js/source/legacy/solGS/kinship.js

   1 /**
   2  * kinship analysis and result plotting using d3
   3  * Isaak Y Tecle <iyt2@cornell.edu>
   4  *
   5  */
   6
   7 var solGS = solGS || function solGS() {};
   8
   9 solGS.kinship = {
  10   canvas: "#kinship_canvas",
  11   kinshipPlotDivPrefix: "#kinship_plot",
  12   kinshipMsgDiv: "#kinship_message",
  13   kinshipPopsSelectMenuId: "#kinship_pops_select",
  14   kinshipPopsDiv: "#kinship_pops_select_div",
  15   kinshipPopsDataDiv: "#kinship_pops_data_div",
  16
  17   getKinshipArgs: function () {
  18     var page = location.pathname;
  19     var kinshipPopId;
  20     var kinshipUrlArgs;
  21     var dataStr;
  22     var trainingPopId;
  23     var selectionPopId;
  24
  25     if (page.match(/solgs\/trait\/|solgs\/model\/combined\/trials\/|\/breeders\/trial\//)) {
  26       trainingPopId = jQuery("#training_pop_id").val();
  27       if (!trainingPopId) {
  28         trainingPopId = jQuery("#trial_id").val();
  29       }
  30       kinshipPopId = trainingPopId;
  31     } else if (page.match(/kinship\/analysis/)) {
  32       kinshipUrlArgs = this.getKinshipArgsFromUrl();
  33       kinshipPopId = kinshipUrlArgs.kinship_pop_id;
  34       dataStr = kinshipUrlArgs.data_structure;
  35       protocolId = kinshipUrlArgs.genotyping_protocol_id;
  36     } else if (page.match(/\/selection\/|\/prediction\//)) {
  37       selectionPopId = jQuery("#selection_pop_id").val();
  38       kinshipPopId = selectionPopId;
  39     } else if (page.match(/solgs\/traits\/all\/population\/|models\/combined\/trials\//)) {
  40       trainingPopId = jQuery("#training_pop_id").val();
  41       kinshipPopId = trainingPopId;
  42     }
  43
  44     if (page.match(/combined/)) {
  45       var comboPopsId = trainingPopId;
  46     }
  47
  48     var listId;
  49     var datasetId;
  50     var datasetName;
  51
  52       if (String(kinshipPopId).match(/list/)) {
  53         dataStr = "list";
  54       } else if (String(kinshipPopId).match(/dataset/)) {
  55         dataStr = "dataset";
  56       }
  57
  58       if (dataStr == "list") {
  59         if (isNaN(kinshipPopId)) {
  60           listId = kinshipPopId.replace("list_", "");
  61         } else {
  62           listId = kinshipPopId;
  63         }
  64       } else if (dataStr == "dataset") {
  65         if (isNaN(kinshipPopId)) {
  66           datasetId = kinshipPopId.replace("dataset_", "");
  67         } else {
  68           datasetId = kinshipPopId;
  69         }
  70       }
  71
  72     var protocolId = jQuery("#genotyping_protocol_id").val();
  73     var traitId = jQuery("#trait_id").val();
  74
  75     return {
  76       kinship_pop_id: kinshipPopId,
  77       training_pop_id: trainingPopId,
  78       list_id: listId,
  79       dataset_id: datasetId,
  80       combo_pops_id: comboPopsId,
  81       selection_pop_id: selectionPopId,
  82       data_structure: dataStr,
  83       genotyping_protocol_id: protocolId,
  84       trait_id: traitId,
  85       analysis_type: "kinship analysis",
  86     };
  87   },
  88
  89   getKinshipArgsFromUrl: function () {
  90     var page = location.pathname;
  91     if (page == "/kinship/analysis/") {
  92       page = "/kinship/analysis";
  93     }
  94     var urlArgs = page.replace("/kinship/analysis", "");
  95
  96     if (urlArgs) {
  97       var args = urlArgs.split(/\/+/);
  98       var selectId = args[1];
  99       var protocolId = args[3];
 100
 101       var dataStr;
 102       var reg = /\d+/;
 103       var popId = selectId.match(reg)[0];
 104       if (selectId.match(/dataset/)) {
 105         dataStr = "dataset";
 106       } else if (selectId.match(/list/)) {
 107         dataStr = "list";
 108       }
 109
 110       var args = {
 111         kinship_pop_id: popId,
 112         data_structure: dataStr,
 113         genotyping_protocol_id: protocolId,
 114       };
 115
