nxhtml/tests/in/josh-091115-cancer_summary.xsl

   1 <xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" version="1.0"
   2                                 xmlns:set="http://exslt.org/sets">
   3
   4   <xsl:output method="html"/>
   5   <xsl:output encoding="utf-8"/>
   6   <xsl:output doctype-system="http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"/>
   7   <xsl:output doctype-public="-//W3C//DTD XHTML 1.0 Transitional//EN"/>
   8
   9   <xsl:template match="/">
  10
  11     <html>
  12       <head>
  13         <title>Cancer Summary: <xsl:value-of select="//individual/@name"/>&#160;<xsl:value-of select="//individual/@gender"/>&#160;<xsl:value-of select="//individual/@id"/></title>
  14
  15         <link rel="shortcut icon" href="/resources/report_resources/apipe_dashboard/images/gc_favicon.png" type="image/png" />
  16
  17         <link rel="stylesheet" href="/resources/report_resources/apipe_dashboard/css/master.css" type="text/css" media="screen" />
  18         <link rel="stylesheet" href="/resources/report_resources/apipe_dashboard/css/tablesorter.css" type="text/css" media="screen" />
  19         <script type="text/javascript" src="/resources/report_resources/jquery/jquery.js"></script>
  20         <script type="text/javascript" src="/resources/report_resources/jquery/jquery.tablesorter.min.js"></script>
  21         <script type="text/javascript">
  22           $(document).ready(function() {
  23           $("#tier_1_snps").tablesorter({
  24           // sort on first column, ascending
  25           // sortList: [[0,0]]
  26           });
  27
  28           $("#tier_1_insertions").tablesorter({
  29           // sort on first column, ascending
  30           //sortList: [[0,0]]
  31           });
  32
  33           $("#tier_1_deletions").tablesorter({
  34           // sort on first column, ascending
  35           //sortList: [[0,0]]
  36           });
  37           });
  38         </script>
  39         <link rel="stylesheet" href="/resources/report_resources/cancer_card/css/zoom2.css" type="text/css" media="screen"></link>
  40         <script type="text/javascript" src="/resources/report_resources/cancer_card/js/dom-drag.js"></script>
  41
  42         <script type="text/javascript" src="/resources/report_resources/cancer_card/js/HotSpot2.js"></script>
  43         <script type="text/javascript">
  44           addEvent(window, 'load', function() {
  45           HotSpotController.init("zoomImage",300, '<xsl:value-of select="//individual/circos-images/@large"/>','ZTbutton'); });
  46
  47           function addEvent(obj, evType, fn) {
  48           if (obj.addEventListener) {
  49           obj.addEventListener(evType, fn, false);
  50           return true;
  51           } else if (obj.attachEvent) {
  52           var r = obj.attachEvent("on" + evType, fn);
  53           return r;
  54           } else {
  55           return false;
  56           }
  57           }
  58         </script>
  59
  60         <script type="text/javascript">
  61                   $(document).ready(function() {
  62                     $("input[type=checkbox]").click(function() {
  63                       alert("Clicked: " + this.value);
  64                         });
  65                   });
  66                 </script>
  67
  68         <style type="text/css" media="screen">
  69           table.info_table_group td {
  70           padding-right: 10px;
  71           }
  72
  73           div.content_padding {
  74           padding: 0 10px 20px 10px;
  75           }
  76
  77           h3.group_header {
  78           border-bottom: 2px solid #CCC;
  79           }
  80           div.circos_graph {
  81           float: left;
  82           width: 920px;
  83           }
  84
  85                   form.status_selector {
  86                     margin: 0;
  87                         padding: 0;
  88                     float: right;
  89                     font-size: 85%;
  90                     font-weight: normal;
  91                   }
  92
  93                   form.status_selector table {
  94                     margin: 0;
  95                         padding: 0;
  96                   }
  97
  98                   form.status_selector table td.lbl {
  99                   padding-right: 10px;
 100                   padding-left: 5px;
 101                   }
 102
 103
 104                   form.status_selector table td.table_lbl {
 105                     font-weight: bold;
 106                         padding-right: 8px;
 107                         padding-left: 3px;
 108                   }
 109         </style>
 110       </head>
 111
 112       <body>
 113         <div class="container">
 114           <div class="background">
 115             <div class="page_header">
