>
 282         </td>
 283         <td>
 284           <select class="form-control" id="accession_properties_format" name="file_format">
 285               <option value=".xlsx">XLSX</option>
 286               <option value=".csv">CSV</option>
 287           </select>
 288         </td>
 289         <td>
 290           <button class="btn btn-primary" type="button" id="accession_properties_download">Download</button>
 291           <input type="hidden" id="accession_properties_download_token" name="accession_properties_download_token"/>
 292         </td>
 293       </tr>
 294       </tbody>
 295   </table>
 296 </form>
 297 </div>
 298
 299
 300 <script>
 301 $(document).ready(function() {
 302
 303     var lo = new CXGN.List();
 304
 305     $('#accession_list5').html(lo.listSelect('accession_properties_accession_list', [ 'accessions' ], 'select', undefined, undefined));
 306
 307     $('#accession_properties_download').click(function() {
 308
 309         var accession_list_id = $('#accession_properties_accession_list_list_select').val();
 310         if (!accession_list_id) {
 311             alert("You need to select an accession list!");
 312             return;
 313         }
 314
 315
 316         if (accession_list_id) {
 317               jQuery('#working_modal').modal('show');
 318               lo.validate(accession_list_id, 'accessions', true).then(
 319               function(r) {
 320                  if (r.valid != 1) {
 321                     alert("The accession list did not pass validation. Please correct the list and try again");
 322                     jQuery('#working_modal').modal('hide');
 323                  }
 324                  else {
 325                     //var ladda = Ladda.create(this);
 326                     //ladda.start();
 327                     //var token = new Date().getTime(); //use the current timestamp as the token name and value
 328                     //manage_dl_with_cookie(token, ladda);
 329                     //jQuery('#accession_properties_download_token').val(token);
 330                     jQuery('#download_accession_properties').submit();
 331                     jQuery('#working_modal').modal('hide');
 332                 }
 333             });
 334         }
 335     });
 336
 337 });
 338 </script>
 339
 340 <!-- END OF DOWNLOAD ACCESSION PROPERTIES -->
 341
 342
 343
 344
 345
 346 <!-- start of code for pedigree download -->
 347
 348 <div class="well well-sm">
 349 <form id="download_pedigree" action="/breeders/download_pedigree_action" method="POST">
 350 <table class="table"  cellpadding="10">
 351   <thead>
 352   <tr><td colspan="2"><h4>Download Pedigrees </h4><p>Select parameter:</p></tr>
 353   <tr>
 354     <th>
 355       Accessions
 356     </th>
 357     <th>
 358       Query
 359     </th>
 360     <th>
 361       Format
 362     </th>
 363     <th>
 364       Action
 365     </th>
 366   </tr>
 367   </thead>
 368   <tbody>
 369   <tr>
 370     <td>
 371       <div id="accession_list4">
 372       </div>
 373     </td>
 374     <td>
 375       <div style="width: 175px">
 376         <p><strong>Depth:</strong></p>
 377         <div class="radio">
 378           <label><input type="radio" id="ped_format_parents" name="ped_format" value="parents_only" checked>Only One Generation</label>
 379         </div>
 380         <div class="radio">
 381           <label><input type="radio" id="ped_format_full" name="ped_format" value="full">All Generations</label>
 382         </div>
 383         <p><strong>Include:</strong></p>
 384         <div class="radio">
 385           <label><input type="radio" id="include_ancestors" name="ped_include" value="ancestors" checked>Only Ancestors</label>
 386         </div>
 387         <div class="radio">
 388           <label><input type="radio" id="include_ancestors_descendants" name="ped_include" value="ancestors_descendants">Ancestors and Descendants</label>
 389         </div>
 390       </div>
 391     </td>
 392     <td>
