mason/breeders_toolbox/add_accessions_dialogs.mas

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