js/source/entries/mixedmodels.js

   1
   2 import '../legacy/jquery.js';
   3 import '../legacy/d3/d3Min.js';
   4
   5 var version = '0.01';
   6
   7 export function init(main_div) {
   8     if (!(main_div instanceof HTMLElement)) {
   9         main_div = document.getElementById(main_div.startsWith("#") ? main_div.slice(1) : main_div);
  10     }
  11
  12     var dataset_id;
  13
  14     alert("WELCOME TO MIXED MODELS!");
  15     get_select_box("datasets", "mixed_model_dataset_select", { "checkbox_name": "mixed_model_dataset_select_checkbox" });
  16
  17     jQuery('#mixed_model_analysis_prepare_button').removeClass('active').addClass('inactive');
  18
  19     $(document).on('click', 'input[name=select_engine]', function (e) {
  20         //alert('clicked select engine!');
  21         get_model_string();
  22     });
  23
  24
  25     $(document).on('click', '#open_store_adjusted_blups_dialog_button', function (e) {
  26         $('#generic_save_analysis_dialog').modal("show");
  27         $('#generic_save_analysis_model_properties').val(model_properties);
  28         $('#generic_save_analysis_protocol').val($('#model_string').html());
  29         $('#generic_save_analysis_dataset_id').val(dataset_id);
  30         $('#generic_save_analysis_accession_names').val(accession_names);
  31         $('#generic_save_analysis_dataset_id').val(get_dataset_id());
  32         $('#generic_save_analysis_trait_names').val(traits);
  33         $('#generic_save_analysis_statistical_ontology_term').val('Adjusted means from BLUPs using LMER R|SGNSTAT:0000034');
  34         $('#generic_save_analysis_model_language').val('R');
  35         $('#generic_save_analysis_model_application_name').val('Breedbase Mixed Model Tool');
  36         $('#generic_save_analysis_model_application_version').val(version);
  37         $('#generic_save_analysis_model_type').val('mixed_model_lmer');
  38         $('#generic_save_analysis_result_values').val(adjusted_blups_data);
  39         $('#generic_save_analysis_result_values_type').val('analysis_result_values_match_accession_names');
  40         $('#generic_save_analysis_result_summary_values').val(result_summary);
  41         $('#generic_save_analysis_model_training_data_file').val(input_file);
  42         $('#generic_save_analysis_model_archived_training_data_file_type').val('mixed_model_input_data');
  43     });
  44
  45     $(document).on('click', '#open_store_blups_dialog_button', function (e) {
  46         $('#generic_save_analysis_dialog').modal("show");
  47         $('#generic_save_analysis_model_properties').val(model_properties);
  48         $('#generic_save_analysis_protocol').val($('#model_string').html());
  49         $('#generic_save_analysis_dataset_id').val(dataset_id);
  50         $('#generic_save_analysis_accession_names').val(accession_names);
  51         $('#generic_save_analysis_dataset_id').val(get_dataset_id());
  52         $('#generic_save_analysis_trait_names').val(traits);
  53         $('#generic_save_analysis_statistical_ontology_term').val('Phenotypic BLUPs using LMER R|SGNSTAT:0000035');
  54         $('#generic_save_analysis_model_language').val('R');
  55         $('#generic_save_analysis_model_application_name').val('Breedbase Mixed Model Tool');
  56         $('#generic_save_analysis_model_application_version').val(version);
  57         $('#generic_save_analysis_model_type').val('mixed_model_lmer');
  58         $('#generic_save_analysis_result_values').val(blups_data);
  59         $('#generic_save_analysis_result_values_type').val('analysis_result_values_match_accession_names');
  60         $('#generic_save_analysis_result_summary_values').val(result_summary);
  61         $('#generic_save_analysis_model_training_data_file').val(input_file);
  62         $('#generic_save_analysis_model_archived_training_data_file_type').val('mixed_model_input_data');
  63     });
  64
  65     $(document).on('click', '#open_store_adjusted_blues_dialog_button', function (e) {
