js/source/legacy/solGS/combineTrials.js

   1 /**
   2 * trials search, selections to combine etc...
   3 * @author Isaak Y Tecle <iyt2@cornell.edu>
   4 *
   5 */
   6
   7 JSAN.use("Prototype");
   8 JSAN.use('jquery.blockUI');
   9
  10
  11 var solGS = solGS || function solGS () {};
  12
  13 solGS.combinedTrials = {
  14
  15      getPopIds: function () {
  16                 var searchedPopsList = jQuery("#searched_trials_table tr").length;
  17          var tableId;
  18
  19          if (searchedPopsList) {
  20              tableId = 'searched_trials_table';
  21          } else {
  22              tableId = 'all_trials_table';
  23          }
  24
  25
  26          jQuery("#trial_search_result_select").show();
  27
  28
  29          jQuery('#' +tableId + ' tr')
  30              .filter(':has(:checkbox:checked)')
  31              .bind('click',  function() {
  32
  33                  jQuery("#select_trials_btn").val('Done selecting');
  34                  var td =  jQuery(this).html();
  35
  36                  var selectedTrial = '<tr>' + td + '</tr>';
  37
  38                  jQuery("#selected_trials_table tr:last").after(selectedTrial);
  39
  40                  jQuery("#selected_trials_table tr").each( function() {
  41                      jQuery(this).find("input[type=checkbox]")
  42                          .attr('onclick', 'solGS.combinedTrials.removeSelectedTrial()')
  43                          .prop('checked', true);
  44                  });
  45              });
  46
  47          jQuery("#selected_trials").show();
  48          jQuery("#combine_trials_div").show();
  49          jQuery("#search_again_div").hide();
  50
  51      },
  52
  53
  54     hideTrialsList: function() {
  55         jQuery("#trial_search_result").empty();
  56         // jQuery("#trial_search_result").empty();
  57         jQuery("#trial_search_result_select").hide();
  58         jQuery("#trial_search_result_message").hide();
  59
  60     },
  61
  62
  63     removeSelectedTrial: function() {
  64
  65         jQuery("#selected_trials_table tr").on("change", function() {
  66
  67         jQuery(this).remove();
  68
  69         if (jQuery("#selected_trials_table td").length == 0) {
  70                 jQuery("#selected_trials").hide();
  71                 jQuery("#combine_trials_div").hide();
  72                 jQuery("#search_again_div").hide();
  73                 jQuery("#select_trials_btn").val('Select');
  74
  75                 //  searchAgain();
  76         }
  77         });
  78
  79     },
  80
  81
  82     searchAgain: function () {
  83
  84         var url = window.location.pathname;
  85
  86         if (url.match(/solgs\/search\/trials\/trait\//) != null) {
  87             var traitId = jQuery("input[name='trait_id']").val();
  88             url = '/solgs/search/result/populations/' + traitId;
  89         } else {
  90             url = '/solgs/search/trials/';
  91         }
  92
  93         // jQuery('#trial_search_result').empty();
  94         jQuery("#trial_search_result").empty();
  95         searchAllTrials(url);
  96         jQuery("#trial_search_result_message").show();
  97         jQuery("#trial_search_result_select").show();
  98         jQuery("#select_trials_btn").val('Select');
  99
 100     },
 101
 102
 103     combineTraitTrials: function () {
 104         var trId = this.getTraitId();
 105         var protocolId = jQuery('#genotyping_protocol_id').val();
 106
 107         var trialIds = this.getSelectedTrials();
 108
 109         var action = "/solgs/combine/trials/trait/" + trId + '/gp/' + protocolId;
 110         var selectedPops = trId + "=" + trialIds + '&' + 'combine=combine';
 111
 112         jQuery.blockUI.defaults.applyPlatformOpacityRules = false;
 113         jQuery.blockUI({message: 'Please wait..'});
 114
 115         jQuery.ajax({
 116             type: 'POST',
 117             dataType: "json",
 118             url: action,
 119             data: selectedPops,
 120             success: function(res) {
 121
 122                 if (res.status) {
 123
 124             var comboPopsId = res.combo_pops_id;
 125             var newUrl = '/solgs/model/combined/trials/' + comboPopsId + '/trait/' + trId  + '/gp/' + protocolId;;
 126
 127                     if (comboPopsId) {
 128                         window.location.href = newUrl;
 129                         jQuery.unblockUI();
 130                     } else if (res.pop_id) {
 131                         var args = {'pop_id': res.pop_id,
 132                                     'trait_id': trId,
 133                                     'genotyping_protocol_id': res.genotyping_protocol_id
 134                                    };
 135
 136                         this.goToSingleTrialTrainingPopPage(args);
 137                         jQuery.unblockUI();
 138                     }
 139
 140                 } else {
 141
 142                     if (res.not_matching_pops){
 143                         alert('populations ' + res.not_matching_pops +
 144                               ' were genotyped using different marker sets. ' +
 145                               'Please make new selections to combine.' );
 146                         window.location.href =  '/solgs/search/result/populations/' + trId;
 147                     }
 148
 149                     if (res.redirect_url) {
 150                         window.location.href = res.redirect_url;
 151                     }
 152                 }
 153             }
 154         });
 155
 156     },
 157
 158
 159     getCombinedPopsId: function (comboPopsList) {
 160
 161         if (!comboPopsList) {
 162             comboPopsList = this.getSelectedTrials();
 163         }
 164
 165         comboPopsList = comboPopsList.unique();
 166
 167         var protocolId = jQuery('#genotyping_protocol_id').val();
 168         var traitId = this.getTraitId();
 169         var referer = window.location.href;
 170
 171         var page;
 172
