mason/breeders_toolbox/add_accessions_dialogs.mas

   1 <%args>
   2 $preferred_species => ""
   3 $editable_stock_props => {}
   4 </%args>
   5
   6 <%perl>
   7     my $user_role = '';
   8     if ($c->user) {
   9         $user_role = $c->user->get_object()->get_user_type();
  10     }
  11 </%perl>
  12
  13 <div class="modal fade" id="add_accessions_dialog" name="add_accessions_dialog" tabindex="-1" role="dialog" aria-labelledby="addAccessionsDialog" data-backdrop="static" data-keyboard="false">
  14   <div class="modal-dialog modal-lg" role="document">
  15     <div class="modal-content">
  16       <div class="modal-header">
  17         <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
  18         <h4 class="modal-title" id="addAccessionsDialog">Add Accessions</h4>
  19       </div>
  20       <div class="modal-body">
  21         <div class="container-fluid">
  22
  23             <ul class="nav nav-pills nav-justified" id="add_new_accessions_tab_select">
  24                 <li class="active" id="add_new_accessions_list_tab"><a data-toggle="tab" href="#with_list_tab">Using Lists</a></li>
  25                 <li id="add_new_accessions_file_tab"><a data-toggle="tab" href="#with_file_tab">Uploading a File</a></li>
  26             </ul>
  27
  28             <div class="tab-content">
  29
  30                 <div id="with_list_tab" class="tab-pane fade in active">
  31                     <hr>
  32                     <form class="form-horizontal" role="form" name="new_accessions_form" id="new_accessions_form">
  33                         <div class="form-group">
  34                             <label class="col-sm-4 control-label">Choose a List of Accessions to Add: </label>
  35                             <div class="col-sm-8" id="list_div" name="list_div">
  36                             </div>
  37                         </div>
  38                         <div class="form-group">
  39                             <label class="col-sm-4 control-label"></label>
  40                             <div class="col-sm-8">
  41                                 <button name="lists_link" class="btn btn-info btn-sm" style="margin:6px 0px 0px 0px" type="button" >Manage Lists</button>
  42                             </div>
  43                         </div>
  44                         <div class="form-group">
  45                             <label class="col-sm-4 control-label">Use Fuzzy Search: </label>
  46                             <div class="col-sm-8">
  47 % if ( $user_role eq 'curator' ) {
  48                                 <input type="checkbox" id="fuzzy_check" name="fuzzy_check" checked></input>
  49 % } else {
  50                                 <input type="checkbox" id="fuzzy_check" name="fuzzy_check" checked disabled></input>
  51 % }
  52                                 <br/>
  53                                 <small>Note: Use the fuzzy search to match similar names to prevent uploading of duplicate accessions. Fuzzy searching is much slower than regular search. Only a curator can disable the fuzzy search.</small>
  54                             </div>
  55                         </div>
  56                     </form>
  57                 </div>
  58
  59                 <div id="with_file_tab" class="tab-pane fade">
  60                     <hr>
  61                     <&| /page/explanation.mas, title=>'Template information' &>
  62                         <p>
  63                             <b>File format information</b>
  64                             <br>
  65                             <a id="accessions_upload_spreadsheet_format_info">Spreadsheet format</a>
  66                         </p>
  67                     </&>
  68
  69                     <form class="form-horizontal" role="form" method="post" enctype="multipart/form-data" encoding="multipart/form-data" id="upload_new_accessions_form" name="upload_new_accessions_form">
  70                         <div class="form-group">
  71                             <label class="col-sm-4 control-label">Upload File: </label>
  72                             <div class="col-sm-8" >
  73                                 <input type="file" name="new_accessions_upload_file" id="new_accessions_upload_file" encoding="multipart/form-data" />
  74                             </div>
  75                         </div>
  76                         <div class="form-group">
  77                             <label class="col-sm-4 control-label">Use Fuzzy Search: </label>
  78                             <div class="col-sm-8">
  79 % if ( $user_role eq 'curator' ) {
  80                                 <input type="checkbox" id="fuzzy_check_upload_accessions" name="fuzzy_check_upload_accessions" checked></input>
