js/CXGN/BreedersToolbox/Accessions.js

   1 /*jslint browser: true, devel: true */
   2 /**
   3
   4 =head1 Accessions.js
   5
   6 Dialogs for managing accessions
   7
   8
   9 =head1 AUTHOR
  10
  11 Jeremy D. Edwards <jde22@cornell.edu>
  12
  13 =cut
  14
  15 */
  16
  17 var $j = jQuery.noConflict();
  18 var list = new CXGN.List();
  19 var accessionList;
  20 var accession_list_id;
  21 var validSpecies;
  22 var fuzzyResponse;
  23
  24 jQuery(document).ready(function ($) {
  25
  26     function disable_ui() {
  27         $('#working_modal').modal("show");
  28     }
  29
  30     function enable_ui() {
  31         $('#working_modal').modal("hide");
  32     }
  33
  34     jQuery('#manage_accessions_populations_new').click(function(){
  35         jQuery("#create_population_list_div").html(list.listSelect("create_population_list_div", ["accessions"] ));
  36         jQuery('#manage_populations_add_population_dialog').modal('show');
  37     });
  38
  39     jQuery("#create_population_submit").click(function(){
  40         jQuery.ajax({
  41             type: 'POST',
  42             url: '/ajax/population/new',
  43             dataType: "json",
  44             data: {
  45                 'population_name': jQuery('#create_population_name').val(),
  46                 'accession_list_id': jQuery('#create_population_list_div_list_select').val(),
  47             },
  48             beforeSend: function(){
  49                 disable_ui();
  50             },
  51             success: function (response) {
  52                 enable_ui();
  53                 if (response.error){
  54                     alert(response.error);
  55                 }
  56                 if (response.success){
  57                     alert(response.success);
  58                 }
  59             },
  60             error: function () {
  61                 alert('An error occurred in adding population. sorry');
  62             }
  63         });
  64     });
  65
  66     jQuery('#manage_accessions_populations_onswitch').click( function() {
  67       var already_loaded_tables = jQuery('#accordion').find("table");
  68       if (already_loaded_tables.length > 0) { return; }
  69
  70       jQuery.ajax ( {
  71         url : '/ajax/manage_accessions/populations',
  72         beforeSend: function() {
  73           disable_ui();
  74         },
  75         success: function(response){
  76           var populations = response.populations;
  77           for (var i in populations) {
  78             var name = populations[i].name;
  79             var population_id = populations[i].stock_id;
  80             var accessions = populations[i].members;
  81             var table_id = name+i+"_pop_table";
  82
  83             var section_html = '<div class="row"><div class="panel panel-default"><div class="panel-heading" >';
  84             section_html += '<div class="panel-title" name="populations_members_table_toggle" data-table_id="#'+table_id+'" data-population_id="'+population_id+'" data-population_name="'+name+'"><div class="row"><div class="col-sm-6" data-toggle="collapse" data-parent="#accordion" data-target="#collapse'+i+'"><a href="#'+table_id+'" class="accordion-toggle">'+name+'</a></div><div class="col-sm-3"><a href="/stock/'+population_id+'/view"><small>[Go To Population Page]</small></a></div><div class="col-sm-3"><a name="manage_populations_add_accessions" data-population_id="'+population_id+'" data-population_name="'+name+'"><small>[Add Accessions To Population]</small></a><br/><a name="manage_populations_delete_population" data-population_id="'+population_id+'" data-population_name="'+name+'"><small>[Delete Population]</small></a></div></div></div></div>';
  85             section_html += '<div id="collapse'+i+'" class="panel-collapse collapse">';
  86             section_html += '<div class="panel-body" style="overflow:hidden"><div class="table-responsive" style="margin-top: 10px;"><table id="'+table_id+'" class="table table-hover table-striped table-bordered" width="100%"></table><div id="populations_members_add_to_list_data_'+population_id+'" style="display:none"></div><br/><div id="populations_members_add_to_list_menu_'+population_id+'"></div></div>';
  87             section_html += '</div><br/></div></div></div><br/>';
  88
  89             jQuery('#accordion').append(section_html);
  90           }
  91           enable_ui();
  92         },
  93         error: function(response) {
  94           enable_ui();
  95           alert('An error occured retrieving population data.');
  96         }
  97       });
  98     });
  99
 100     jQuery(document).on("click", "div[name='populations_members_table_toggle']", function(){
 101         var table_id = jQuery(this).data('table_id');
