mason/brapiclient/germplasm_search.mas

   1 <%args>
   2 </%args>
   3
   4 <& /util/import_javascript.mas, classes => [ 'brapi.Table' ] &>
   5
   6 <& /page/page_title.mas, title=>"Germplasm Search and Exchange" &>
   7
   8 <h4>Database Select</h4>
   9 <select name="brapi_home_url_select" id="brapi_home_url_select" class="form-control" />
  10     <option value="">local</option>
  11     <option value="https://cassbase.org">cassbase.org</option>
  12     <option value="https://cassavabase.org">cassavabase.org</option>
  13     <option value="https://musabase.org">musabase.org</option>
  14     <option value="https://sweetpotatobase.org">sweetpotatobase.org</option>
  15     <option value="https://yambase.org">yambase.org</option>
  16     <option value="https://fernbase.org">fernbase.org</option>
  17     <option value="https://solgenomics.net">solgenomics.net</option>
  18     <option value="https://www.crop-diversity.org/mgis">crop-diversity.org</option>
  19 </select>
  20
  21 <h4>Germplasm Search</h4>
  22
  23 <div id="brapi_germplasm_search_home_div" class="well">
  24
  25 <input name="brapi_germplasm_search_germplasmName" id="brapi_germplasm_search_germplasmname" class="form-control" type="text" placeholder="GermplasmName(s) e.g. TMEB419,TMEB529" />
  26 <input name="brapi_germplasm_search_accessionNumber" id="brapi_germplasm_search_accessionNumber" class="form-control" type="text" placeholder="AccessionNumber" />
  27 <input name="brapi_germplasm_search_germplasmGenus" id="brapi_germplasm_search_germplasmGenus" class="form-control" type="text" placeholder="GermplasmGenus" />
  28 <input name="brapi_germplasm_search_germplasmSpecies" id="brapi_germplasm_search_germplasmSpecies" class="form-control" type="text" placeholder="GermplasmSpecies" />
  29 <input name="brapi_germplasm_search_germplasmDbId" id="brapi_germplasm_search_germplasmDbId" class="form-control" type="text" placeholder="GermplasmDbId" />
  30 <input name="brapi_germplasm_search_germplasmPUI" id="brapi_germplasm_search_germplasmPUI" class="form-control" type="text" placeholder="GermplasmPUI" />
  31 <select name="brapi_germplasm_search_matchMethod" id="brapi_germplasm_search_matchMethod" class="form-control" />
  32     <option value="exact">Exact</option>
  33     <option value="wildcard">Wildcard. Wildcard allows % or * for multiple characters and ? for single characters.</option>
  34 </select>
  35 <br/>
  36 <button class="btn btn-primary" name="brapi_germplasm_search_submit" id="brapi_germplasm_search_submit">Search</button>
  37
  38 <br/><br/>
  39
  40 <div id="brapi_germplasm_search_result_div">
  41 </div>
  42 <div id="brapi_germplasm_search_result_div_collection">
  43 </div>
  44
  45 <div class="modal fade" id="brapi_germplasm_saved_message_modal" name="brapi_germplasm_saved_message_modal" tabindex="-1" role="dialog" aria-labelledby="brapiGermplasmSearchSavedDialog">
  46     <div class="modal-dialog" role="document">
  47         <div class="modal-content">
  48             <div class="modal-header" style="text-align: center">
  49                 <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
  50                 <h4 class="modal-title" id="brapiGermplasmSearchSavedDialog">BrAPI Germplasm Exchange</h4>
  51             </div>
  52             <div class="modal-body">
  53                 <div class="container-fluid">
  54                     <div id="brapi_germplasm_saved_message"></div>
  55                 </div>
  56             </div>
  57             <div class="modal-footer">
  58                 <button id="close_brapi_germplasm_saved_message_modal" type="button" class="btn btn-default" data-dismiss="modal">Close</button>
  59             </div>
  60         </div>
  61     </div>
  62 </div>
  63
  64 </div>
  65
  66 <script>
  67
  68 var allowed_organism_results = [];
  69
  70 jQuery(document).ready(function() {
  71     var return_url;
  72     var selected_results = [];
  73     var selected_organism_results = [];
  74
  75     jQuery("#brapi_germplasm_search_submit").click(function() {