 116               <table cellpadding="0" cellspacing="0" border="0">
 117                 <tr>
 118                   <td>
 119                     <img src="/resources/report_resources/apipe_dashboard/images/gc_header_logo2.png" width="44" height="45" align="absmiddle" />
 120                   </td>
 121                   <td>
 122                     <h1><xsl:value-of select="//individual/@name"/>&#160;<xsl:value-of select="//individual/@gender"/>&#160;<xsl:value-of select="//individual/@id"/>&#160;Cancer Summary</h1>
 123                   </td>
 124                 </tr>
 125               </table>
 126             </div>
 127             <div class="page_padding">
 128               <!-- <h2 class="page_title icon_instrument_data">Flow Cell <xsl:value-of select="//flow-cell/@id"/> Status</h2> -->
 129               <table cellpadding="0" cellspacing="0" border="0" class="info_table_group">
 130                 <tr>
 131                   <td>
 132                     <h3 class="group_header">Clinical Data</h3>
 133                     <table border="0" cellpadding="0" cellspacing="0">
 134                       <tr>
 135                         <td>
 136                           <table border="0" cellpadding="0" cellspacing="0" class="info_table" width="100%">
 137                             <colgroup>
 138                               <col/>
 139                               <col width="100%"/>
 140                             </colgroup>
 141                             <tr><td class="label">Name:</td><td class="value"><xsl:value-of select="//individual/@name"/></td></tr>
 142                             <tr>
 143                               <td class="label">Gender:</td>
 144                               <td class="value">
 145                                 <xsl:choose>
 146                                   <xsl:when test="string(//individual/@gender)">
 147                                     <xsl:value-of select="//individual/@gender"/>
 148                                   </xsl:when>
 149                                   <xsl:otherwise>
 150                                     Not Provided
 151                                   </xsl:otherwise>
 152                                 </xsl:choose>
 153                               </td>
 154                             </tr>
 155                             <tr><td class="label">ID:</td><td class="value"><xsl:value-of select="//individual/@id"/></td></tr>
 156
 157                           </table>
 158                         </td>
 159                         <td>
 160                           <table border="0" cellpadding="0" cellspacing="0" class="info_table" width="100%" style="float: left;">
 161                             <colgroup>
 162                               <col/>
 163                               <col width="100%"/>
 164                             </colgroup>
 165
 166                             <tr><td class="label">Year Diagnosed:</td><td class="value"><xsl:value-of select="//clinical-data/@diagnosis-year"/></td></tr>
 167                             <tr><td class="label">Diagnosed at Age:</td><td class="value"><xsl:value-of select="//clinical-data/@diagnosis-age"/></td></tr>
 168                             <xsl:choose>
 169                               <xsl:when test="//clinical-data/@alive = '1'">
 170                                 <tr><td class="label">Survived:</td><td class="value">Yes</td></tr>
 171                               </xsl:when>
 172                               <xsl:otherwise>
 173                                 <tr><td class="label">Survived:</td><td class="value">No</td></tr>
 174                                 <tr><td class="label">Days Survived:</td><td class="value"><xsl:value-of select="//clinical-data/@days-survived"/></td></tr>
 175                               </xsl:otherwise>
 176                             </xsl:choose>
 177                           </table>
 178                         </td>
 179                         <td>
 180                           <table border="0" cellpadding="0" cellspacing="0" class="info_table" width="100%" style="float: left;">
 181                             <colgroup>
 182                               <col/>
 183                               <col width="100%"/>
 184                             </colgroup>
 185
 186                             <tr><td class="label">Treatment:</td><td class="value"><xsl:value-of select="//clinical-data/@treatment"/></td></tr>
 187                             <tr><td class="label">Outcome:</td><td class="value"><xsl:value-of select="//clinical-data/@outcome"/></td></tr>
 188                             <tr><td class="label">AMP:</td><td class="value"><xsl:value-of select="//clinical-data/@amp"/></td></tr>