  66         $('#generic_save_analysis_dialog').modal("show");
  67         $('#generic_save_analysis_model_properties').val(model_properties);
  68         $('#generic_save_analysis_protocol').val($('#model_string').html());
  69         $('#generic_save_analysis_dataset_id').val(dataset_id);
  70         $('#generic_save_analysis_accession_names').val(accession_names);
  71         $('#generic_save_analysis_dataset_id').val(get_dataset_id());
  72         $('#generic_save_analysis_trait_names').val(traits);
  73         $('#generic_save_analysis_statistical_ontology_term').val('Adjusted means from BLUEs using LMER R|SGNSTAT:0000036');
  74         $('#generic_save_analysis_model_language').val('R');
  75         $('#generic_save_analysis_model_application_name').val('Breedbase Mixed Model Tool');
  76         $('#generic_save_analysis_model_application_version').val(version);
  77         $('#generic_save_analysis_model_type').val('mixed_model_lmer');
  78         $('#generic_save_analysis_result_summary_values').val(result_summary);
  79         $('#generic_save_analysis_result_values_type').val('analysis_result_values_match_accession_names');
  80         $('#generic_save_analysis_model_training_data_file').val(input_file);
  81         $('#generic_save_analysis_model_archived_training_data_file_type').val('mixed_model_input_data');
  82     });
  83
  84     $(document).on('click', '#open_store_blues_dialog_button', function (e) {
  85         $('#generic_save_analysis_dialog').modal("show");
  86         $('#generic_save_analysis_model_properties').val(model_properties);
  87         $('#generic_save_analysis_protocol').val($('#model_string').html());
  88         $('#generic_save_analysis_dataset_id').val(dataset_id);
  89         $('#generic_save_analysis_accession_names').val(accession_names);
  90         $('#generic_save_analysis_dataset_id').val(get_dataset_id());
  91         $('#generic_save_analysis_trait_names').val(traits);
  92         $('#generic_save_analysis_statistical_ontology_term').val('Phenotypic BLUEs using LMER R|SGNSTAT:0000037');
  93         $('#generic_save_analysis_model_language').val('R');
  94         $('#generic_save_analysis_model_application_name').val('Breedbase Mixed Model Tool');
  95         $('#generic_save_analysis_model_application_version').val(version);
  96         $('#generic_save_analysis_model_type').val('mixed_model_lmer');
  97         $('#generic_save_analysis_result_values_type').val('analysis_result_values_match_accession_names');
  98         $('#generic_save_analysis_result_summary_values').val(result_summary);
  99         $('#generic_save_analysis_model_training_data_file').val(input_file);
 100         $('#generic_save_analysis_model_archived_training_data_file_type').val('mixed_model_input_data');
 101     });
 102
 103     $('#mixed_model_analysis_prepare_button').click(function () {
 104
 105         dataset_id = get_dataset_id();
 106         if (dataset_id != false) {
 107             $.ajax({
 108                 url: '/ajax/mixedmodels/prepare',
 109                 data: { 'dataset_id': get_dataset_id() },
 110                 success: function (r) {
 111                     if (r.error) {
 112                         alert(r.error);
 113                     }
 114                     else {
 115                         $('#dependent_variable').html(r.dependent_variable);
 116                         var html = "";
 117
 118                         for (var n = 0; n < r.factors.length; n++) {
 119                             html += "<div id=\"factor_" + n + "\" class=\"container factor\">" + r.factors[n] + "</div>";
 120                         }
 121                         $('#factors').html(html);
 122
 123                         for (var n = 0; n < r.factors.length; n++) {
 124                             $('#factor_' + n).draggable({ helper: "clone", revert: "invalid" });
 125                         }
 126
 127                         $('#tempfile').html(r.tempfile);
 128                         //$('#workflow').