  76         var germplasmNames = jQuery("#brapi_germplasm_search_germplasmname").val();
  77         if (germplasmNames){
  78             germplasmNames = germplasmNames.split(',');
  79         } else {
  80             germplasmNames = [];
  81         }
  82         var accessionNumbers = jQuery("#brapi_germplasm_search_accessionNumber").val();
  83         if (accessionNumbers){
  84             accessionNumbers = accessionNumbers.split(',');
  85         } else {
  86             accessionNumbers = [];
  87         }
  88         var genusNames = jQuery("#brapi_germplasm_search_germplasmGenus").val();
  89         if (genusNames){
  90             genusNames = genusNames.split(',');
  91         } else {
  92             genusNames = [];
  93         }
  94         var subtaxaNames = jQuery("#brapi_germplasm_search_germplasmSubTaxa").val();
  95         if (subtaxaNames){
  96             subtaxaNames = subtaxaNames.split(',');
  97         } else {
  98             subtaxaNames = [];
  99         }
 100         var speciesNames = jQuery("#brapi_germplasm_search_germplasmSpecies").val();
 101         if (speciesNames){
 102             speciesNames = speciesNames.split(',');
 103         } else {
 104             speciesNames = [];
 105         }
 106         var germplasmDbIds = jQuery("#brapi_germplasm_search_germplasmDbId").val();
 107         if (germplasmDbIds){
 108             germplasmDbIds = germplasmDbIds.split(',');
 109         } else {
 110             germplasmDbIds = [];
 111         }
 112         var germplasmPUIs = jQuery("#brapi_germplasm_search_germplasmPUI").val();
 113         if (germplasmPUIs){
 114             germplasmPUIs = germplasmPUIs.split(',');
 115         } else {
 116             germplasmPUIs = [];
 117         }
 118         var search_query_data = {
 119             'germplasmNames' :  germplasmNames,
 120             'accessionNumbers' : accessionNumbers,
 121             'germplasmGenus' : genusNames,
 122             'germplasmSubTaxa' : subtaxaNames,
 123             'germplasmSpecies' : speciesNames,
 124             'germplasmDbIds' : germplasmDbIds,
 125             'germplasmPUIs' : germplasmPUIs,
 126             'matchMethod' : jQuery("#brapi_germplasm_search_matchMethod").val(),
 127         };
 128         return_url = jQuery('#brapi_home_url_select').val()+'/brapi/v1/germplasm-search';
 129         jQuery.ajax( {
 130           'url': jQuery('#brapi_home_url_select').val()+'/brapi/v1/germplasm-search',
 131           'method': 'POST',
 132           'beforeSend': function(){
 133             jQuery('#working_modal').modal('show');
 134           },
 135           'data': search_query_data,
 136           'success': function(response) {
 137             //console.log(response);
 138             brapi_create_paginated_table(response.result.data, response.metadata.pagination, 'brapi_germplasm_search_result_div', return_url, { "germplasmName": ["germplasmPUI", ""] }, search_query_data, ['germplasmName','commonCropName','genus','species','accessionNumber','germplasmPUI','synonyms'], 'germplasmName', ['species']);
 139             jQuery('#working_modal').modal('hide');
 140           },
 141           error: function(response) {
 142             jQuery('#working_modal').modal('hide');
 143             alert('An error occurred');
 144           }
 145         });
 146     });
 147
 148     jQuery(document).on('click', '#brapi_table_select_submit_brapi_germplasm_search_result_div', function(){
 149         jQuery.each(jQuery('input[name="brapi_table_select_'+return_url+'"]:checked'), function(){
 150             if (jQuery.inArray(jQuery(this).val(), selected_results) == -1){
 151                 selected_results.push(jQuery(this).val());
 152             }
 153             if (jQuery.inArray(jQuery(this).data("species"), selected_organism_results) == -1){
 154                 selected_organism_results.push(jQuery(this).data("species"));
 155             }
 156         });
 157         console.log(selected_results);
 158         console.log(selected_organism_results);
 159
 160         jQuery.ajax({