 116       return args;
 117     } else {
 118       return {};
 119     }
 120   },
 121
 122
 123   getTableTdId: function (kinshipPopId) {
 124     return `kinship_${kinshipPopId}`;
 125   },
 126
 127
 128   createTable: function (tableId) {
 129     var kinshipTable =
 130       `<table id="${tableId}" class="table table-striped"><thead><tr>` +
 131       "<th>Population</th>" +
 132       "<th>Data structure type</th>" +
 133       "<th>Ownership</th>" +
 134       "<th>Data type</th>" +
 135       "<th>Run Kinship</th>" +
 136       "</tr></thead></table>";
 137
 138     return kinshipTable;
 139   },
 140
 141   getKinshipPopId: function (selectedId, dataStr) {
 142
 143     var pcaPopId;
 144     if (dataStr) {
 145       pcaPopId = `${dataStr}_${selectedId}`;
 146     } else {
 147       pcaPopId = selectedId;
 148     }
 149
 150     return pcaPopId;
 151   },
 152
 153   createRowElements: function (kinshipPop) {
 154     var popId = kinshipPop.id;
 155     var popName = kinshipPop.name;
 156     var dataStr = kinshipPop.data_str;
 157
 158     var kinshipPopId = solGS.kinship.getKinshipPopId(popId, dataStr);
 159
 160     var dataTypeOpts = this.getDataTypeOpts({
 161       id: popId,
 162       name: popName,
 163       data_str: dataStr,
 164     });
 165
 166     dataTypeOpts = this.createDataTypeSelect(dataTypeOpts, kinshipPopId);
 167
 168
 169     var listId;
 170     var datasetId;
 171
 172     if (dataStr.match(/dataset/)) {
 173       datasetId = popId;
 174     } else if (dataStr.match(/list/)) {
 175       listId = popId;
 176     }
 177     var protocolId = solGS.genotypingProtocol.getGenotypingProtocolId("kinship_div");
 178
 179     var kinshipArgs = {
 180       kinship_pop_id: kinshipPopId,
 181       data_structure: dataStr,
 182       dataset_id: datasetId,
 183       list_id: listId,
 184       kinship_pop_name: popName,
 185       genotyping_protocol_id: protocolId,
 186       analysis_type: "kinship analysis",
 187     };
 188
 189     kinshipArgs = JSON.stringify(kinshipArgs);
 190
 191     var runKinshipBtnId = this.getRunKinshipBtnId(kinshipPopId);
 192     var runKinshipBtn =
 193       `<button type="button" id=${runKinshipBtnId}` +
 194       ` class="btn btn-success" data-selected-pop='${kinshipArgs}'>Run kinship</button>`;
 195
 196     if (dataStr.match(/dataset/)) {
 197       popName = `<a href="/dataset/${popId}">${popName}</a>`;
 198     }
 199     var rowData = [popName,
 200       dataStr, kinshipPop.owner, dataTypeOpts, runKinshipBtn, `${dataStr}_${popId}`];
 201
 202     return rowData;
 203   },
 204
 205   displayKinshipPopsTable: function (tableId, data) {
 206
 207     var table = jQuery(`#${tableId}`).DataTable({
 208       'searching': true,
 209       'ordering': true,
 210       'processing': true,
 211       'paging': true,
 212       'info': false,
 213       'pageLength': 5,
 214       'rowId': function (a) {
 215         return a[5]
 216       }
 217     });
 218
 219     table.rows.add(data).draw();
 220
 221   },
 222
 223
 224   getKinshipPopsRows: function(kinshipPops) {
 225
 226     var kinshipPopsRows = [];
 227
 228     for (var i = 0; i < kinshipPops.length; i++) {
 229       if (kinshipPops[i]) {
 230         var kinshipPopRow = this.createRowElements(kinshipPops[i]);
 231         kinshipPopsRows.push(kinshipPopRow);
 232       }
 233     }
 234
 235     return kinshipPopsRows;
 236
 237   },
 238
 239   getKinshipPops: function () {
 240
 241     var list = new solGSList();
 242     var lists = list.getLists(["accessions", "trials"]);
 243     lists = list.addDataStrAttr(lists);
 244
 245     var datasets = solGS.dataset.getDatasetPops(["accessions", "trials"]);
 246
 247     var kinshipPops = [lists, datasets];
 248
 249     return kinshipPops.flat();
 250
 251   },
 252
 253   getDataTypeOpts: function (args) {
 254     var dataTypeOpts = ["Genotype"];
 255     return dataTypeOpts;