 129
 130                     }
 131                     $('#fixed_factors').droppable({
 132                         drop: function (event, ui) {
 133                             $(this)
 134                                 //.addClass( "ui-state-highlight" )
 135                                 .find("p")
 136                                 .html("Dropped!");
 137                             var droppable = $(this);
 138                             var draggable = ui.draggable;
 139                             // Move draggable into droppable
 140                             var clone = draggable.clone();
 141                             clone.draggable({ revert: "invalid", helper: "clone" });
 142                             clone.css("z-index", 3);
 143                             if (!isCloned(clone)) {
 144                                 setClonedTagProperties(clone);
 145                             }
 146
 147                             clone.appendTo(droppable);
 148                             get_model_string();
 149                         }
 150                     });
 151
 152                     $('#random_factors').droppable({
 153                         drop: function (event, ui) {
 154                             $(this)
 155                                 //.addClass( "ui-state-highlight" )
 156                                 .find("p")
 157                                 .html("Dropped!");
 158                             var droppable = $(this);
 159                             var draggable = ui.draggable;
 160                             // Move draggable into droppable
 161                             var clone = draggable.clone();
 162                             clone.draggable({ revert: "invalid", helper: "clone" });
 163                             clone.css("z-index", 3);
 164                             if (!isCloned(clone)) {
 165                                 setClonedTagProperties(clone);
 166                             }
 167
 168                             clone.appendTo(droppable);
 169                             get_model_string();
 170                         }
 171                     });
 172
 173                 },
 174                 error: function (r) {
 175                     alert("ERROR!!!!!");
 176                 }
 177             });
 178         }
 179     });
 180
 181
 182     $('#add_interaction_factor_button').click(function (e) {
 183
 184         add_sub_div("interaction_factors_collection", "interaction", "Interaction");
 185     });
 186
 187     $('#add_variable_slope_intersect_button').click(function (e) {
 188         add_sub_div("variable_slope_intersect_collection", "variable_slope_intersect", "Variable slope/intersect");
 189     });
 190
 191
 192     var factor_count;
 193     var accession_names;
 194
 195     var adjusted_blups_data;
 196     var blups_data;
 197
 198     var adjusted_blues_data;
 199     var blues_data;
 200
 201     var traits;
 202     var stat_ontology_term;
 203
 204     var model_properties;
 205     var result_summary;
 206     var input_file;
 207
 208     function add_sub_div(collection_div, div_prefix, collection_name) {
 209
 210         if (factor_count === undefined) { factor_count = 0; }
 211
 212         var previous_div = factor_count;
 213         factor_count++;
 214
 215         var div_name = div_prefix + factor_count;
 216
 217         var div = '<div id="' + div_name + '_panel" class="panel panel-default" style="border-width:0px"><div id="' + div_name + '_header" class="panel-header"><span id="close_interaction_div_' + factor_count + '" class="remove">X</span> ' + collection_name + ' Term ' + factor_count + '</div><div id="' + div_name + '" class="panel-body factor_panel" ></div></div>';
 218
 219         $('#' + collection_div).append(div);
 220
 221         $('#' + div_name).droppable({
 222             drop: function (event, ui) {
 223                 var droppable = $(this);
 224                 var draggable = ui.draggable;
 225                 // Move draggable into droppable
 226                 var clone = draggable.clone();
 227                 clone.draggable({ revert: "invalid", helper: "clone" });
 228                 clone.css("z-index", 2);
 229                 if (!isCloned(clone)) {
 230                     setClonedTagProperties(clone);
 231                 }
 232
 233                 clone.appendTo(droppable);
 234                 get_model_string();
 235             }
 236         });
 237
 238         $(document).on("click", "span.remove", function (e) {
 239             this.parentNode.parentNode.remove(); get_model_string();
 240         });
 241
 242
 243     }
 244
 245     function isCloned(e) {
 246         if (e.text().includes('X')) {
 247             return true;
 248         }
 249
 250         return false;
 251     }
 252     //onclick="this.parentNode.parentNode.removeChild(this.parentNode); return false;">
 253     function setClonedTagProperties(e) {
 254         e.id = e.html() + 'C';
 255         var html = '<span id="' + e.id + '_remove" class="remove_factor">X</a></span> ' + e.html();
 256         e.html(html);
 257         $(document).on("click", "span.remove_factor", function (e) { this.parentNode.remove(); get_model_string() });
 258     }
 259
 260     $('#dependent_variable').click('#dependent_variable_select', function () {
 261         var tempfile = $('#tempfile').html();
 262         var trait_selected = [];
 263         $('.trait_box:checked').each(function () {
 264             trait_selected.push($(this).val());