 189
 190                           </table>
 191                         </td>
 192                       </tr>
 193                     </table>
 194                   </td>
 195                   <td>
 196                     <h3 class="group_header">Sequencing Stats</h3>
 197                     <table border="0" cellpadding="0" cellspacing="0" class="info_table" width="100%">
 198                       <colgroup>
 199                         <col/>
 200                         <col width="100%"/>
 201                       </colgroup>
 202                       <tr><td class="label">Normal Coverage:</td><td class="value"><xsl:value-of select="//samples/sample/models/model/@normal-haploid-coverage"/>X</td></tr>
 203                       <tr><td class="label">Tumor Coverage:</td><td class="value"><xsl:value-of select="//samples/sample/models/model/@tumor-haploid-coverage"/>X</td></tr>
 204                     </table>
 205                   </td>
 206                 </tr>
 207               </table>
 208               <hr style="margin-bottom: 0;"/>
 209               <h2 class="report_section" style="margin-bottom: 0; margin-top: 0">Circos Graph&#160;&#160;&#160;<a id="ZTbutton" href="javascript: void(0);" style="font-size: 85%; font-weight: normal;">[toggle zoom]</a></h2>
 210               <p id="ZTthumbnail">
 211                 <img>
 212                   <xsl:attribute name="id">zoomImage</xsl:attribute>
 213                   <xsl:attribute name="src"><xsl:value-of select="//individual/circos-images/@small"/></xsl:attribute>
 214                   <xsl:attribute name="width">920</xsl:attribute>
 215                   <xsl:attribute name="height">920</xsl:attribute>
 216                 </img>
 217               </p>
 218               <h2 class="report_section" style="margin-bottom: 0">Tier 1 SNPs
 219 <!--                      <form class="status_selector">
 220                                 <input type="hidden" name="table" value="tier_1_snps"/>
 221                                 <table cellpadding="0" cellspacing="0">
 222                                   <tr>
 223                                         <td class="table_lbl">Show:</td>
 224                                         <xsl:for-each select="set:distinct(//variants/snps/snp/@validation-status)">
 225                                           <td class="cb">
 226                                                 <input type="checkbox"><xsl:attribute name="value"><xsl:value-of select="."/></xsl:attribute></input>
 227                                           </td>
 228                                           <td class="lbl">
 229                                                 <xsl:value-of select="."/>
 230                                           </td>
 231                                         </xsl:for-each>
 232                                   </tr>
 233                                 </table>
 234                           </form>
 235 -->
 236
 237                           </h2>
 238               <table id="tier_1_snps" class="list tablesorter" width="100%" cellspacing="0" cellpadding="0" border="0" style="margin-top: 0;">
 239                 <xsl:choose>
 240                   <xsl:when test="count(//variants/snps/snp) > 0">
 241
 242                     <thead>
 243                       <tr>
 244                         <th>validation status</th>
 245                         <th>chromosome</th>
 246                         <th class="last">start</th>
 247                         <th class="last">reference</th>
 248                         <th class="last">variant</th>
 249                         <th class="last">gene</th>
 250                         <th class="last">amino acid change</th>
 251                                                 <th class="last">trv type</th>
 252                       </tr>
 253                     </thead>
 254                     <tbody>
 255                       <xsl:for-each select="//variants/snps/snp">
 256                         <xsl:sort select="@validation-status" data-type="text" order="ascending"/>
 257                         <xsl:sort select="@chromosome" data-type="number" order="ascending"/>
 258                         <tr>
 259                                                   <td class="validation_status"><xsl:value-of select="@validation-status"/></td>
 260                                                   <td><xsl:value-of select="@chromosome"/></td>
 261                           <td class="last">
 262                                                         <xsl:variable name="start" select="@start"/><xsl:value-of select="format-number($start, '#,##0')"/>
 263                                                   </td>