 102         var population_id = jQuery(this).data('population_id');
 103         var population_name = jQuery(this).data('population_name');
 104
 105         var table = jQuery(table_id).DataTable({
 106             ajax: '/ajax/manage_accessions/population_members/'+population_id,
 107             destroy: true,
 108             columns: [
 109                 { title: "Accession Name", "data": null, "render": function ( data, type, row ) { return "<a href='/stock/"+row.stock_id+"/view'>"+row.name+"</a>"; } },
 110                 { title: "Description", "data": "description" },
 111                 { title: "Synonyms", "data": "synonyms[, ]" },
 112                 { title: "Remove From Population", "data": null, "render": function ( data, type, row ) { return "<a name='populations_member_remove' data-stock_relationship_id='"+row.stock_relationship_id+"'>X</a>"; } },
 113             ],
 114             "fnInitComplete": function(oSettings, json) {
 115                 console.log(json);
 116                 var html = "";
 117                 for(var i=0; i<json.data.length; i++){
 118                     html += json.data[i].name+"\n";
 119                 }
 120                 jQuery("#populations_members_add_to_list_data_"+population_id).html(html);
 121                 addToListMenu("populations_members_add_to_list_menu_"+population_id, "populations_members_add_to_list_data_"+population_id, {
 122                     selectText: true,
 123                     listType: 'accessions',
 124                     listName: population_name
 125                 });
 126             }
 127         });
 128
 129     });
 130
 131     var population_id;
 132     var population_name;
 133
 134     jQuery(document).on("click", "a[name='manage_populations_add_accessions']", function(){
 135         population_id = jQuery(this).data('population_id');
 136         population_name = jQuery(this).data('population_name');
 137         jQuery("#add_accession_to_population_list_div").html(list.listSelect("add_accession_to_population_list_div", ["accessions"] ));
 138         jQuery('#add_accession_population_name').html(population_name);
 139         jQuery('#manage_populations_add_accessions_dialog').modal('show');
 140     });
 141
 142     jQuery(document).on("click", "a[name='manage_populations_delete_population']", function(){
 143         population_id = jQuery(this).data('population_id');
 144         population_name = jQuery(this).data('population_name');
 145         jQuery('#delete_population_name').html(population_name);
 146         jQuery('#manage_populations_delete_dialog').modal('show');
 147     });
 148
 149     jQuery("#add_accessions_to_population_submit").click(function(){
 150         jQuery.ajax({
 151             type: 'POST',
 152             url: '/ajax/population/add_accessions',
 153             dataType: "json",
 154             data: {
 155                 'population_name': population_name,
 156                 'accession_list_id': jQuery('#add_accession_to_population_list_div_list_select').val(),
 157             },
 158             beforeSend: function(){
 159                 disable_ui();
 160             },
 161             success: function (response) {
 162                 enable_ui();
 163                 if (response.error){
 164                     alert(response.error);
 165                 }
 166                 if (response.success){
 167                     alert(response.success);
 168                 }
 169             },
 170             error: function () {
 171                 alert('An error occurred in adding accessions to population. sorry');
 172             }
 173         });
 174     });
 175
 176     jQuery("#delete_population_submit").click(function(){
 177         jQuery.ajax({
 178             type: 'POST',
 179             url: '/ajax/population/delete',
 180             dataType: "json",
 181             data: {
 182                 'population_id': population_id,
 183                 'population_name': population_name,
 184             },
 185             beforeSend: function(){
 186                 disable_ui();
 187             },
 188             success: function (response) {
 189                 enable_ui();
 190                 if (response.error){
 191                     alert(response.error);
 192                 }
 193                 if (response.success){
 194                     alert(response.success);
 195                 }
 196             },
 197             error: function () {
 198                 alert('An error occurred in deleting population. sorry');
 199             }
 200         });
 201     });
 202
 203     jQuery(document).on("click", "a[name='populations_member_remove']", function(){
 204         var stock_relationship_id= jQuery(this).data("stock_relationship_id");