 393       <select class="form-control" id="pedigree_file_format" name="file_format">
 394         <option value=".txt">Plain Text</option>
 395         <option value=".helium">Helium Format</option>
 396       </select>
 397     </td>
 398     <td>
 399       <button class="btn btn-primary" type="button" id="pedigree">Download</button>
 400       <input type="hidden" id="pedigree_download_token" name="pedigree_download_token"/>
 401     </td>
 402   </tr>
 403   </tbody>
 404   </table>
 405 </form>
 406 </div>
 407
 408
 409 <script>
 410 $(document).ready(function() {
 411
 412     var lo = new CXGN.List();
 413
 414     $('#accession_list4').html(lo.listSelect('pedigree_accession_list', [ 'accessions' ], 'select', undefined, undefined));
 415
 416     $('#pedigree').click(function() {
 417
 418         var accession_list_id = $('#pedigree_accession_list_list_select').val();
 419         if (!accession_list_id) {
 420             alert("You need to select an accession list!");
 421             return;
 422         }
 423
 424         if (accession_list_id) {
 425            accession_validation = lo.validate(accession_list_id, 'accessions', true).then(
 426              function(r) {
 427                  if(r.valid != 1) {
 428                    alert("The accession list did not pass validation. Please correct the list and try again");
 429                  }
 430                  else {
 431                     //var ladda = Ladda.create(this);
 432                     //ladda.start();
 433                     //var token = new Date().getTime(); //use the current timestamp as the token name and value
 434                     //manage_dl_with_cookie(token, ladda);
 435                     //jQuery('#pedigree_download_token').val(token);
 436                     jQuery('#working_modal').modal('show');
 437                     var http = new XMLHttpRequest();
 438                     http.open('POST', '/breeders/download_pedigree_action', true);
 439                     http.setRequestHeader('Content-type', 'application/x-www-form-urlencoded');
 440                     http.onreadystatechange = () => {
 441                       if( http.readyState == 4 ) {
 442                         jQuery('#working_modal').modal('hide');
 443                         if ( http.status == 200) {
 444                           var blob = new Blob([http.response], { type : 'plain/text' });
 445                           var fileName = http.getResponseHeader("FileName");
 446                           var link = document.createElement('a');
 447                           link.href = window.URL.createObjectURL(blob);
 448                           link.download = fileName;
 449                           link.click();
 450                         }
 451                       }
 452                     }
 453                     http.send(jQuery("#download_pedigree").serialize());
 454                  }
 455              });
 456         } });
 457 });
 458
 459 </script>
 460
 461 <!-- end of code for pedigree download -->
 462
 463
 464
 465 <!-- start of code for download seedlot matinenance events -->
 466
 467 % if ( $seedlot_maintenance_enabled ) {
 468
 469 <div class="well well-sm">
 470   <form id="download_seedlot_maintenance_events" action="/breeders/download_seedlot_maintenance_events_action" method="POST">
 471       <table class="table"  cellpadding="10">
 472         <thead>
 473           <tr><td colspan="2"><h4>Download Seedlot Maintenance Events</h4><p>Select parameters:</p></tr>
 474           <tr>
 475             <th>Seedlots</th>
 476             <th>Format</th>
 477             <th>Action</th>
 478           </tr>
 479         </thead>
 480         <tbody>
 481         <tr>
 482           <td>
 483             <div id="seedlot_list1"></div>
 484           </td>
 485           <td>
 486             <select class="form-control" id="seedlot_maintenance_events_format" name="file_format">
 487                 <option value=".xlsx">XLSX</option>
 488             </select>
 489           </td>