 256
 257   },
 258
 259
 260   createDataTypeSelect: function (opts) {
 261     var dataTypeGroup = '<select class="form-control" id="kinship_data_type_select">';
 262
 263     for (var i = 0; i < opts.length; i++) {
 264       dataTypeGroup += '<option value="' + opts[i] + '">' + opts[i] + "</option>";
 265     }
 266     dataTypeGroup += "</select>";
 267
 268     return dataTypeGroup;
 269   },
 270
 271   getSelectedPopKinshipArgs: function (runKinshipElemId) {
 272     var kinshipArgs;
 273
 274     var selectedPopDiv = document.getElementById(runKinshipElemId);
 275     if (selectedPopDiv) {
 276       var selectedPopData = selectedPopDiv.dataset;
 277
 278       kinshipArgs = JSON.parse(selectedPopData.selectedPop);
 279       var kinshipPopId = kinshipArgs.data_str + "_" + kinshipArgs.id;
 280
 281       var protocolId = solGS.genotypingProtocol.getGenotypingProtocolId("kinship_div");
 282       var page = `/kinship/analysis/${kinshipPopId}/gp/${protocolId}`;
 283
 284       kinshipArgs["analysis_type"] = "kinship analysis";
 285       kinshipArgs["genotyping_protocol_id"] = protocolId;
 286       kinshipArgs["analysis_page"] = page;
 287     }
 288
 289     return kinshipArgs;
 290   },
 291
 292   checkCachedKinship: function (page, args) {
 293     args = JSON.stringify(args);
 294
 295     var checkCached = jQuery.ajax({
 296       type: "POST",
 297       dataType: "json",
 298       data: {
 299         page: page,
 300         arguments: args,
 301       },
 302       url: "/solgs/check/cached/result/",
 303     });
 304
 305     return checkCached;
 306   },
 307
 308   runKinshipAnalysis: function (args) {
 309     var kinArgs = JSON.stringify(args);
 310
 311     var runKinship = jQuery.ajax({
 312       type: "POST",
 313       dataType: "json",
 314       data: { arguments: kinArgs },
 315       url: "/run/kinship/analysis/",
 316     });
 317
 318     return runKinship;
 319   },
 320
 321   addDowloandLinks: function (res) {
 322     var popName = res.kinship_pop_name;
 323     var kinFileId = res.kinship_file_id;
 324     var kinshipFile = res.kinship_table_file;
 325
 326     var aveFile = res.kinship_averages_file;
 327     var inbreedingFile = res.inbreeding_file;
 328
 329     var fileNameKinship = kinshipFile.split("/").pop();
 330     var fileNameAve = aveFile.split("/").pop();
 331     var fileNameInbreeding = inbreedingFile.split("/").pop();
 332
 333     kinshipFile =
 334       '<a href="' + kinshipFile + '" download=' + fileNameKinship + ">Kinship matrix</a>";
 335
 336     aveFile = '<a href="' + aveFile + '" download=' + fileNameAve + ">Average kinship</a>";
 337
 338     inbreedingFile =
 339       '<a href="' +
 340       inbreedingFile +
 341       '" download=' +
 342       fileNameInbreeding +
 343       ">Inbreeding coefficients</a>";
 344
 345     var kinDownloadBtn = "download_" + "kinship_plot_" + kinFileId;
 346     var kinPlotLink =
 347       "<a href='#'  onclick='event.preventDefault();' id='" + kinDownloadBtn + "'> plot</a>";
 348
 349     var links = "<strong>Download:</strong> ";
 350
 351     if (popName) {
 352       links = links + popName + " ";
 353     }
 354
 355     links = links + kinshipFile + " | " + aveFile + " | " + inbreedingFile + " | " + kinPlotLink;
 356
 357     return links;
 358   },
 359
 360   getRunKinshipBtnId: function (rowId) {
 361     if (location.pathname.match(/kinship\/analysis/) && rowId) {
 362       return `run_kinship_${rowId}`;
 363     } else {
 364       return "run_kinship";
 365     }
 366   },
 367
 368   getKinshipPopId: function (selectId, dataStr) {
 369     var kinshipPopId;
 370     if (dataStr) {
 371       kinshipPopId = `${dataStr}_${selectId}`;
 372     } else {
 373       kinshipPopId = selectId;
 374     }
 375
 376     return kinshipPopId;
 377   },
 378
 379   ///////
 380 };
 381
 382 jQuery(document).ready(function () {
