mason/brapiclient/phenotypes_search.mas

   1 <%args>
   2 </%args>
   3
   4 <& /util/import_javascript.mas, classes => [ 'brapi.Table' ] &>
   5
   6 <& /page/page_title.mas, title=>"Phenotype Retrieval" &>
   7
   8 <h4>Database Select</h4>
   9 <select name="brapi_home_phenotypes_url_select" id="brapi_home_phenotypes_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>Phenotype Search</h4>
  22
  23 <div id="brapi_home_phenotype_search_div" class="well">
  24
  25     <input name="brapi_home_phenosearch_germplasmDbIds" id="brapi_home_phenosearch_germplasmDbIds" class="form-control" type="text" placeholder="GermplasmDbIds e.g. 139" />
  26     <input name="brapi_home_phenosearch_studyDbIds" id="brapi_home_phenosearch_studyDbIds" class="form-control" type="text" placeholder="StudyDbIds e.g. 139,137" />
  27     <input name="brapi_home_phenosearch_observationVariableDbIds" id="brapi_home_phenoseach_observationVariableDbIds" class="form-control" type="text" placeholder="ObservationDbIds e.g. 70741,70666,70773" />
  28     <input name="brapi_home_phenosearch_locationDbIds" id="brapi_home_phenosearch_locationDbIds" class="form-control" type="text" placeholder="LocationDbIds e.g. 23" value="23"/>
  29     <input name="brapi_home_phenosearch_years" id="brapi_home_phenosearch_years" class="form-control" type="text" placeholder="Years e.g. 2014,2015" />
  30     <select name="brapi_home_phenosearch_observations_level" id="brapi_home_phenosearch_observations_level" class="form-control" />
  31         <option value="all">All</option>
  32         <option value="plot">Plot</option>
  33         <option value="plant">Plant</option>
  34     </select>
  35     <br/>
  36     <button class="btn btn-primary" name="brapi_home_phenosearch_submit" id="brapi_home_phenosearch_submit">Search Phenotypes</button>
  37     <br/><br/>
  38     <div id="brapi_phenosearch_data_result_div">
  39     </div>
  40
  41 </div>
  42
  43 <br/>
  44 <h4>Phenotypes For a Study in Table Format</h4>
  45
  46 <div id="brapi_home_phenotype_study_table_div" class="well">
  47
  48     <select name="brapi_phenotype_studies_table_format" id="brapi_phenotype_studies_table_format" class="form-control" />
  49         <option value="csv">CSV</option>
  50         <option value="tsv">TSV</option>
  51         <option value="xls">Excel (xls)</option>
  52         <option value="json">JSON</option>
  53     </select>
  54
  55     <div id="brapi_home_phenotype_study_table_studies_div">
  56     </div>
  57
  58     <div id="brapi_pheno_studies_table_data_result_div">
  59     </div>
  60
  61 </div>
  62
  63 <br/>
  64 <h4>Phenotypes For a Study in ObservationUnits Format</h4>
  65
  66 <div id="brapi_home_phenotype_study_observation_units_div" class="well">
  67
  68     <div id="brapi_home_phenotype_study_observation_units_studies_div">
  69     </div>
  70
  71     <div id="brapi_pheno_studies_observation_units_data_result_div">
  72     </div>
  73
  74 </div>
  75
  76 <br/>
  77 <h4>Phenotypes For a Study in Granular Format</h4>
  78
  79 <div id="brapi_home_phenotype_study_granular_div" class="well">
  80
  81     <div id="brapi_home_phenotype_study_granular_studies_div">
  82     </div>
  83
  84     <div id="brapi_pheno_studies_granular_data_result_div">
  85     </div>
  86
  87 </div>
  88
  89 <script>
  90
  91 var selected_results = [];
  92 var studies_return_url;
  93
  94 jQuery(document).ready(function() {
  95
  96     brapi_phenotypes_get_studies(jQuery('#brapi_home_phenotypes_url_select').val(), 'brapi_home_phenotype_study_table_studies_div');
  97     brapi_phenotypes_get_studies(jQuery('#brapi_home_phenotypes_url_select').val(), 'brapi_home_phenotype_study_observation_units_studies_div');
  98     brapi_phenotypes_get_studies(jQuery('#brapi_home_phenotypes_url_select').val(), 'brapi_home_phenotype_study_granular_studies_div');
  99
 100     jQuery('#brapi_home_phenotypes_url_select').change(function(){
 101         brapi_phenotypes_get_studies(jQuery('#brapi_home_phenotypes_url_select').val(), 'brapi_home_phenotype_study_table_studies_div');
 102         brapi_phenotypes_get_studies(jQuery('#brapi_home_phenotypes_url_select').val(), 'brapi_home_phenotype_study_observation_units_studies_div');
 103         brapi_phenotypes_get_studies(jQuery('#brapi_home_phenotypes_url_select').val(), 'brapi_home_phenotype_study_granular_studies_div');
 104     });
 105
 106     jQuery("#brapi_home_phenosearch_submit").click(function() {
 107
 108         var observationVariableDbIds = jQuery('#brapi_home_phenosearch_observationVariableDbIds').val();
 109         if (observationVariableDbIds){
 110             observationVariableDbIds = observationVariableDbIds.split(',');
 111         } else {
 112             observationVariableDbIds = [];
 113         }