 490           <td>
 491             <button class="btn btn-primary" type="button" id="seedlot_maintenance_events_download">Download</button>
 492             <input type="hidden" id="seedlot_maintenance_events_download_token" name="seedlot_maintenance_events_download_token"/>
 493           </td>
 494         </tr>
 495         </tbody>
 496     </table>
 497   </form>
 498 </div>
 499
 500 <script>
 501 $(document).ready(function() {
 502
 503     var lo = new CXGN.List();
 504
 505     $('#seedlot_list1').html(lo.listSelect('seedlot_maintenance_events_list', [ 'seedlots' ], 'select', undefined, undefined));
 506
 507     $('#seedlot_maintenance_events_download').click(function() {
 508
 509         var seedlot_list_id = $('#seedlot_maintenance_events_list_list_select').val();
 510         if (!seedlot_list_id) {
 511             alert("You need to select a seedlot list!");
 512             return;
 513         }
 514
 515         var seedlot_validation = 1;
 516         if (seedlot_list_id) {
 517             seedlot_validation = lo.validate(seedlot_list_id, 'seedlots', true);
 518         }
 519
 520         if (seedlot_validation != 1) {
 521             alert("The seedlot list did not pass validation. Please correct the list and try again");
 522             return;
 523         }
 524
 525         var ladda = Ladda.create(this);
 526         ladda.start();
 527         var token = new Date().getTime(); //use the current timestamp as the token name and value
 528         manage_dl_with_cookie(token, ladda);
 529         jQuery('#seedlot_maintenance_events_download_token').val(token);
 530         jQuery('#download_seedlot_maintenance_events').submit();
 531
 532     });
 533 });
 534
 535 </script>
 536
 537 % }
 538
 539 <!-- end of code for seedlot maintenance event download -->
 540
 541
 542 <div class="well well-sm">
 543 <form id="download_gbs" action="/breeders/download_gbs_action" method="POST">
 544 <table class="table"  cellpadding="10">
 545   <thead>
 546   <tr><td colspan="2"><h4>Download Genotypes </h4><p>Select parameter:</p></tr>
 547   <tr>
 548     <th>
 549       Accessions
 550     </th>
 551     <th>
 552       Genotyping Protocol
 553     </th>
 554     <th>
 555       Action
 556     </th>
 557   </tr>
 558   </thead>
 559   <tbody>
 560   <tr>
 561     <td>
 562       <div id="accession_list2">
 563       </div>
 564     </td>
 565     <td>
 566       <div id="protocol_list">
 567       </div>
 568     </td>
 569     <td>
 570       <button class="btn btn-primary" type="button" id="genotype">Download</button>
 571       <input type="hidden" id="gbs_download_token" name="gbs_download_token"/>
 572     </td>
 573   </tr>
 574   </tbody>
 575   </table>
 576 </form>
 577 </div>
 578
 579 <script>
 580   $(document).ready(function() {
 581
 582       var lo = new CXGN.List();
 583
 584       $('#accession_list2').html(lo.listSelect('genotype_accession_list', [ 'accessions' ], 'select', undefined, undefined));
 585       get_select_box("genotyping_protocol", "protocol_list");
 586
 587       $('#genotype').click(function() {
 588
 589       var accession_list_id = $('#genotype_accession_list_list_select').val();
 590       var protocol_list_id = $('#protocol_list').val();
 591
 592       var accession_validation = 1;
 593       if (accession_list_id) {
 594   accession_validation = lo.validate(accession_list_id, 'accessions', true).then(
 595      function(r) {
 596          if (!( accession_list_id || protocol_list_id) ) {
 597              alert("You need to select a list of accessions and a protocol !");
 598          }
 599          else if(r.valid != 1)  {
 600              alert("The accession list could not be validated. Please correct the list(s) and try again");
 601          }
 602   else  {
 603
 604
 605       //var ladda = Ladda.create(this);
 606       //ladda.start();
 607       //var token = new Date().getTime(); //use the current timestamp as the token name and value
 608       //manage_dl_with_cookie(token, ladda);