  81 % } else {
  82                                 <input type="checkbox" id="fuzzy_check_upload_accessions" name="fuzzy_check_upload_accessions" checked disabled></input>
  83 % }
  84                                 <br/>
  85                                 <small>Note: Use the fuzzy search to match similar names to prevent uploading of duplicate accessions. Fuzzy searching is much slower than regular search. Only a curator can disable the fuzzy search.</small>
  86                             </div>
  87                         </div>
  88                     </form>
  89
  90                 </div>
  91
  92             </div>
  93
  94         </div>
  95       </div>
  96       <div class="modal-footer">
  97         <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>
  98         <button type="button" class="btn btn-primary" name="new_accessions_submit" id="new_accessions_submit">Continue</button>
  99       </div>
 100     </div>
 101   </div>
 102 </div>
 103
 104 <div class="modal fade" id="accessions_upload_spreadsheet_format_modal" name="accessions_upload_spreadsheet_format_modal" tabindex="-1" role="dialog" aria-labelledby="uploadAccessionsInfoDialog">
 105     <div class="modal-dialog modal-xl" role="document">
 106         <div class="modal-content">
 107             <div class="modal-header" style="text-align: center">
 108                 <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
 109                 <h4 class="modal-title" id="uploadAccessionsInfoDialog">Upload Accessions Template Information</h4>
 110             </div>
 111             <div class="modal-body">
 112                 <div class="container-fluid">
 113                     <b>Accessions may be uploaded in an Excel file (.xls)</b>
 114                     <br />
 115                     (.xlsx format not supported)
 116                     <br /><br />
 117                     <b>Header:</b>
 118                     <br>
 119                     The first row (header) should contain the following:
 120                     <br />
 121
 122                     <table class="table table-hover table-bordered table-condensed" >
 123                         <thead></thead>
 124                         <tbody>
 125                             <tr>
 126                                 <td>accession_name</td>
 127                                 <td>species_name</td>
 128                                 <td>population_name</td>
 129                                 <td>organization_name(s)</td>
 130                                 <td>synonym(s)</td>
 131 % if (exists($editable_stock_props->{'location_code'})){
 132                                 <td>location_code(s)</td>
 133 % }
 134 % if (exists($editable_stock_props->{'ploidy_level'})){
 135                                 <td>ploidy_level(s)</td>
 136 % }
 137 % if (exists($editable_stock_props->{'genome_structure'})){
 138                                 <td>genome_structure(s)</td>
 139 % }
 140 % if (exists($editable_stock_props->{'variety'})){
 141                                 <td>variety(s)</td>
 142 % }
 143 % if (exists($editable_stock_props->{'donor'})){
 144                                 <td>donor(s)</td>
 145 % }
 146 % if (exists($editable_stock_props->{'donor institute'})){
 147                                 <td>donor_institute(s)</td>
 148 % }
 149 % if (exists($editable_stock_props->{'donor PUI'})){
 150                                 <td>donor_PUI(s)</td>
 151 % }
 152 % if (exists($editable_stock_props->{'country of origin'})){
 153                                 <td>country_of_origin(s)</td>
 154 % }
 155 % if (exists($editable_stock_props->{'state'})){
 156                                 <td>state(s)</td>
 157 % }
 158 % if (exists($editable_stock_props->{'institute code'})){
 159                                 <td>institute_code(s)</td>
 160 % }
 161 % if (exists($editable_stock_props->{'institute name'})){
 162                                 <td>institute_name(s)</td>
 163 % }
 164 % if (exists($editable_stock_props->{'biological status of accession code'})){
 165                                 <td>biological_status_of_accession_code(s)</td>
 166 % }
 167 % if (exists($editable_stock_props->{'notes'})){
 168                                 <td>notes(s)</td>
 169 % }
 170 % if (exists($editable_stock_props->{'accession number'})){
 171                                 <td>accession_number(s)</td>
 172 % }
 173 % if (exists($editable_stock_props->{'PUI'})){
 174                                 <td>PUI(s)</td>
 175 % }
 176 % if (exists($editable_stock_props->{'seed source'})){
 177                                 <td>seed_source(s)</td>
 178 % }
 179 % if (exists($editable_stock_props->{'type of germplasm storage code'})){