 173         var args = {
 174             'trials': comboPopsList,
 175             'genotyping_protocol_id': protocolId
 176         };
 177
 178         if (comboPopsList.length > 1) {
 179             jQuery.ajax({
 180                 type: 'POST',
 181                 dataType: "json",
 182                 url: "/solgs/get/combined/populations/id",
 183                 data: args,
 184                 success: function(res) {
 185                     if (res.status) {
 186                         var comboPopsId = res.combo_pops_id;
 187
 188                         if (window.Prototype) {
 189                             delete Array.prototype.toJSON;
 190                         }
 191
 192                         var args = {
 193                             'combo_pops_id'   : [ comboPopsId ],
 194                             'combo_pops_list' : comboPopsList,
 195                             'trait_id'        : traitId,
 196                             'genotyping_protocol_id': res.genotyping_protocol_id
 197                         };
 198
 199                         solGS.combinedTrials.downloadCombinedTrialsTrainingPopData(args);
 200                     }
 201
 202                 },
 203                 error: function(res) {
 204                     alert('Error occured getting combined trials unique id');
 205                 }
 206
 207             });
 208
 209         } else {
 210             var popId = comboPopsList;
 211             var args = {
 212                 'trial_id': popId,
 213                 'trait_id': traitId,
 214                 'genotyping_protocol_id': protocolId
 215             };
 216
 217             this.downloadSingleTrialTrainingPopData(args);
 218         }
 219
 220     },
 221
 222
 223     downloadCombinedTrialsTrainingPopData: function (args) {
 224
 225         if (window.Prototype) {
 226             delete Array.prototype.toJSON;
 227         }
 228
 229         args['analysis_type'] = 'combine_populations';
 230         args['data_set_type'] = 'multiple_populations';
 231
 232         var comboPopsId = args.combo_pops_id;
 233         comboPopsId = comboPopsId[0];
 234         var protocolId = args.genotyping_protocol_id;
 235
 236         var referer = window.location.href;
 237         var page;
 238
 239         if (referer.match(/search\/trials\/trait\//)) {
 240             var traitId = args.trait_id;
 241
 242             page = '/solgs/model/combined/trials/' + comboPopsId
 243                 + '/trait/' + traitId
 244                 + '/gp/' + protocolId;
 245
 246         } else {
 247             page = '/solgs/populations/combined/' + comboPopsId + '/gp/' + protocolId;
 248         }
 249
 250         solGS.waitPage(page, args);
 251
 252     },
 253
 254
 255     displayCombinedTrialsTrainingPopPage: function(args) {
 256
 257         var trialsIds = args.combo_pops_list;
 258         var protocolId = args.genotyping_protocol_id;
 259
 260         if (!trialsIds) {
 261             trialsIds = this.getSelectedTrials();
 262         }
 263
 264         var action = "/solgs/retrieve/populations/data";
 265
 266         jQuery.blockUI.defaults.applyPlatformOpacityRules = false;
 267         jQuery.blockUI({message: 'Please wait..'});
 268
 269         jQuery.ajax({
 270             type: 'POST',
 271             dataType: "json",
 272             url: action,
 273             data: {'trials': trialsIds, 'genotyping_protocol_id': protocolId},
 274             success: function(res) {
 275                 if (res.not_matching_pops == null) {
 276
 277                     var combinedPopsId = res.combined_pops_id;
 278                     var protocolId     = res.genotyping_protocol_id;
 279
 280                     if (combinedPopsId) {
 281                         solGS.combinedTrials.goToCombinedTrialsTrainingPopPage(combinedPopsId, protocolId);
 282                         jQuery.unblockUI();
 283                     } else if (res.pop_id) {
 284
 285                         var args = {
 286                             'pop_id': res.pop_id,
 287                             'trait_id': trId,
 288                             'genotyping_protocol_id': res.genotyping_protocol_id
 289                         };
 290
 291                         solGS.combinedTrials.goToSingleTrialTrainingPopPage(args);
 292                         jQuery.unblockUI();
 293                     }
 294
 295                 } else if(res.not_matching_pops )  {
 296
 297                     jQuery.unblockUI();
 298                     alert('populations ' + res.not_matching_pops +
 299                           ' were genotyped using different marker sets. ' +
 300                           'Please make new selections to combine.' );
 301
 302                 }
 303             },
 304             error: function(res) {
 305                 jQuery.unblockUI();
 306                 alert('An error occured retrieving phenotype' +
 307                       'and genotype data for trials..');
 308             }
 309         });
 310
 311     },
 312
 313
 314     getSelectedTrials: function () {
 315
 316         var trialIds = [];
 317
 318         if (jQuery("#selected_trials_table").length) {
 319             jQuery("#selected_trials_table tr")
 320                 .each(function () {
 321
 322                     var trialId = jQuery(this)
 323                         .find("input[type=checkbox]")
 324                         .val();
 325
 326                 if (trialId) {
 327                     trialIds.push(trialId);
 328                 }
 329             });
 330         }
 331
 332         return trialIds.sort();
 333
 334     },
 335
 336
 337     goToCombinedTrialsTrainingPopPage: function (comboPopsId, protocolId) {
 338
 339         var page = '/solgs/populations/combined/' + comboPopsId + '/gp/' + protocolId;
 340
 341         if (comboPopsId) {
 342             window.location = page;
 343         } else {
 344             alert('combined Trials id missing.')