 265         });
 266
 267         if (trait_selected.length > 1 || trait_selected.length == 0) {
 268             jQuery('#trait_histogram').html('Please select only one trait at a time to see the histogram!');
 269         } else {
 270
 271             var trait = trait_selected[0];
 272
 273
 274             $.ajax({
 275                 url: '/ajax/mixedmodels/grabdata',
 276                 data: { 'file': tempfile },
 277                 success: function (r) {
 278                     var v = {
 279                         "$schema": "https://vega.github.io/schema/vega-lite/v2.json",
 280                         "width": 200,
 281                         "height": 100,
 282                         "padding": 5,
 283                         "data": { 'values': r.data },
 284                         "mark": "bar",
 285                         "encoding": {
 286                             "x": {
 287                                 "bin": true,
 288                                 "field": trait,
 289                                 "type": "quantitative"
 290                             },
 291                             "y": {
 292                                 "aggregate": "count",
 293                                 "type": "quantitative"
 294                             }
 295                         }
 296                     };
 297
 298                     vegaEmbed("#trait_histogram", v);
 299                 },
 300
 301
 302                 error: function (e) { alert('error!'); }
 303             });
 304
 305         }
 306
 307     });
 308
 309     $('#run_mixed_model_button').click(function () {
 310         var model = $('#model_string').text();
 311         var fixed_factors = parse_simple_factors("fixed_factors");
 312         //alert("FIXED FACTORS: "+fixed_factors);
 313         var random_factors = parse_simple_factors("random_factors");
 314         var engine = $('input[name="select_engine"]:checked').val();
 315         //alert("Engine is "+engine);
 316         var tempfile = $('#tempfile').text();
 317
 318         var dependent_variables = [];
 319
 320         $('input[name=dependent_variable_select]:checked').each(function () {
 321             dependent_variables.push(jQuery(this).val());
 322         });
 323         console.log(dependent_variables);
 324         $('#working_modal').modal("show");
 325         $.ajax({
 326             "url": '/ajax/mixedmodels/run',
 327             "method": "POST",
 328             "data": {
 329                 "model": model,
 330                 "tempfile": tempfile,
 331                 "dependent_variables": dependent_variables,
 332                 "fixed_factors": fixed_factors,
 333                 "random_factors": random_factors,
 334                 "engine": engine
 335             },
 336             "success": function (r) {
 337                 $('#working_modal').modal("hide");
 338                 if (r.error) { alert(r.error); }
 339                 else {
 340                     if (r.method === 'random') {
 341                         $('#mixed_models_adjusted_blups_results_div').html(r.adjusted_blups_html);
 342                         $('#mixed_models_blups_results_div').html(r.blups_html);
 343
 344                         $('#adjusted_blups_tab_link').show();
 345                         $('#adjusted_blups_tab_link').addClass('active');
 346                         $('#blups_tab_link').show();
 347
 348                         $('#adjusted_blues_tab_link').removeClass('active');
 349                         $('#adjusted_blues_tab_link').hide();
 350                         $('#blues_tab_link').hide();
 351                     }
 352                     else {
 353                         $('#mixed_models_adjusted_blues_results_div').html(r.adjusted_blues_html);
 354                         $('#mixed_models_blues_results_div').html(r.blues_html);
 355
 356
 357                         $('#adjusted_blups_tab_link').removeClass('active');
 358                         $('#adjusted_blups_tab_link').hide();
 359                         $('#blups_tab_link').hide();
 360
 361
 362                         $('#adjusted_blues_tab_link').tab('show');
 363                         $('#adjusted_blues_tab_link').addClass('active');
 364                         $('#blues_tab_link').show();
 365                     }
 366
 367                     accession_names = JSON.stringify(r.accession_names);
 368
 369                     adjusted_blups_data = JSON.stringify(r.adjusted_blups_data);
 370
 371                     adjusted_blues_data = JSON.stringify(r.adjusted_blues_data);
 372                     blups_data = JSON.stringify(r.blups_data);
 373                     blues_data = JSON.stringify(r.blues_data);
 374                     traits = JSON.stringify(r.traits);
 375                     input_file = r.input_file;
 376                     result_summary = '{ "method" : "Breedbase mixed model analysis tool" }';
 377
 378                     var model_properties_data = { "properties": { "traits": traits } };
 379                     model_properties = JSON.stringify(model_properties_data);
 380
 381
 382                 }
 383             },
 384             "error": function (r) {
 385                 alert(r);
 386             }
 387         });
 388     });
 389
 390 }
 391
 392 function get_dataset_id() {
 393     var selected_datasets = [];
 394     jQuery('input[name="mixed_model_dataset_select_checkbox"]:checked').each(function () {