 205         jQuery.ajax({
 206             url: '/ajax/population/remove_member?stock_relationship_id='+stock_relationship_id,
 207             dataType: "json",
 208             beforeSend: function(){
 209                 disable_ui();
 210             },
 211             success: function (response) {
 212                 enable_ui();
 213                 if (response.error){
 214                     alert(response.error);
 215                 }
 216                 if (response.success){
 217                     alert(response.success);
 218                 }
 219             },
 220             error: function () {
 221                 alert('An error occurred in removing accession from population. sorry');
 222             }
 223         });
 224     });
 225
 226     function add_accessions(accessionsToAdd, speciesName, populationName, organizationName  ) {
 227         var full_info = []
 228         for(var i=0; i<accessionsToAdd.length; i++){
 229             full_info.push({
 230                 'species':speciesName,
 231                 'defaultDisplayName':accessionsToAdd[i],
 232                 'germplasmName':accessionsToAdd[i],
 233                 'organizationName':organizationName,
 234                 'populationName':populationName,
 235             });
 236         }
 237         $.ajax({
 238             type: 'POST',
 239             url: '/ajax/accession_list/add',
 240             dataType: "json",
 241             timeout: 36000000,
 242             data: {
 243                 'full_info': JSON.stringify(full_info),
 244                 'allowed_organisms': JSON.stringify([speciesName]),
 245             },
 246             beforeSend: function(){
 247                 disable_ui();
 248             },
 249             success: function (response) {
 250                 enable_ui();
 251                 if (response.error) {
 252                     alert(response.error);
 253                 } else {
 254                     var html = 'The following stocks were added!<br/>';
 255                     for (var i=0; i<response.added.length; i++){
 256                         html = html + '<a href="/stock/'+response.added[i][0]+'/view">'+response.added[i][1]+'</a><br/>';
 257                     }
 258                     jQuery('#add_accessions_saved_message').html(html);
 259                     jQuery('#add_accessions_saved_message_modal').modal('show');
 260                 }
 261             },
 262             error: function () {
 263                 alert('An error occurred in processing. sorry');
 264             }
 265         });
 266     }
 267
 268     function verify_species_name() {
 269         var speciesName = $("#species_name_input").val();
 270         validSpecies = 0;
 271         $.ajax({
 272             type: 'GET',
 273             url: '/organism/verify_name',
 274             dataType: "json",
 275             data: {
 276                 'species_name': speciesName,
 277             },
 278             success: function (response) {
 279                 if (response.error) {
 280                     alert(response.error);
 281                     validSpecies = 0;
 282                 } else {
 283                     validSpecies = 1;
 284                 }
 285             },
 286             error: function () {
 287                 alert('An error occurred verifying species name. sorry');
 288                 validSpecies = 0;
 289             }
 290         });
 291     }
 292
 293     $('#species_name_input').focusout(function () {
 294         verify_species_name();
 295     });
 296
 297     $('#review_absent_accessions_submit').click(function () {
 298         var speciesName = $("#species_name_input").val();
 299         var populationName = $("#population_name_input").val();
 300         var organizationName = $("#organization_name_input").val();
 301         var accessionsToAdd = accessionList;
 302         if (!speciesName) {
 303             alert("Species name required");
 304             return;
 305         }
 306         if (!populationName) {
 307             populationName = '';
 308         }
 309         if (!accessionsToAdd || accessionsToAdd.length == 0) {
 310             alert("No accessions to add");
 311             return;
 312         }
 313         add_accessions(accessionsToAdd, speciesName, populationName, organizationName);
 314         $('#review_absent_dialog').modal("hide");
 315         //window.location.href='/breeders/accessions';
 316     });
 317
 318     $('#new_accessions_submit').click(function () {
 319         accession_list_id = $('#list_div_list_select').val();
 320         verify_accession_list(accession_list_id);
 321         $('#add_accessions_dialog').modal("hide");
 322     });
 323