 180                                 <td>type_of_germplasm_storage_code(s)</td>
 181 % }
 182 % if (exists($editable_stock_props->{'acquisition date'})){
 183                                 <td>acquisition_date(s)</td>
 184 % }
 185 % if (exists($editable_stock_props->{'transgenic'})){
 186                                 <td>transgenic</td>
 187 % }
 188 % if (exists($editable_stock_props->{'introgression_parent'})){
 189                                 <td>introgression_parent</td>
 190 % }
 191 % if (exists($editable_stock_props->{'introgression_backcross_parent'})){
 192                                 <td>introgression_backcross_parent</td>
 193 % }
 194 % if (exists($editable_stock_props->{'introgression_map_version'})){
 195                                 <td>introgression_map_version</td>
 196 % }
 197 % if (exists($editable_stock_props->{'introgression_chromosome'})){
 198                                 <td>introgression_chromosome</td>
 199 % }
 200 % if (exists($editable_stock_props->{'introgression_start_position_bp'})){
 201                                 <td>introgression_start_position_bp</td>
 202 % }
 203 % if (exists($editable_stock_props->{'introgression_end_position_bp'})){
 204                                 <td>introgression_end_position_bp</td>
 205 % }
 206                             </tr>
 207                         </tbody>
 208                     </table>
 209
 210                     <b>Required fields:</b>
 211                     <ul>
 212                     <li>accession_name (must be unique)</li>
 213                     <li>species_name (must exist in the database)</li>
 214                     </ul>
 215                     <b>Optional fields:</b>
 216                     <ul>
 217                     <li>population_name (a population is a grouping of accessions. if the population already exists in the database, the accession will be added into it, otherwise, the new population will be created.)</li>
 218                     <li>organization_names (the name(s) of the organization(s) which use this accession. multiple organizations can be given with comma separation (e.g. NARO,IITA))</li>
 219                     <li>synonyms (an accession can be known by many names including local popular names. a synonym name can be used instead of the accession_name throughout the database; because of this, synonyms must themselves be unique. multiple synonyms can be given with comma separation (e.g. accession_synonym1,accession_synonym001))</li>
 220 % if (exists($editable_stock_props->{'location_code'})){
 221                     <li>location_code(s) (location code(s) for the accession. many can be uploaded at once in comma separated list)</li>
 222 % }
 223 % if (exists($editable_stock_props->{'ploidy_level'})){
 224                     <li>ploidy_level(s) (a number indicating the ploidy (e.g. 2 for diploid, 3 for triploid), numeric. many values can be uploaded as comma separated list.)</li>
 225 % }
 226 % if (exists($editable_stock_props->{'genome_structure'})){
 227                     <li>genome_structure(s) (genome structure(s) for accession which take into account ploidy and ancestral genome info e.g. AAA, AB. many can be uploaded as comma separated list.)</li>
 228 % }
 229 % if (exists($editable_stock_props->{'variety'})){
 230                     <li>variety(s) (variety can be defined as a group of individuals or plants having similar traits that can be reproduced "true to type" from generation to generation. may be uploaded as comma separated list.)</li>
 231 % }
 232 % if (exists($editable_stock_props->{'donor'})){
 233                     <li>donor(s) (the accession_name of the donor accession. may be uploaded as comma separated list.)</li>
 234 % }
 235 % if (exists($editable_stock_props->{'donor institute'})){
 236                     <li>donor_institute(s) (the institute of the donor accession. may be uploaded as comma separated list.)</li>
 237 % }
 238 % if (exists($editable_stock_props->{'donor PUI'})){
 239                     <li>donor_PUI(s) (the permanent unique identifier of the donor accession. may be uploaded as comma separated list.)</li>
 240 % }
 241 % if (exists($editable_stock_props->{'country of origin'})){
 242                     <li>country_of_origin(s) (the country of origin. may be uploaded as comma separated list.)</li>
 243 % }
 244 % if (exists($editable_stock_props->{'state'})){
 245                     <li>state(s) (the state of origin. may be uploaded as comma separated list.)</li>
 246 % }
 247 % if (exists($editable_stock_props->{'institute code'})){
 248                     <li>institute_code(s) (the institute code of origin. may be uploaded as comma separated list.)</li>
 249 % }