 383   jQuery("#kinship_div").on("click", function (e) {
 384     var runKinshipBtnId = e.target.id;
 385     if (runKinshipBtnId.match(/run_kinship/)) {
 386       var kinshipArgs = solGS.kinship.getKinshipArgs();
 387       var kinshipPopId = kinshipArgs.kinship_pop_id;
 388       if (!kinshipPopId) {
 389         kinshipArgs = solGS.kinship.getSelectedPopKinshipArgs(runKinshipBtnId);
 390       }
 391
 392       kinshipPopId = kinshipArgs.kinship_pop_id;
 393       var protocolId = solGS.genotypingProtocol.getGenotypingProtocolId("kinship_div");
 394
 395       var canvas = solGS.kinship.canvas;
 396       var kinshipPlotDivId = solGS.kinship.kinshipPlotDivPrefix;
 397       var kinshipMsgDiv = solGS.kinship.kinshipMsgDiv;
 398       runKinshipBtnId = `#${runKinshipBtnId}`;
 399       var kinshipUrl = `/kinship/analysis/${kinshipPopId}/gp/${protocolId}`;
 400       //    solGS.kinship.generateKinshipUrl(kinshipPopId);
 401       kinshipArgs["analysis_page"] = kinshipUrl;
 402
 403       jQuery(runKinshipBtnId).hide();
 404       jQuery(`${canvas} .multi-spinner-container`).show();
 405
 406       jQuery(runKinshipBtnId).hide();
 407       jQuery(kinshipMsgDiv).text("Running kinship... please wait...it may take minutes.").show();
 408
 409       jQuery(`${canvas} .multi-spinner-container`).show();
 410       solGS.kinship
 411         .checkCachedKinship(kinshipUrl, kinshipArgs)
 412         .done(function (res) {
 413           if (res.data) {
 414             jQuery(kinshipMsgDiv).html("Generating heatmap... please wait...").show();
 415
 416             kinshipPlotDivId = `${kinshipPlotDivId}_${res.kinship_file_id}`;
 417
 418             var links = solGS.kinship.addDowloandLinks(res);
 419             solGS.heatmap.plot(res.data, canvas, kinshipPlotDivId, links);
 420
 421             jQuery(`${canvas} .multi-spinner-container`).hide();
 422             jQuery(kinshipMsgDiv).empty();
 423             jQuery(runKinshipBtnId).show();
 424           } else {
 425
 426                         jQuery(`${canvas} .multi-spinner-container`).hide();
 427             jQuery(kinshipMsgDiv).empty();
 428
 429             var title =
 430               "<p>This analysis may take a long time. " +
 431               "Do you want to submit the analysis and get an email when it completes?</p>";
 432
 433             var jobSubmit = '<div id= "kinship_submit">' + title + "</div>";
 434
 435             jQuery(jobSubmit).appendTo("body");
 436
 437             jQuery("#kinship_submit").dialog({
 438               height: "auto",
 439               width: "auto",
 440               modal: true,
 441               title: "Kinship job submission",
 442               buttons: {
 443                 OK: {
 444                   text: "Yes",
 445                   class: "btn btn-success",
 446                   id: "queue_job",
 447                   click: function () {
 448                     jQuery(this).dialog("close");
 449
 450                     solGS.submitJob.checkUserLogin(kinshipUrl, kinshipArgs);
 451                   },
 452                 },
 453
 454                 No: {
 455                   text: "No, I will wait till it completes.",
 456                   class: "btn btn-warning",
 457                   id: "no_queue",
 458                   click: function () {
 459                     jQuery(this).dialog("close");
 460
 461                                         jQuery(kinshipMsgDiv).text("Running kinship... please wait...it may take minutes.").show();
 462                                         jQuery(`${canvas} .multi-spinner-container`).show();
 463
 464                     solGS.kinship
 465                       .runKinshipAnalysis(kinshipArgs)
 466                       .done(function (res) {
 467                         if (res.data) {
 468                           jQuery(kinshipMsgDiv)
 469                             .html("Generating heatmap... please wait...")