 324     $('#add_accessions_link').click(function () {
 325         var list = new CXGN.List();
 326         var accessionList;
 327         var accession_list_id;
 328         var validSpecies;
 329         var fuzzyResponse;
 330         $('#add_accessions_dialog').modal("show");
 331         $('#review_found_matches_dialog').modal("hide");
 332         $('#review_fuzzy_matches_dialog').modal("hide");
 333         $('#review_absent_dialog').modal("hide");
 334         $("#list_div").html(list.listSelect("list_div", ["accessions"] ));
 335     });
 336
 337     $('body').on('hidden.bs.modal', '.modal', function () {
 338         $(this).removeData('bs.modal');
 339     });
 340
 341         $(document).on('change', 'select[name="fuzzy_option"]', function() {
 342                 var value = $(this).val();
 343                 if ($('#add_accession_fuzzy_option_all').is(":checked")){
 344                         $('select[name="fuzzy_option"] option[value='+value+']').attr('selected','selected');
 345                 }
 346         });
 347
 348     $('#review_fuzzy_matches_download').click(function(){
 349         //console.log(fuzzyResponse);
 350         openWindowWithPost(JSON.stringify(fuzzyResponse));
 351         //window.open('/ajax/accession_list/fuzzy_download?fuzzy_response='+JSON.stringify(fuzzyResponse));
 352     });
 353
 354 });
 355
 356 function openWindowWithPost(fuzzyResponse) {
 357     var f = document.getElementById('add_accession_fuzzy_match_download');
 358     f.fuzzy_response.value = fuzzyResponse;
 359     window.open('', 'TheWindow');
 360     f.submit();
 361 }
 362
 363 function verify_accession_list(accession_list_id) {
 364     accession_list = JSON.stringify(list.getList(accession_list_id));
 365     doFuzzySearch = jQuery('#fuzzy_check').attr('checked'); //fuzzy search is always checked in a hidden input
 366     //alert("should be disabled");
 367     //alert(accession_list);
 368
 369     jQuery.ajax({
 370         type: 'POST',
 371         url: '/ajax/accession_list/verify',
 372         timeout: 36000000,
 373         //async: false,
 374         dataType: "json",
 375         data: {
 376             'accession_list': accession_list,
 377             'do_fuzzy_search': doFuzzySearch,
 378         },
 379         beforeSend: function(){
 380             disable_ui();
 381         },
 382         success: function (response) {
 383             enable_ui();
 384             if (response.error) {
 385                 alert(response.error);
 386             } else {
 387                 review_verification_results(response, accession_list_id);
 388             }
 389         },
 390         error: function () {
 391             enable_ui();
 392             alert('An error occurred in processing. sorry');
 393         }
 394     });
 395 }
 396
 397 function review_verification_results(verifyResponse, accession_list_id){
 398     var i;
 399     var j;
 400     //console.log(verifyResponse);
 401     //console.log(accession_list_id);
 402
 403     if (verifyResponse.found) {
 404         jQuery('#count_of_found_accessions').html("Total number already in the database("+verifyResponse.found.length+")");
 405         var found_html = '<table class="table" id="found_accessions_table"><thead><tr><th>Search Name</th><th>Found in Database</th></tr></thead><tbody>';
 406         for( i=0; i < verifyResponse.found.length; i++){
 407             found_html = found_html
 408                 +'<tr><td>'+verifyResponse.found[i].matched_string
 409                 +'</td><td>'
 410                 +verifyResponse.found[i].unique_name
 411                 +'</td></tr>';
 412         }
 413         found_html = found_html +'</tbody></table>';
 414
 415         jQuery('#view_found_matches').html(found_html);
 416
 417         jQuery('#review_found_matches_dialog').modal('show');
 418
 419         jQuery('#found_accessions_table').DataTable({});
 420
 421         accessionList = verifyResponse.absent;
 422
 423     }
 424
 425     if (verifyResponse.fuzzy.length > 0) {
 426         fuzzyResponse = verifyResponse.fuzzy;
 427         var fuzzy_html = '<table id="add_accession_fuzzy_table" class="table"><thead><tr><th class="col-xs-4">Name in Your List</th><th class="col-xs-4">Existing Name(s) in Database</th><th class="col-xs-4">Options&nbsp;&nbsp;&nbsp&nbsp;<input type="checkbox" id="add_accession_fuzzy_option_all"/> Use Same Option for All</th></tr></thead><tbody>';
 428         for( i=0; i < verifyResponse.fuzzy.length; i++) {
 429             fuzzy_html = fuzzy_html + '<tr id="add_accession_fuzzy_option_form'+i+'"><td>'+ verifyResponse.fuzzy[i].name + '<input type="hidden" name="fuzzy_name" value="'+ verifyResponse.fuzzy[i].name + '" /></td>';
 430             fuzzy_html = fuzzy_html + '<td><select class="form-control" name ="fuzzy_select">';
