mason/breeders_toolbox/upload_nirs_spreadsheet.mas

   1
   2 <%args>
   3 </%args>
   4
   5 <& /util/import_javascript.mas, classes => [ 'jquery', 'jqueryui', 'jquery.iframe-post-form', 'CXGN.BreedersToolbox.UploadPhenotype', 'CXGN.BreederSearch', 'CXGN.Trial' ] &>
   6
   7 <div class="modal fade" id="upload_phenotype_spreadsheet_dialog" name="upload_phenotype_spreadsheet_dialog" tabindex="-1" role="dialog" aria-labelledby="addSpreadsheetNIRSDialog">
   8   <div class="modal-dialog" role="document">
   9     <div class="modal-content">
  10       <div class="modal-header">
  11         <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
  12         <h4 class="modal-title" id="addSpreadsheetNIRSDialog">Upload NIRS Spreadsheet</h4>
  13       </div>
  14       <div class="modal-body">
  15         <div class="container-fluid">
  16
  17             <&| /page/explanation.mas, title=>'Template Information' &>
  18                 <p>
  19                 <b>File format information</b>
  20                 <br>
  21                 <a id="phenotype_upload_spreadsheet_format_info">Spreadsheet Format</a>
  22                 </p>
  23             </&>
  24
  25             <form class="form-horizontal" role="form" method="post" enctype="multipart/form-data" encoding="multipart/form-data" id="upload_spreadsheet_phenotype_file_form" name="upload_spreadsheet_phenotype_file_form">
  26                 <div class="form-group">
  27                     <label class="col-sm-3 control-label">Spreadsheet Format: </label>
  28                     <div class="col-sm-9" >
  29                         <select class="form-control" id="upload_spreadsheet_phenotype_file_format" name="upload_spreadsheet_phenotype_file_format">
  30                             <option value="nirs">Simple NIRS</option>
  31                             <option value="scio">SCiO NIRS</option>
  32                         </select>
  33                     </div>
  34                 </div>
  35                 <div class="form-group">
  36                     <label class="col-sm-3 control-label">Timestamps Included: </label>
  37                     <div class="col-sm-9" >
  38                         <input type="checkbox" id="upload_spreadsheet_phenotype_timestamp_checkbox" name="upload_spreadsheet_phenotype_timestamp_checkbox" />
  39                     </div>
  40                 </div>
  41                 <div id="upload_spreadsheet_phenotype_data_level_div">
  42                     <div class="form-group">
  43                         <label class="col-sm-3 control-label">Data Level: </label>
  44                         <div class="col-sm-9" >
  45                             <select class="form-control" id="upload_spreadsheet_phenotype_data_level" name="upload_spreadsheet_phenotype_data_level">
  46                                 <option value="plots">Plots</option>
  47                                 <option value="plants">Plants</option>
  48                                 <option value="subplots">Subplots</option>
  49                                 <option value="tissue_samples">Tissue Samples</option>
  50                             </select>
  51                         </div>
  52                     </div>
  53                 </div>
  54                 <div class="form-group">
  55                     <label class="col-sm-3 control-label">NIRS Spreadsheet: </label>
  56                     <div class="col-sm-9" >
  57                         <input type="file" id="upload_spreadsheet_phenotype_file_input" name="upload_spreadsheet_phenotype_file_input" encoding="multipart/form-data" />
  58                     </div>
  59                 </div>
  60
  61
  62                 <div id="upload_phenotype_spreadsheet_verify_status"></div>
  63                 </div>
  64             </form><br/>
  65
  66         </div>
  67
  68         <div class="modal-footer">
  69             <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>
  70             <button type="button" class="btn btn-info" name="upload_spreadsheet_phenotype_submit_verify" id="upload_spreadsheet_phenotype_submit_verify">Verify</button>
  71             <button disabled type="button" class="btn btn-primary" name="upload_spreadsheet_phenotype_submit_store" id="upload_spreadsheet_phenotype_submit_store" title="First Verify Your File">Store</button>
  72         </div>
  73
  74     </div>
  75   </div>
  76 </div>
  77
  78 <div class="modal fade" id="phenotype_upload_spreadsheet_info_dialog" name="phenotype_upload_spreadsheet_info_dialog" tabindex="-1" role="dialog" aria-labelledby="phenotypeUploadInfoDialog">
  79   <div class="modal-dialog" role="document">
  80     <div class="modal-content">
  81       <div class="modal-header">
  82         <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
  83         <h4 class="modal-title" id="phenotypeUploadInfoDialog">Template Information</h4>
  84       </div>
  85       <div class="modal-body">
  86         <div class="container-fluid">
  87
  88             <h5>There are two possible formats for uploading NIRS data</h5>
  89
  90             <h3>Simple NIRS .xls:</h3>
  91             <ul>
  92                 <li>The simple nirs spreadsheet format is built on top of the simple phenotype format.</li>
  93                 <li>It consists of a column called 'observationunit_name' followed by trait columns derived from the NIR spectra, followed by columns of NIR spectra data themselves.</li>
  94                 <li>Trait column names must come from the trait ontology, but NIR spectra column names should simply be copied from whateve standard output file the NIR device produces.</li>
  95                 <li><a href="https://docs.google.com/spreadsheets/d/1bPsM71mrw8I2ffg6xQo8PC5nDgSz_IzTml3JVb5FWwE/edit?usp=sharing">Simple NIRS .xls template</a></li>
  96             </ul>
  97
  98             <h3>SCIO NIRS .csv:</h3>
  99             <ul>
 100                 <li>The SCIO nirs spreadsheet format is generated when doing a direct download from the SCIO server.</li>
 101                 <li>It consists of a series of metadata fields at the beginning of the file, followed by a header for all of the individual measurements, followed by a row for each of the individual measurements themselves.</li>
 102                 <li>The User_input_id field must be a valid observation_unit in the database.</li>
 103                 <li><a href="https://docs.google.com/spreadsheets/d/17_egaPcoTyf6mtZ9xIyNnm4vgdci2TbK5sJ67ySR5Hw/edit?usp=sharing">SCIO NIRS .csv template</a></li>
 104             </ul>
 105         </div>
 106       </div>
 107       <div class="modal-footer">
 108         <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>
 109       </div>
 110     </div>
 111   </div>
 112 </div>
 113
 114
 115 <script defer="defer">
 116
 117 jQuery(document).ready(function() {
 118
 119     jQuery('#upload_spreadsheet_phenotypes_link').click( function() {
 120         jQuery('#upload_phenotype_spreadsheet_dialog').modal("show");
 121     });
 122
 123     jQuery("#phenotype_upload_spreadsheet_format_info").click( function () {
 124         jQuery("#phenotype_upload_spreadsheet_info_dialog" ).modal("show");
 125     });
 126
 127 });
 128
 129 </script>