 345         }
 346     },
 347
 348
 349     goToSingleTrialTrainingPopPage: function (args) {
 350
 351         var referer = window.location.href;
 352         var page;
 353         var protocolId = args.genotyping_protocol_id;
 354
 355         if (referer.match(/search\/trials\/trait\//)) {
 356             page = '/solgs/trait/' + args.trait_id + '/population/' + args.pop_id + '/gp/' + protocolId;
 357
 358         } else {
 359
 360             //var hostName = window.location.protocol + '//' + window.location.host;
 361             page = '/solgs/population/' + args.pop_id + '/gp/' + protocolId ;
 362         }
 363
 364         window.location = page;
 365
 366     },
 367
 368
 369     downloadSingleTrialTrainingPopData: function (args) {
 370
 371         var referer = window.location.href;
 372         var page;
 373         var popId = args.trial_id;
 374         var traitId = args.trait_id;
 375         var protocolId = args.genotyping_protocol_id;
 376
 377         if (referer.match(/search\/trials\/trait\//)) {
 378             page = '/solgs/trait/' + traitId + '/population/' + popId + '/gp/' + protocolId;
 379
 380         } else {
 381             //var hostName = window.location.protocol + '//' + window.location.host;
 382             page = '/solgs/population/' + popId + '/gp/' + protocolId;
 383         }
 384
 385         var pageArgs = {
 386             'population_id'   : [ popId],
 387             'analysis_type'   : 'training_dataset',
 388             'data_set_type'   : 'single_population',
 389             'trait_id'        :  traitId,
 390             'genotyping_protocol_id': args.genotyping_protocol_id,
 391         };
 392
 393         solGS.waitPage(page, pageArgs);
 394
 395     },
 396
 397
 398     getTraitId: function() {
 399
 400         var id = jQuery("input[name='trait_id']").val();
 401
 402         return id;
 403     }
 404
 405 /////
 406 }
 407 /////
 408
 409
 410 Array.prototype.unique =
 411     function() {
 412     var a = [];
 413     var l = this.length;
 414     for(var i=0; i<l; i++) {
 415       for(var j=i+1; j<l; j++) {
 416         // If this[i] is fo3und later in the array
 417         if (this[i] === this[j])
 418           j = ++i;
 419       }
 420       a.push(this[i]);
 421     }
 422     return a;
 423     };
 424
 425
 426 jQuery(document).ready(function() {
 427     jQuery('#select_trials_btn').on('click', function() {
 428         solGS.combinedTrials.hideTrialsList();
 429     });
 430
 431 });
 432
 433
 434 jQuery(document).ready(function() {
 435     jQuery('#combine_trait_trials').on('click', function() {
 436         //combineTraitTrials();
 437         solGS.combinedTrials.getCombinedPopsId();
 438     });
 439
 440 });
 441
 442
 443 jQuery(document).ready(function() {
 444     jQuery('#combine_trials').on('click', function() {
 445
 446         solGS.combinedTrials.getCombinedPopsId();
 447     });
 448
 449 });
 450
 451 // jQuery(document).ready(function() {
 452 //     jQuery('#search_again').on('click', function() {
 453 //      searchAgain();
 454 //     });
 455
 456 // });
 457
 458 jQuery(document).ready(function() {
 459
 460 var tableId = "#searched_trials_table";
 461 var table = document.querySelector(tableId);
 462
 463 if (table) {
 464   var rowsCount = table.rows.length;
 465
 466   if (rowsCount > 1) {
 467         jQuery("#trial_search_result_select").show();
 468   }
 469 }
 470
 471 });