 114         var germplasmDbIds = jQuery('#brapi_home_phenosearch_germplasmDbIds').val();
 115         if (germplasmDbIds){
 116             germplasmDbIds = germplasmDbIds.split(',');
 117         } else {
 118             germplasmDbIds = [];
 119         }
 120         var studyDbIds = jQuery('#brapi_home_phenosearch_studyDbIds').val();
 121         if (studyDbIds){
 122             studyDbIds = studyDbIds.split(',');
 123         } else {
 124             studyDbIds = [];
 125         }
 126         var locationDbIds = jQuery('#brapi_home_phenosearch_locationDbIds').val();
 127         if (locationDbIds){
 128             locationDbIds = locationDbIds.split(',');
 129         } else {
 130             locationDbIds = [];
 131         }
 132         var seasonDbIds = jQuery('#brapi_home_phenosearch_years').val();
 133         if (seasonDbIds){
 134             seasonDbIds = seasonDbIds.split(',');
 135         } else {
 136             seasonDbIds = [];
 137         }
 138
 139         var return_url = jQuery('#brapi_home_phenotypes_url_select').val()+'/brapi/v1/phenotypes-search';
 140         jQuery.ajax( {
 141           'url': return_url,
 142           'data' : {
 143             'observationVariableDbIds':observationVariableDbIds,
 144             'germplasmDbIds':germplasmDbIds,
 145             'observationLevel':jQuery('#brapi_home_phenosearch_observations_level').val(),
 146             'studyDbIds':studyDbIds,
 147             'locationDbIds':locationDbIds,
 148             'seasonDbIds':seasonDbIds
 149           },
 150           'method': 'POST',
 151           'beforeSend': function() {
 152             jQuery('#working_modal').modal('show');
 153           },
 154           'success': function(response) {
 155             jQuery('#working_modal').modal('hide');
 156             console.log(response);
 157             brapi_create_paginated_table(response.result.data, response.metadata.pagination, 'brapi_phenosearch_data_result_div', return_url, undefined, {}, ['observationUnitName','replicate','germplasmName','blockNumber', 'X', 'Y', 'entryType', 'studyName','studyLocation','observationLevel','observations'], 'observationUnitName', []);
 158
 159           },
 160           error: function(response) {
 161             jQuery('#working_modal').modal('hide');
 162             alert('An error occurred');
 163           }
 164         });
 165     });
 166
 167     jQuery(document).on('click', '#brapi_table_select_submit_brapi_home_phenotype_study_table_studies_div', function(){
 168         jQuery.each(jQuery('input[name="brapi_table_select_'+studies_return_url+'"]:checked'), function(){
 169             if (jQuery.inArray(jQuery(this).val(), selected_results) == -1){
 170                 selected_results.push(jQuery(this).val());
 171             }
 172         });
 173         console.log(selected_results);
 174
 175         var format = jQuery('#brapi_phenotype_studies_table_format').val();
 176         var return_url = jQuery('#brapi_home_phenotypes_url_select').val()+'/brapi/v1/studies/'+selected_results[0]+'/table?format='+format;
 177         jQuery.ajax( {
 178             'url': return_url,
 179             'beforeSend': function(){
 180                 jQuery('#working_modal').modal('show');
 181             },
 182             'success': function(response) {
 183                 //console.log(response);
 184                 if (response.metadata.datafiles.length > 0){
 185                     var html = "<h4>Download Study Phenotype File(s) From Here: <br/>";
 186                     for (var j=0; j<response.metadata.datafiles.length; j++){
 187                         html = html + "<a href='"+response.metadata.datafiles[j]+"'>"+response.metadata.datafiles[j]+"</a><br/>";
 188                     }
 189                     jQuery('#brapi_pheno_studies_table_data_result_div').html(html);
 190                 } else {
 191                     brapi_create_paginated_table(response.result.data, response.metadata.pagination, 'brapi_pheno_studies_table_data_result_div', return_url, undefined, {}, ['headerRow','observationVariableDbIds','observationVariableNames','data'], 'observationVariableNames', []);
 192                 }
 193                 jQuery('#working_modal').modal('hide');
 194             },
 195             error: function(response) {
 196                 jQuery('#working_modal').modal('hide');
 197                 alert('An error occurred');
 198             }
 199         });
 200
 201     });
 202
 203     jQuery(document).on('click', '#brapi_table_select_submit_brapi_home_phenotype_study_observation_units_studies_div', function(){
 204         jQuery.each(jQuery('input[name="brapi_table_select_'+studies_return_url+'"]:checked'), function(){