 264                           <td class="last"><xsl:value-of select="@reference-allele"/></td>
 265                           <td class="last"><xsl:value-of select="@variant-allele"/></td>
 266                           <td class="last"><xsl:value-of select="@gene"/></td>
 267                           <td class="last"><xsl:value-of select="@amino-acid-change"/></td>
 268                                                   <td class="last"><xsl:value-of select="@trv-type"/></td>
 269                         </tr>
 270                       </xsl:for-each>
 271                     </tbody>
 272                   </xsl:when>
 273                   <xsl:otherwise>
 274                     <tr><td><span class="note">None found.</span></td></tr>
 275                   </xsl:otherwise>
 276                 </xsl:choose>
 277               </table>
 278
 279               <h2 class="report_section" style="margin-bottom: 0">Tier 1 Insertions</h2>
 280               <table id="tier_1_insertions" class="list tablesorter" width="100%" cellspacing="0" cellpadding="0" border="0" style="margin-top: 0;">
 281                 <xsl:choose>
 282                   <xsl:when test="count(//variants/insertions/insertion) > 0">
 283                     <thead>
 284                       <tr>
 285                                                 <th>validation status</th>
 286                         <th>chromosome</th>
 287                         <th class="last">start</th>
 288                         <th class="last">stop</th>
 289                         <th class="last">variant</th>
 290                         <th class="last">gene</th>
 291                         <th class="last">amino acid change</th>
 292                         <th class="last">trv type</th>
 293                       </tr>
 294                     </thead>
 295                     <tbody>
 296                       <xsl:for-each select="//variants/insertions/insertion">
 297                         <xsl:sort select="@validation-status" data-type="text" order="ascending"/>
 298                         <xsl:sort select="@chromosome" data-type="number" order="ascending"/>
 299                         <tr>
 300                           <td class="validation_status"><xsl:value-of select="@validation-status"/></td>
 301                           <td><xsl:value-of select="@chromosome"/></td>
 302                           <td class="last">
 303                                                         <xsl:variable name="start" select="@start"/><xsl:value-of select="format-number($start, '#,##0')"/>
 304                                                   </td>
 305                           <td class="last">
 306                                                         <xsl:variable name="stop" select="@stop"/><xsl:value-of select="format-number($stop, '#,##0')"/>
 307                                                   </td>
 308                           <td class="last"><xsl:value-of select="@variant-allele"/></td>
 309                           <td class="last"><xsl:value-of select="@gene"/></td>
 310                           <td class="last"><xsl:value-of select="@amino-acid-change"/></td>
 311                                                   <td class="last"><xsl:value-of select="@trv-type"/></td>
 312                         </tr>
 313                       </xsl:for-each>
 314                     </tbody>
 315                   </xsl:when>
 316                   <xsl:otherwise>
 317                     <tr><td><span class="note">None found.</span></td></tr>
 318                   </xsl:otherwise>
 319                 </xsl:choose>
 320               </table>
 321
 322               <h2 class="report_section" style="margin-bottom: 0">Tier 1 Deletions</h2>
 323               <table id="tier_1_deletions" class="list tablesorter" width="100%" cellspacing="0" cellpadding="0" border="0" style="margin-top: 0;">
 324                 <xsl:choose>
 325                   <xsl:when test="count(//variants/deletions/deletion) > 0">
 326                     <thead>
 327                       <tr>
 328                         <th>validation status</th>
 329                         <th>chromosome</th>
 330                         <th class="last">start</th>
 331                         <th class="last">stop</th>
 332                         <th class="last">reference</th>
 333                         <th class="last">gene</th>
 334                         <th class="last">amino acid change</th>
 335                                                 <th class="last">trv type</th>
 336                       </tr>
 337                     </thead>
 338                     <tbody>
 339                       <xsl:for-each select="//variants/deletions/deletion">
 340                         <xsl:sort select="@validation-status" data-type="text" order="ascending"/>