 609       //jQuery('#gbs_download_token').val(token);
 610       jQuery('#download_gbs').submit();
 611    }
 612   }, function(e) { alert('An error occurred.'); });
 613   }
 614
 615   });
 616   });
 617 </script>
 618
 619 <div class="well well-sm">
 620 <form id="gbs_qc" action="/breeders/gbs_qc_action" method="POST">
 621 <table class="table" cellpadding="10">
 622   <thead>
 623   <tr><td colspan="3"><h4>Genotyping QC</h4><p>Select parameter:</p></tr>
 624   <tr>
 625     <th>
 626       Trials
 627     </th>
 628     <th>
 629       Accessions
 630     </th>
 631     <th>
 632       Genotyping Protocol
 633     </th>
 634     <th>
 635       Action
 636     </th>
 637   </tr>
 638   </thead>
 639   <tbody>
 640   <tr>
 641     <td>
 642       <div id="trial_list3">
 643       </div>
 644     </td>
 645     <td>
 646       <div id="accession_list3">
 647       </div>
 648     </td>
 649     <td>
 650       <div id="protocol_list2">
 651       </div>
 652     </td>
 653     <td>
 654       <button class="btn btn-primary" type="button" id="genotype_qc">Download</button>
 655       <input type="hidden" id="qc_download_token" name="qc_download_token"/>
 656     </td>
 657   </tr>
 658   </tbody>
 659   </table>
 660 </form>
 661 </div>
 662
 663 </div>
 664
 665 <script>
 666   $(document).ready(function() {
 667
 668       var lo = new CXGN.List();
 669
 670       $('#accession_list3').html(lo.listSelect('genotype_qc_accession_list', [ 'accessions' ], 'select', undefined, undefined));
 671       $('#trial_list3').html(lo.listSelect('genotype_trial_list', [ 'trials' ], 'select', undefined, undefined ));
 672       get_select_box("genotyping_protocol", "protocol_list2", {'id':'protocol_list2_select', 'name':'protocol_list2_select'});
 673
 674       $('#genotype_qc').click(function() {
 675
 676         $('#working').dialog( {
 677                 height: 100,
 678                 width:  300,
 679                 modal: true,
 680                 autoOpen: false,
 681                 closeOnEscape: true,
 682                 draggable: true,
 683                 resizable: true,
 684                 open: function() { $(this).closest('.ui-dialog').find('.ui-dialog-titlebar-close').hide(); },
 685                 title: 'Downloading genotype...'
 686                 });
 687
 688       var lists = new Array();
 689
 690       var accession_list_id = $('#genotype_qc_accession_list_list_select').val();
 691       var trial_list_id = $('#genotype_trial_list_list_select').val();
 692
 693
 694       if (! (accession_list_id || trial_list_id) ) {
 695         alert("You need to select an accession or a trial, or both!");
 696         return;
 697       }
 698
 699       var lists = new Array();
 700       var types = new Array();
 701
 702   if (accession_list_id) {
 703   lists.push(accession_list_id);
 704   types.push('accessions');
 705   }
 706
 707   if(trial_list_id) {
 708   lists.push(trial_list_id);
 709   types.push('trials');
 710   }
 711
 712
 713       validateLists(lists, types).then(function(r) {
 714          console.log('validation results: '+JSON.stringify(r));
 715          var names_str = '';
 716          for (var n=0; n < r.invalid_lists.length; n++) {
 717             names_str += r.invalid_lists[n][1];
 718          }
 719          if(names_str.length > 0) {
 720             alert('Some lists ('+names_str+') are not valid, please check.');
 721             jQuery('#working_modal').modal('hide');
 722          }
 723          else {
 724            //      var ladda = Ladda.create(this);
 725 //         ladda.start();
 726 //         var token = new Date().getTime(); //use the current timestamp as the token name and value
 727 //          manage_dl_with_cookie(token, ladda);
 728 //          jQuery('#qc_download_token').val(token);
 729             jQuery('#gbs_qc').submit();
 730
 731             jQuery('#working_modal').modal('hide');
 732
 733         }
 734
 735       });
 736
 737
 738     });
 739
 740   });
 741 </script>