 250 % if (exists($editable_stock_props->{'institute name'})){
 251                     <li>institute_name(s) (the institute name of origin. may be uploaded as comma separated list.)</li>
 252 % }
 253 % if (exists($editable_stock_props->{'biological status of accession code'})){
 254                     <li>biological_status_of_accession_code(s) (code indicating the state of accession. may be uploaded as comma separated list.)</li>
 255 % }
 256 % if (exists($editable_stock_props->{'notes'})){
 257                     <li>notes(s) (free text for notes. may be uploaded as comma separated list.)</li>
 258 % }
 259 % if (exists($editable_stock_props->{'accession number'})){
 260                     <li>accession_number(s) (accession number for accession from germplasm bank. may be uploaded as comma separated list.)</li>
 261 % }
 262 % if (exists($editable_stock_props->{'PUI'})){
 263                     <li>PUI(s) (permanent unique identifier of the accession. may be uploaded as comma separated list.)</li>
 264 % }
 265 % if (exists($editable_stock_props->{'seed source'})){
 266                     <li>seed_source(s) (origin of seed source. may be uploaded as comma separated list.)</li>
 267 % }
 268 % if (exists($editable_stock_props->{'type of germplasm storage code'})){
 269                     <li>type_of_germplasm_storage_code(s) (code indicating the type of germplasm storage. may be uploaded as comma separated list.)</li>
 270 % }
 271 % if (exists($editable_stock_props->{'acquisition date'})){
 272                     <li>acquisition_date(s) (date(s) of acquisition YYYYMMDD for accession. may be uploaded as comma separated list.)</li>
 273 % }
 274 % if (exists($editable_stock_props->{'transgenic'})){
 275                     <li>transgenic (indicates if accession is transgenic. Please indicate 1 if transgenic and empty if otherwise.)</li>
 276 % }
 277 % if (exists($editable_stock_props->{'introgression_parent'})){
 278                     <li>introgression_parent (if the accession you are adding has an introgression that originated from one of the parents, you can specify the parent here)</li>
 279 % }
 280 % if (exists($editable_stock_props->{'introgression_backcross_parent'})){
 281                     <li>introgression_backcross_parent (the backcross parent for introducing an introgression into the accession being added)</li>
 282 % }
 283 % if (exists($editable_stock_props->{'introgression_map_version'})){
 284                     <li>introgression_map_version (the map version for identifying the start and stop position of the introgression. e.g. AGPv2)</li>
 285 % }
 286 % if (exists($editable_stock_props->{'introgression_chromosome'})){
 287                     <li>introgression_chromosome (the chromosome number that the introgression is on.)</li>
 288 % }
 289 % if (exists($editable_stock_props->{'introgression_start_position_bp'})){
 290                     <li>introgression_start_position_bp (the start position of the introgression in base pairs)</li>
 291 % }
 292 % if (exists($editable_stock_props->{'introgression_end_position_bp'})){
 293                     <li>introgression_start_position_bp (the end position of the introgression in base pairs)</li>
 294 % }
 295                     </ul>
 296                 </div>
 297             </div>
 298             <div class="modal-footer">
 299                 <button id="close_trial_upload_dialog" type="button" class="btn btn-default" data-dismiss="modal">Close</button>
 300             </div>
 301         </div>
 302     </div>
 303 </div>
 304
 305 <div class="modal fade" id="review_absent_dialog" name="review_absent_dialog" tabindex="-1" role="dialog" aria-labelledby="reviewAbsentDialog" data-backdrop="static" data-keyboard="false">
 306   <div class="modal-dialog modal-xl" role="document">
 307     <div class="modal-content ui-front">
 308       <div class="modal-header">
 309         <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
 310         <h4 class="modal-title" id="reviewAbsentDialog">Accessions to be Added</h4>
 311       </div>
 312       <div class="modal-body">
 313         <div class="container-fluid">
 314             <div id="add_accessions_using_list_inputs" style="display:none">
 315                 <label for="species_name_input">Species name for added accessions</label>
 316                 <input class="form-control" type="text" id="species_name_input" value="<% $preferred_species %>"></input>
 317                 <br><br>
 318                 <label for="population_name_input">Population name for added accessions (optional)</label>
 319                 <input class="form-control" type="text" id="population_name_input"></input>
 320                 <br><br>
 321                 <label for="organization_name_input">Organization name for added accessions (optional)</label>