 341                         <xsl:sort select="@chromosome" data-type="number" order="ascending"/>
 342                         <tr>
 343                           <td class="validation_status"><xsl:value-of select="@validation-status"/></td>
 344                           <td><xsl:value-of select="@chromosome"/></td>
 345                           <td class="last">
 346                                                         <xsl:variable name="start" select="@start"/><xsl:value-of select="format-number($start, '#,##0')"/>
 347                                                   </td>
 348                           <td class="last">
 349                                                         <xsl:variable name="stop" select="@stop"/><xsl:value-of select="format-number($stop, '#,##0')"/>
 350                                                   </td>
 351                           <td class="last"><xsl:value-of select="@reference-allele"/></td>
 352                           <td class="last"><xsl:value-of select="@gene"/></td>
 353                           <td class="last"><xsl:value-of select="@amino-acid-change"/></td>
 354                                                   <td class="last"><xsl:value-of select="@trv-type"/></td>
 355                         </tr>
 356                       </xsl:for-each>
 357                     </tbody>
 358                   </xsl:when>
 359                   <xsl:otherwise>
 360                     <tr><td><span class="note">None found.</span></td></tr>
 361                   </xsl:otherwise>
 362                 </xsl:choose>
 363               </table>
 364
 365               <h2 class="report_section" style="margin-bottom: 0;">Structural Variations (translocations)</h2>
 366               <table id="sv_translocations" class="list" width="100%" cellspacing="0" cellpadding="0" border="0" style="margin-top: 0;">
 367                 <xsl:choose>
 368                   <xsl:when test="count(//structural-variants/translocations/translocation) > 0">
 369                     <thead>
 370                       <tr>
 371                         <th>validation status</th>
 372                         <th class="last">chromosome</th>
 373                         <th class="last">position</th>
 374                         <th>&#160;</th>
 375                         <th class="last">chromosome</th>
 376                         <th class="last">position</th>
 377                       </tr>
 378                     </thead>
 379                     <tbody>
 380                       <xsl:for-each select="//structural-variants/translocations/translocation">
 381                         <xsl:sort select="@validation-status" data-type="text" order="ascending"/>
 382                         <xsl:sort select="start/@chromosome" data-type="number" order="ascending"/>
 383                         <tr>
 384                           <td class="validation_status"><xsl:value-of select="@validation-status"/></td>
 385                           <td class="last"><xsl:value-of select="start/@chromosome"/></td>
 386                           <td class="last">
 387                                                         <xsl:variable name="start_position" select="start/@position"/><xsl:value-of select="format-number($start_position, '#,##0')"/>
 388                                                   </td>
 389
 390                           <td class="last"><span style="font-size: 100%; font-weight: bold;">&#8594;</span></td>
 391
 392                           <td class="last"><xsl:value-of select="stop/@chromosome"/></td>
 393                           <td class="last">
 394                                                         <xsl:variable name="stop_position" select="stop/@position"/><xsl:value-of select="format-number($stop_position, '#,##0')"/>
 395                                                   </td>
 396                         </tr>
 397                       </xsl:for-each>
 398                     </tbody>
 399                   </xsl:when>
 400                   <xsl:otherwise>
 401                     <tr><td><span class="note">None found.</span></td></tr>
 402                   </xsl:otherwise>
 403                 </xsl:choose>
 404               </table>
 405
 406               <h2 class="report_section" style="margin-bottom: 0;">Structural Variations (insertions)</h2>
 407               <table id="sv_insertions" class="list" width="100%" cellspacing="0" cellpadding="0" border="0" style="margin-top: 0;">
 408                 <tbody>
 409                   <xsl:choose>
 410                     <xsl:when test="count(//structural-variants/insertions/insertion) > 0">
 411                       <thead>
 412                         <tr>