 161             'url': '/ajax/accession_list/verify',
 162             'method': 'POST',
 163             'beforeSend': function(){
 164                 jQuery('#working_modal').modal('show');
 165             },
 166             'data': {
 167                 'accession_list' : JSON.stringify(selected_results),
 168                 'organism_list' : JSON.stringify(selected_organism_results),
 169                 'do_fuzzy_search' : 'true'
 170             },
 171             'success': function(response){
 172                 if(response.error){
 173                     alert(response.error);
 174                     jQuery('#working_modal').modal('hide');
 175                     return false;
 176                 }
 177                 console.log(response);
 178
 179                 var html = '<h3>How Selected Organisms Compare to This Database:</h3>';
 180                 html = html + '<table class="table table-bordered"><thead><tr><th>Species</th><th>Status</th><th>Possible Matches</th></tr></thead><tbody>';
 181                 for (var i=0; i<response.found_organisms.length; i++){
 182                     html = html + '<tr><td>' + response.found_organisms[i].unique_name + '</td><td class="bg-success">Exact Species Found in This Database</td><td>Exact Match</td></tr>';
 183                     allowed_organism_results.push(response.found_organisms[i].unique_name);
 184                 }
 185                 for (var i=0; i<response.fuzzy_organisms.length; i++){
 186                     html = html + '<tr><td>' + response.fuzzy_organisms[i].name + '</td><td class="bg-danger">Possible Species Matches Found in This Database, but Not Exact Match. Please Contact Us to Add Your Organism, or change Your Species to Match Our Species Name!</td>';
 187                     html = html + '<td><select class="form-control">'
 188                     for (var j=0; j<response.fuzzy_organisms[i].matches.length; j++){
 189                         html = html + '<option value="'+response.fuzzy_organisms[i].matches[j].name+'">'+response.fuzzy_organisms[i].matches[j].name+'</option>'
 190                     }
 191                     html = html + '</select></td></tr>';
 192                 }
 193                 for (var i=0; i<response.absent_organisms.length; i++){
 194                     html = html + '<tr><td>' + response.absent_organisms[i] + '</td><td class="bg-danger">Please Contact Us to Add Your Organism, or change Your Species to Match Our Species Name!</td><td>No Match</td></tr>';
 195                 }
 196                 html = html + '</tbody></table>';
 197
 198                 html = html + '<h3>How Selected GermplasmNames Compare to This Database:</h3>';
 199                 html = html + '<table class="table table-bordered"><thead><tr><th>Select</th><th>GermplasmName</th><th>Status</th><th>Possible Matches</th></tr></thead><tbody>';
 200                 for (var i=0; i<response.found.length; i++){
 201                     html = html + '<tr><td><input type="checkbox" name="brapi_germplasm_search_collection_select" disabled/></td><td>' + response.found[i].unique_name + '</td><td class="bg-success">Exact GermplasmName Found in This Database</td><td>Exact Match</td></tr>';
 202                 }
 203                 for (var i=0; i<response.fuzzy.length; i++){
 204                     html = html + '<tr><td><input type="checkbox" name="brapi_germplasm_search_collection_select" value="' + response.fuzzy[i].name + '"/></td><td>' + response.fuzzy[i].name + '</td><td class="bg-info">Possible GermplasmName Matches Found in This Database</td>';
 205                     html = html + '<td><select class="form-control">'
 206                     for (var j=0; j<response.fuzzy[i].matches.length; j++){
 207                         html = html + '<option value="'+response.fuzzy[i].matches[j].name+'">'+response.fuzzy[i].matches[j].name+'</option>'
 208                     }
 209                     html = html + '</select></td></tr>';
 210                 }
 211                 for (var i=0; i<response.absent.length; i++){