 470                             .show();
 471
 472                           kinshipPlotDivId = `${kinshipPlotDivId}_${res.kinship_file_id}`;
 473
 474                           var links = solGS.kinship.addDowloandLinks(res);
 475                           solGS.heatmap.plot(res.data, canvas, kinshipPlotDivId, links);
 476
 477                           jQuery(`${canvas} .multi-spinner-container`).hide();
 478                           jQuery(kinshipMsgDiv).empty();
 479                           jQuery(runKinshipBtnId).show();
 480                         } else {
 481                           jQuery(`${canvas} .multi-spinner-container`).hide();
 482                           jQuery(kinshipMsgDiv)
 483                             .css({
 484                               "padding-left": "0px",
 485                             })
 486                             .html("This population has no kinship output data.")
 487                             .fadeOut(8400);
 488
 489                           jQuery(runKinshipBtnId).show();
 490                         }
 491                       })
 492                       .fail(function () {
 493                         jQuery(kinshipMsgDiv)
 494                           .html("Error occured running the kinship.")
 495                           .show()
 496                           .fadeOut(8400);
 497
 498                         jQuery(`${canvas} .multi-spinner-container`).hide();
 499                       });
 500                   },
 501                 },
 502
 503                 Cancel: {
 504                   text: "Cancel",
 505                   class: "btn btn-info",
 506                   id: "cancel_queue_info",
 507                   click: function () {
 508                     jQuery(this).dialog("close");
 509                     jQuery(runKinshipBtnId).show();
 510                   },
 511                 },
 512               },
 513             });
 514           }
 515         })
 516         .fail(function () {
 517           jQuery(kinshipMsgDiv).html("Error occured running the kinship.").show().fadeOut(8400);
 518           jQuery(`${canvas} .multi-spinner-container`).hide();
 519         });
 520     }
 521   });
 522 });
 523
 524 jQuery(document).ready(function () {
 525   var url = location.pathname;
 526
 527   if (url.match(/kinship\/analysis/)) {
 528     var args = solGS.kinship.getKinshipArgsFromUrl();
 529     if (args.kinship_pop_id) {
 530       if (args.data_structure) {
 531         args["kinship_pop_id"] = args.data_structure + "_" + args.kinship_pop_id;
 532       }
 533       solGS.kinship.checkCachedKinship(url, args).done(function (res) {
 534         if (res.data) {
 535           var kinshipMsgDiv = solGS.kinship.kinshipMsgDiv;
 536           var canvas = solGS.kinship.canvas;
 537
 538           jQuery(kinshipMsgDiv).html("Generating heatmap... please wait...").show();
 539           jQuery(`${canvas} .multi-spinner-container`).show();
 540
 541           var kinshipPlotDivId = solGS.kinship.kinshipPlotDivPrefix;
 542           kinshipPlotDivId = `${kinshipPlotDivId}_${res.kinship_file_id}`;
 543
 544           var links = solGS.kinship.addDowloandLinks(res);
 545           solGS.heatmap.plot(res.data, canvas, kinshipPlotDivId, links);
 546
 547           jQuery(`${canvas} .multi-spinner-container`).hide();
 548           jQuery(kinshipMsgDiv).empty();
 549         }
 550     })
 551   }
 552 }
 553 });
 554
 555 jQuery(document).ready(function () {
 556   var kinshipCanvas = solGS.kinship.canvas;
 557   jQuery(kinshipCanvas).on("click", "a", function (e) {
 558     var buttonId = e.target.id;
 559     var kinshipPlotId = buttonId.replace(/download_/, "");
 560     saveSvgAsPng(document.getElementById("#" + kinshipPlotId), kinshipPlotId + ".png", { scale: 1 });
 561   });
 562 });
 563
 564 jQuery(document).ready(function () {
 565   var url = location.pathname;
 566
 567   if (url.match(/kinship\/analysis/)) {
 568     kinshipPopsDataDiv = solGS.kinship.kinshipPopsDataDiv;
 569     var tableId = 'kinship_pops_table';
 570     var kinshipPopsTable = solGS.kinship.createTable(tableId);
 571     jQuery(kinshipPopsDataDiv).append(kinshipPopsTable).show();
 572
 573     var kinshipPops = solGS.kinship.getKinshipPops();
 574     var kinshipPopsRows = solGS.kinship.getKinshipPopsRows(kinshipPops);
 575
 576     solGS.kinship.displayKinshipPopsTable(tableId, kinshipPopsRows);
 577     jQuery("#add_new_pops").show();
 578   }
 579 });