 413                                                   <th>validation status</th>
 414                           <th class="last">chromosome</th>
 415                           <th class="last">start</th>
 416                           <th class="last">stop</th>
 417                           <th class="last">size</th>
 418                         </tr>
 419                       </thead>
 420                       <xsl:for-each select="//structural-variants/insertions/insertion">
 421                         <xsl:sort select="@validation-status" data-type="number" order="ascending"/>
 422                         <xsl:sort select="start/@chromosome" data-type="number" order="ascending"/>
 423                         <tr>
 424                           <td class="validation_status"><xsl:value-of select="@validation-status"/></td>
 425                           <td class="last"><xsl:value-of select="start/@chromosome"/></td>
 426                           <td class="last">
 427                                                         <xsl:variable name="start_position" select="start/@position"/><xsl:value-of select="format-number($start_position, '#,##0')"/>
 428                                                   </td>
 429                           <td class="last">
 430                                                         <xsl:variable name="stop_position" select="stop/@position"/><xsl:value-of select="format-number($stop_position, '#,##0')"/>
 431                                                   </td>
 432                                                   <xsl:variable name="size" select="@size"/><xsl:value-of select="format-number($size, '#,##0')"/>
 433
 434                         </tr>
 435                       </xsl:for-each>
 436                     </xsl:when>
 437                     <xsl:otherwise>
 438                       <tr><td><span class="note">None found.</span></td></tr>
 439                     </xsl:otherwise>
 440                   </xsl:choose>
 441                 </tbody>
 442               </table>
 443
 444               <h2 class="report_section" style="margin-bottom: 0;">Structural Variations (deletions)</h2>
 445               <table id="sv_deletions" class="list" width="100%" cellspacing="0" cellpadding="0" border="0" style="margin-top: 0;">
 446                 <xsl:choose>
 447                   <xsl:when test="count(//structural-variants/deletions/deletion) > 0">
 448                     <thead>
 449                       <tr>
 450                         <th>validation status</th>
 451                         <th class="last">chromosome</th>
 452                         <th class="last">start</th>
 453                         <th class="last">stop</th>
 454                         <th class="last">size</th>
 455                       </tr>
 456                     </thead>
 457                     <tbody>
 458                       <xsl:for-each select="//structural-variants/deletions/deletion">
 459                         <xsl:sort select="@validation-status" data-type="number" order="ascending"/>
 460                         <xsl:sort select="start/@chromosome" data-type="number" order="ascending"/>
 461                         <tr>
 462                           <td class="validation_status"><xsl:value-of select="@validation-status"/></td>
 463                           <td class="last"><xsl:value-of select="start/@chromosome"/></td>
 464                           <td class="last">
 465                                                         <xsl:variable name="start_position" select="start/@position"/><xsl:value-of select="format-number($start_position, '#,##0')"/>
 466                                                   </td>
 467                           <td class="last">
 468                                                         <xsl:variable name="stop_position" select="stop/@position"/><xsl:value-of select="format-number($stop_position, '#,##0')"/>
 469                                                   </td>
 470                           <td class="last">
 471                                                         <xsl:variable name="size" select="@size"/><xsl:value-of select="format-number($size, '#,##0')"/>
 472                                                   </td>
 473                         </tr>
 474                       </xsl:for-each>
 475                     </tbody>
 476                   </xsl:when>
 477                   <xsl:otherwise>
 478                     <tr><td><span class="note">None found.</span></td></tr>
 479                   </xsl:otherwise>
 480                 </xsl:choose>
 481               </table>
 482             </div>
 483           </div>
 484         </div>
 485       </body>
 486     </html>
 487
 488   </xsl:template>
 489
 490 </xsl:stylesheet>