 205             if (jQuery.inArray(jQuery(this).val(), selected_results) == -1){
 206                 selected_results.push(jQuery(this).val());
 207             }
 208         });
 209         console.log(selected_results);
 210
 211         var return_url = jQuery('#brapi_home_phenotypes_url_select').val()+'/brapi/v1/studies/'+selected_results[0]+'/observationunits';
 212         jQuery.ajax( {
 213             'url': return_url,
 214             'beforeSend': function(){
 215                 jQuery('#working_modal').modal('show');
 216             },
 217             'success': function(response) {
 218                 //console.log(response);
 219                 if (response.metadata.datafiles.length > 0){
 220                     var html = "<h4>Download Study Phenotype File(s) From Here: <br/>";
 221                     for (var j=0; j<response.metadata.datafiles.length; j++){
 222                         html = html + "<a href='"+response.metadata.datafiles[j]+"'>"+response.metadata.datafiles[j]+"</a><br/>";
 223                     }
 224                     jQuery('#brapi_pheno_studies_observation_units_data_result_div').html(html);
 225                 } else {
 226                     brapi_create_paginated_table(response.result.data, response.metadata.pagination, 'brapi_pheno_studies_observation_units_data_result_div', return_url, undefined, {}, ['observationUnitName','replicate','germplasmName','blockNumber', 'X', 'Y', 'entryType', 'plotNumber','observations'], 'observationUnitName', []);
 227                 }
 228                 jQuery('#working_modal').modal('hide');
 229             },
 230             error: function(response) {
 231                 jQuery('#working_modal').modal('hide');
 232                 alert('An error occurred');
 233             }
 234         });
 235
 236     });
 237
 238     jQuery(document).on('click', '#brapi_table_select_submit_brapi_home_phenotype_study_granular_studies_div', function(){
 239         jQuery.each(jQuery('input[name="brapi_table_select_'+studies_return_url+'"]:checked'), function(){
 240             if (jQuery.inArray(jQuery(this).val(), selected_results) == -1){
 241                 selected_results.push(jQuery(this).val());
 242             }
 243         });
 244         console.log(selected_results);
 245
 246         var return_url = jQuery('#brapi_home_phenotypes_url_select').val()+'/brapi/v1/studies/'+selected_results[0]+'/observations';
 247         jQuery.ajax( {
 248             'url': return_url,
 249             'beforeSend': function(){
 250                 jQuery('#working_modal').modal('show');
 251             },
 252             'success': function(response) {
 253                 //console.log(response);
 254                 if (response.metadata.datafiles.length > 0){
 255                     var html = "<h4>Download Study Phenotype File(s) From Here: <br/>";
 256                     for (var j=0; j<response.metadata.datafiles.length; j++){
 257                         html = html + "<a href='"+response.metadata.datafiles[j]+"'>"+response.metadata.datafiles[j]+"</a><br/>";
 258                     }
 259                     jQuery('#brapi_pheno_studies_granular_data_result_div').html(html);
 260                 } else {
 261                     brapi_create_paginated_table(response.result.data, response.metadata.pagination, 'brapi_pheno_studies_granular_data_result_div', return_url, undefined, {}, ['observationUnitName','observationLevel','observationDbId','observationVariableName','germplasmName','observationTimestamp', 'operator', 'value'], 'observationDbId', []);
 262                 }
 263                 jQuery('#working_modal').modal('hide');
 264             },
 265             error: function(response) {
 266                 jQuery('#working_modal').modal('hide');
 267                 alert('An error occurred');
 268             }
 269         });
 270
 271     });
 272
 273 });
 274
 275
 276 function brapi_phenotypes_get_studies(url, div_id) {
 277     studies_return_url = url+'/brapi/v1/studies-search';
 278     jQuery.ajax( {
 279         'url': url+'/brapi/v1/studies-search',
 280         'beforeSend': function(){
 281             jQuery('#working_modal').modal('show');
 282         },
 283         'success': function(response) {
 284             //console.log(response);
 285             brapi_create_paginated_table(response.result.data, response.metadata.pagination, div_id, studies_return_url, undefined, {}, ['studyName','trialName','programName','locationName'], 'studyDbId', []);
 286             jQuery('#working_modal').modal('hide');
 287         },
 288         error: function(response) {
 289             jQuery('#working_modal').modal('hide');
 290             alert('An error occurred');
 291         }
 292     });
 293 }
 294
 295 </script>