 322                 <input class="form-control" type="text" id="organization_name_input"></input>
 323                 <br><br>
 324                 <b>The following accessions are new and will be added to the database:</b>
 325                 <div id="count_of_absent_accessions"></div>
 326                 <br>
 327                 <div id="view_absent"></div>
 328             </div>
 329             <div id="view_infoToAdd"></div>
 330         </div>
 331       </div>
 332       <div class="modal-footer">
 333         <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>
 334         <button type="button" class="btn btn-primary" name="review_absent_accessions_submit" id="review_absent_accessions_submit">Add Accessions</button>
 335       </div>
 336     </div>
 337   </div>
 338 </div>
 339
 340 <div class="modal fade" id="review_fuzzy_matches_dialog" name="review_fuzzy_matches_dialog" tabindex="-1" role="dialog" aria-labelledby="reviewFuzzyDialog" data-backdrop="static" data-keyboard="false">
 341   <div class="modal-dialog modal-xl" role="document">
 342     <div class="modal-content">
 343       <div class="modal-header">
 344         <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
 345         <h4 class="modal-title" id="reviewFuzzyDialog">Fuzzy Matches</h4>
 346       </div>
 347       <div class="modal-body">
 348         <div class="container-fluid">
 349           <b>Accessions were found with similar names.</b>
 350           <br/><br/>
 351           <div id="view_fuzzy_matches"></div>
 352         </div>
 353       </div>
 354       <div class="modal-footer">
 355         <button type="button" class="btn btn-default" name="review_fuzzy_matches_download" id="review_fuzzy_matches_download">Download Fuzzy Matches</button>
 356         <button type="button" class="btn btn-primary" name="review_fuzzy_matches_continue" id="review_fuzzy_matches_continue" data-dismiss="modal">Make Changes and Continue</button>
 357       </div>
 358     </div>
 359   </div>
 360 </div>
 361
 362 <div class="modal fade" id="review_found_matches_dialog" name="review_found_matches_dialog" tabindex="-1" role="dialog" aria-labelledby="reviewFoundDialog" data-backdrop="static" data-keyboard="false">
 363   <div class="modal-dialog modal-xl" role="document">
 364     <div class="modal-content">
 365       <div class="modal-header">
 366         <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
 367         <h4 class="modal-title" id="reviewFoundDialog">Found Accessions</h4>
 368       </div>
 369       <div class="modal-body">
 370         <div class="container-fluid">
 371           <b>The following accessions already exist in the database:</b>
 372           <div id="count_of_found_accessions"></div>
 373           <br/>
 374           <div id="view_found_matches"></div>
 375         </div>
 376       </div>
 377       <div class="modal-footer">
 378         <button type="button" class="btn btn-primary" name="review_found_matches_hide" id="review_found_matches_hide" data-dismiss="modal">Continue</button>
 379       </div>
 380     </div>
 381   </div>
 382 </div>
 383
 384 <div class="modal fade" id="add_accessions_saved_message_modal" name="add_accessions_saved_message_modal" tabindex="-1" role="dialog" aria-labelledby="addAccessionsSavedDialog">
 385     <div class="modal-dialog" role="document">
 386         <div class="modal-content">
 387             <div class="modal-header" style="text-align: center">
 388                 <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
 389                 <h4 class="modal-title" id="addAccessionsSavedDialog">Accessions Saved</h4>
 390             </div>
 391             <div class="modal-body">
 392                 <div class="container-fluid">
 393                     <div id="add_accessions_saved_message"></div>
 394                 </div>
 395             </div>
 396             <div class="modal-footer">
 397                 <button id="close_add_accessions_saved_message_modal" type="button" class="btn btn-default" data-dismiss="modal">Close</button>
 398             </div>
 399         </div>
 400     </div>
 401 </div>
 402
 403 <form id="add_accession_fuzzy_match_download" method="post" action="/ajax/accession_list/fuzzy_download" target="TheWindow">
 404     <input type="hidden" name="fuzzy_response" value="" />
 405 </form>
 406
 407 <style>
 408 .ui-autocomplete {
 409   max-height: 100px;
 410   overflow-y: auto;
 411   /* prevent horizontal scrollbar */
 412   overflow-x: hidden;
 413 }
 414
 415 /* IE 6 doesn't support max-height
 416 * we use height instead, but this forces the menu to always be this tall
 417 */
 418 * html .ui-autocomplete {
 419   height: 100px;
 420 }
 421 </style>