 212                     html = html + '<tr><td><input type="checkbox" name="brapi_germplasm_search_collection_select" value="' + response.absent[i] + '"/></td><td>' + response.absent[i] + '</td><td class="bg-warning">GermplasmName Not Found in This Database</td><td>No Match</td></tr>';
 213                 }
 214                 html = html + '</tbody></table><button class="btn btn-primary" name="brapi_germplasm_search_submit_final" id="brapi_germplasm_search_submit_final">Save in Database</button>';
 215                 jQuery('#working_modal').modal('hide');
 216                 jQuery('#brapi_germplasm_search_result_div_collection').html(html);
 217             },
 218             'error': function(response){
 219                 jQuery('#working_modal').modal('hide');
 220                 alert('An error occurred in fuzzy search!');
 221             }
 222         })
 223     });
 224
 225     jQuery(document).on('click', '#brapi_germplasm_search_submit_final', function(){
 226         jQuery('#working_modal').modal('show');
 227         var selected_to_save = [];
 228         jQuery.each(jQuery('input[name="brapi_germplasm_search_collection_select"]:checked'), function(){
 229             if (jQuery.inArray(jQuery(this).val(), selected_to_save) == -1){
 230                 selected_to_save.push(jQuery(this).val());
 231             }
 232         });
 233         console.log(selected_to_save);
 234         var to_save = [];
 235         var num_requests = selected_to_save.length;
 236         var request = 1;
 237         for (var i=0; i<num_requests; i++){
 238             jQuery.ajax({
 239                 'method':'GET',
 240                 'url': jQuery('#brapi_home_url_select').val()+'/brapi/v1/germplasm-search?matchMethod=exact&germplasmName='+selected_to_save[i],
 241                 'success': function(response){
 242                     //console.log(response);
 243                     if (jQuery.inArray(response.result.data[0].species, allowed_organism_results) == -1){
 244                         alert('Will Skip '+response.result.data[0].germplasmName+' because the species '+response.result.data[0].species+' is not in this database!');
 245                     } else {
 246                         to_save.push(response.result.data[0]);
 247                     }
 248                     if (request == num_requests){
 249                         perform_save(to_save);
 250                     }
 251                     request++;
 252                 },
 253                 'error': function(response){
 254                     alert('An error occurred getting details to save!');
 255                 }
 256             });
 257         }
 258
 259     });
 260
 261 });
 262
 263 function perform_save(to_save){
 264     console.log(to_save);
 265     jQuery.ajax({
 266         'url': '/ajax/accession_list/add',
 267         'method': 'POST',
 268         'data': {
 269             'full_info' : JSON.stringify(to_save),
 270             'allowed_organisms' : JSON.stringify(allowed_organism_results)
 271         },
 272         'success': function(response){
 273             console.log(response);
 274             if(response.error){
 275                 alert(response.error);
 276                 jQuery('#working_modal').modal('hide');
 277                 return false;
 278             }
 279             if(response.success){
 280                 var html = 'The following stocks were added!<br/>';
 281                 for (var i=0; i<response.added.length; i++){
 282                     html = html + '<a href="/stock/'+response.added[i][0]+'/view">'+response.added[i][1]+'</a><br/>';
 283                 }
 284                 jQuery('#brapi_germplasm_saved_message').html(html);
 285                 jQuery('#brapi_germplasm_saved_message_modal').modal('show');
 286             }
 287             jQuery('#working_modal').modal('hide');
 288         },
 289         'error': function(response){
 290             alert('An error occurred in fuzzy search!');
 291             jQuery('#working_modal').modal('hide');
 292         }
 293     })
 294 }
 295 </script>