 431             for(j=0; j < verifyResponse.fuzzy[i].matches.length; j++){
 432                 if (verifyResponse.fuzzy[i].matches[j].is_synonym){
 433                     fuzzy_html = fuzzy_html + '<option value="' + verifyResponse.fuzzy[i].matches[j].synonym_of + '">' + verifyResponse.fuzzy[i].matches[j].name + ' (SYNONYM OF: '+verifyResponse.fuzzy[i].matches[j].synonym_of+')</option>';
 434                 } else {
 435                     fuzzy_html = fuzzy_html + '<option value="' + verifyResponse.fuzzy[i].matches[j].name + '">' + verifyResponse.fuzzy[i].matches[j].name + '</option>';
 436                 }
 437             }
 438             fuzzy_html = fuzzy_html + '</select></td><td><select class="form-control" name="fuzzy_option"><option value="keep">Continue saving name in your list</option><option value="replace">Replace name in your list with selected existing name</option><option value="remove">Remove name in your list and ignore</option><option value="synonymize">Add name in your list as a synonym to selected existing name</option></select></td></tr>';
 439         }
 440         fuzzy_html = fuzzy_html + '</tbody></table>';
 441         jQuery('#view_fuzzy_matches').html(fuzzy_html);
 442
 443         //Add to absent
 444         for( i=0; i < verifyResponse.fuzzy.length; i++) {
 445             verifyResponse.absent.push(verifyResponse.fuzzy[i].name);
 446         }
 447         accessionList = verifyResponse.absent;
 448     }
 449
 450     if (verifyResponse.absent.length > 0 && verifyResponse.fuzzy.length == 0) {
 451         populate_review_absent_dialog(verifyResponse.absent);
 452     }
 453
 454     jQuery('#review_found_matches_hide').click(function(){
 455         if (verifyResponse.fuzzy.length > 0){
 456             jQuery('#review_fuzzy_matches_dialog').modal('show');
 457         } else {
 458             jQuery('#review_fuzzy_matches_dialog').modal('hide');
 459             if (verifyResponse.absent.length > 0){
 460                 jQuery('#review_absent_dialog').modal('show');
 461             } else {
 462                 alert('All accessions in your list are now saved in the database. 3');
 463             }
 464         }
 465     });
 466
 467     jQuery(document).on('click', '#review_fuzzy_matches_continue', function(){
 468         process_fuzzy_options(accession_list_id);
 469     });
 470
 471 }
 472
 473 function populate_review_absent_dialog(absent){
 474     jQuery('#count_of_absent_accessions').html("Total number to be added("+absent.length+")");
 475     var absent_html = '';
 476     jQuery("#species_name_input").autocomplete({
 477         source: '/organism/autocomplete'
 478     });
 479
 480     for( i=0; i < absent.length; i++){
 481         absent_html = absent_html
 482         +'<div class="left">'+absent[i]
 483         +'</div>';
 484     }
 485     jQuery('#view_absent').html(absent_html);
 486 }
 487
 488 function process_fuzzy_options(accession_list_id) {
 489     var data={};
 490     jQuery('#add_accession_fuzzy_table').find('tr').each(function(){
 491         var id=jQuery(this).attr('id');
 492         if (id !== undefined){
 493             var row={};
 494             jQuery(this).find('input,select').each(function(){
 495                 var type = jQuery(this).attr('type');
 496                 if (type == 'radio'){
 497                     if (jQuery(this).is(':checked')){
 498                         row[jQuery(this).attr('name')]=jQuery(this).val();
 499                     }
 500                 } else {
 501                     row[jQuery(this).attr('name')]=jQuery(this).val();
 502                 }
 503             });
 504             data[id]=row;
 505         }
 506     });
 507     //console.log(data);
 508
 509     jQuery.ajax({
 510         type: 'POST',
 511         url: '/ajax/accession_list/fuzzy_options',
 512         dataType: "json",
 513         data: {
 514             'accession_list_id': accession_list_id,
 515             'fuzzy_option_data': JSON.stringify(data),
 516             'names_to_add': JSON.stringify(accessionList)
 517         },
 518         success: function (response) {
 519             //console.log(response);
 520             accessionList = response.names_to_add;
 521             if (accessionList.length > 0){
 522                 populate_review_absent_dialog(accessionList);
 523                 jQuery('#review_absent_dialog').modal('show');
 524             } else {
 525                 alert('All accessions in your list are now saved in the database. 2');
 526             }
 527         },
 528         error: function () {
 529             alert('An error occurred checking your fuzzy options! Do not try to add a synonym to a synonym!');
 530         }
 531     });
 532 }
 533