 395         selected_datasets.push(jQuery(this).val());
 396     });
 397     if (selected_datasets.length < 1) {
 398         alert('Please select at least one dataset!');
 399         return false;
 400     } else if (selected_datasets.length > 1) {
 401         alert('Please select only one dataset!');
 402         return false;
 403     } else {
 404         var dataset_id = selected_datasets[0];
 405         return dataset_id;
 406     }
 407 }
 408
 409 function extract_model_parameters() {
 410
 411     var fixed_factors = parse_simple_factors("fixed_factors");
 412
 413     var interaction_factors = parse_factor_collection("interaction_factor_collection_panel");
 414
 415     var variable_slope_intersects = parse_factor_collection("variable_slope_intersect_collection_panel");
 416
 417     var random_factors = parse_simple_factors("random_factors");
 418
 419     var engine = jQuery('input[name=select_engine]:checked').val();
 420
 421     //alert("ENGINE IS NOW: "+engine);
 422
 423     // var random_factors = $('#random_factors').text();
 424     // random_factors = random_factors.replace(/X /g, '","');
 425     // random_factors = random_factors.replace(/\s/g, '');
 426     // random_factors = random_factors.substr(3);
 427     // if (random_factors) {
 428     //     random_factors = '["'+random_factors+'"]';
 429     // }
 430     // var random_factors_json;
 431     // if (random_factors) {
 432     //     random_factors_json = JSON.parse(random_factors);
 433     // }
 434
 435     var dependent_variables = [];
 436     $('input[name=dependent_variable_select]:checked').each(function () {
 437         dependent_variables.push(jQuery(this).val());
 438     });
 439
 440     var json = {
 441         'fixed_factors': fixed_factors,
 442         'fixed_factors_interaction': interaction_factors,
 443         'variable_slope_intersects': variable_slope_intersects,
 444         'random_factors': random_factors,
 445         'dependent_variables': dependent_variables,
 446         'engine': engine
 447     };
 448     console.log(json);
 449     return json;
 450 }
 451
 452 function parse_simple_factors(simple_div) {
 453
 454     var factors = $('#' + simple_div).children();
 455     var factor_list = new Array();
 456     for (var n = 0; n < factors.length; n++) {
 457         var factor_string = $(factors[n]).text();
 458         factor_string = factor_string.replace(/X /g, '');
 459
 460         if (factor_string) {
 461             factor_list.push(factor_string);
 462         }
 463     }
 464     return factor_list;
 465 }
 466
 467 function parse_factor_collection(collection_div) {
 468
 469     // Structure:
 470     // interaction_factors_collection panel
 471     //    interaction_factors_collection panel-header
 472     //    interaction_1_panel panel
 473     //       interaction_1_header panel-header
 474     //       interaction_1  panel-body
 475     //         factor_1 span X FACTOR_NAME1
 476     //         factor_2 span X FACTOR_NAME2
 477     //       interaction_2_header panel-header
 478     //         factor_3 span X FACTOR_NAME3
 479     //         factor_4 span X FACTOR_NAME4
 480     //
 481
 482     var collection_divs = $('#' + collection_div).children();
 483
 484     var collection = new Array();
 485     var grouped_factors = new Array();
 486
 487     for (var i = 1; i < collection_divs.length; i++) { // skip interaction_factors_collection panel header
 488
 489         var $div = $(collection_divs[i]);
 490
 491         var top_panels = $div.children();
 492
 493         for (var n = 0; n < top_panels.length; n++) {
 494
 495             var panel_components = $(top_panels[n]).children();
 496             var $panel_body = $(panel_components[1]);
 497
 498             var factors = $panel_body.children();
 499
 500             for (var m = 0; m < factors.length; m++) {
 501                 var $factor = $(factors[m]);
 502                 var label = $factor.text();
 503
 504                 // remove X closing box
 505                 label = label.substr(2);
 506                 grouped_factors.push(label);
 507             }
 508             collection.push(grouped_factors);
 509             grouped_factors = new Array();
 510         }
 511     }
 512
 513     var fixed_factors_interaction_json;
 514     if (collection) {
 515         //fixed_factors_interaction_collection = '[["'+fixed_factors_interaction_collection+'"]]';
 516     }
 517     return collection;
 518
 519 }
 520
 521 function parse_random_factors() {
 522
 523
 524 }
 525
 526
 527 function get_model_string() {
 528     var params = extract_model_parameters();
 529
 530     //alert("PARAMS: "+JSON.stringify(params));
 531     $.ajax({
 532         url: '/ajax/mixedmodels/modelstring',
 533         method: 'POST',
 534         data: params,
 535         error: function (e) {
 536             alert("An error occurred" + e);
 537         },
 538         success: function (r) {
 539             if (r.error) {
 540                 alert(r.error);
 541             }
 542             else {
 543
 544                 console.log("ENGINE AGAIN: " + r.engine + " " + JSON.stringify(r));
 545                 if (r.engine == 'sommer') {
 546                     jQuery('#model_string').text(r.model[0] + " , random = " + r.model[1]);
 547                 }
 548                 else {
 549                     jQuery('#model_string').text(r.model);
 550                 }
 551             }
 552         }
 553     });
 554 }
 555
 556 function store_blup_file() {
 557
 558
 559
 560
 561 }