diff options
Diffstat (limited to 'emacs.d/nxhtml/tests/in/josh-091115-cancer_summary.xsl')
| -rw-r--r-- | emacs.d/nxhtml/tests/in/josh-091115-cancer_summary.xsl | 490 |
1 files changed, 490 insertions, 0 deletions
diff --git a/emacs.d/nxhtml/tests/in/josh-091115-cancer_summary.xsl b/emacs.d/nxhtml/tests/in/josh-091115-cancer_summary.xsl new file mode 100644 index 0000000..043e9d2 --- /dev/null +++ b/emacs.d/nxhtml/tests/in/josh-091115-cancer_summary.xsl @@ -0,0 +1,490 @@ +<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" version="1.0" + xmlns:set="http://exslt.org/sets"> + + <xsl:output method="html"/> + <xsl:output encoding="utf-8"/> + <xsl:output doctype-system="http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"/> + <xsl:output doctype-public="-//W3C//DTD XHTML 1.0 Transitional//EN"/> + + <xsl:template match="/"> + + <html> + <head> + <title>Cancer Summary: <xsl:value-of select="//individual/@name"/> <xsl:value-of select="//individual/@gender"/> <xsl:value-of select="//individual/@id"/></title> + + <link rel="shortcut icon" href="/resources/report_resources/apipe_dashboard/images/gc_favicon.png" type="image/png" /> + + <link rel="stylesheet" href="/resources/report_resources/apipe_dashboard/css/master.css" type="text/css" media="screen" /> + <link rel="stylesheet" href="/resources/report_resources/apipe_dashboard/css/tablesorter.css" type="text/css" media="screen" /> + <script type="text/javascript" src="/resources/report_resources/jquery/jquery.js"></script> + <script type="text/javascript" src="/resources/report_resources/jquery/jquery.tablesorter.min.js"></script> + <script type="text/javascript"> + $(document).ready(function() { + $("#tier_1_snps").tablesorter({ + // sort on first column, ascending + // sortList: [[0,0]] + }); + + $("#tier_1_insertions").tablesorter({ + // sort on first column, ascending + //sortList: [[0,0]] + }); + + $("#tier_1_deletions").tablesorter({ + // sort on first column, ascending + //sortList: [[0,0]] + }); + }); + </script> + <link rel="stylesheet" href="/resources/report_resources/cancer_card/css/zoom2.css" type="text/css" media="screen"></link> + <script type="text/javascript" src="/resources/report_resources/cancer_card/js/dom-drag.js"></script> + + <script type="text/javascript" src="/resources/report_resources/cancer_card/js/HotSpot2.js"></script> + <script type="text/javascript"> + addEvent(window, 'load', function() { + HotSpotController.init("zoomImage",300, '<xsl:value-of select="//individual/circos-images/@large"/>','ZTbutton'); }); + + function addEvent(obj, evType, fn) { + if (obj.addEventListener) { + obj.addEventListener(evType, fn, false); + return true; + } else if (obj.attachEvent) { + var r = obj.attachEvent("on" + evType, fn); + return r; + } else { + return false; + } + } + </script> + + <script type="text/javascript"> + $(document).ready(function() { + $("input[type=checkbox]").click(function() { + alert("Clicked: " + this.value); + }); + }); + </script> + + <style type="text/css" media="screen"> + table.info_table_group td { + padding-right: 10px; + } + + div.content_padding { + padding: 0 10px 20px 10px; + } + + h3.group_header { + border-bottom: 2px solid #CCC; + } + div.circos_graph { + float: left; + width: 920px; + } + + form.status_selector { + margin: 0; + padding: 0; + float: right; + font-size: 85%; + font-weight: normal; + } + + form.status_selector table { + margin: 0; + padding: 0; + } + + form.status_selector table td.lbl { + padding-right: 10px; + padding-left: 5px; + } + + + form.status_selector table td.table_lbl { + font-weight: bold; + padding-right: 8px; + padding-left: 3px; + } + </style> + </head> + + <body> + <div class="container"> + <div class="background"> + <div class="page_header"> + <table cellpadding="0" cellspacing="0" border="0"> + <tr> + <td> + <img src="/resources/report_resources/apipe_dashboard/images/gc_header_logo2.png" width="44" height="45" align="absmiddle" /> + </td> + <td> + <h1><xsl:value-of select="//individual/@name"/> <xsl:value-of select="//individual/@gender"/> <xsl:value-of select="//individual/@id"/> Cancer Summary</h1> + </td> + </tr> + </table> + </div> + <div class="page_padding"> + <!-- <h2 class="page_title icon_instrument_data">Flow Cell <xsl:value-of select="//flow-cell/@id"/> Status</h2> --> + <table cellpadding="0" cellspacing="0" border="0" class="info_table_group"> + <tr> + <td> + <h3 class="group_header">Clinical Data</h3> + <table border="0" cellpadding="0" cellspacing="0"> + <tr> + <td> + <table border="0" cellpadding="0" cellspacing="0" class="info_table" width="100%"> + <colgroup> + <col/> + <col width="100%"/> + </colgroup> + <tr><td class="label">Name:</td><td class="value"><xsl:value-of select="//individual/@name"/></td></tr> + <tr> + <td class="label">Gender:</td> + <td class="value"> + <xsl:choose> + <xsl:when test="string(//individual/@gender)"> + <xsl:value-of select="//individual/@gender"/> + </xsl:when> + <xsl:otherwise> + Not Provided + </xsl:otherwise> + </xsl:choose> + </td> + </tr> + <tr><td class="label">ID:</td><td class="value"><xsl:value-of select="//individual/@id"/></td></tr> + + </table> + </td> + <td> + <table border="0" cellpadding="0" cellspacing="0" class="info_table" width="100%" style="float: left;"> + <colgroup> + <col/> + <col width="100%"/> + </colgroup> + + <tr><td class="label">Year Diagnosed:</td><td class="value"><xsl:value-of select="//clinical-data/@diagnosis-year"/></td></tr> + <tr><td class="label">Diagnosed at Age:</td><td class="value"><xsl:value-of select="//clinical-data/@diagnosis-age"/></td></tr> + <xsl:choose> + <xsl:when test="//clinical-data/@alive = '1'"> + <tr><td class="label">Survived:</td><td class="value">Yes</td></tr> + </xsl:when> + <xsl:otherwise> + <tr><td class="label">Survived:</td><td class="value">No</td></tr> + <tr><td class="label">Days Survived:</td><td class="value"><xsl:value-of select="//clinical-data/@days-survived"/></td></tr> + </xsl:otherwise> + </xsl:choose> + </table> + </td> + <td> + <table border="0" cellpadding="0" cellspacing="0" class="info_table" width="100%" style="float: left;"> + <colgroup> + <col/> + <col width="100%"/> + </colgroup> + + <tr><td class="label">Treatment:</td><td class="value"><xsl:value-of select="//clinical-data/@treatment"/></td></tr> + <tr><td class="label">Outcome:</td><td class="value"><xsl:value-of select="//clinical-data/@outcome"/></td></tr> + <tr><td class="label">AMP:</td><td class="value"><xsl:value-of select="//clinical-data/@amp"/></td></tr> + + </table> + </td> + </tr> + </table> + </td> + <td> + <h3 class="group_header">Sequencing Stats</h3> + <table border="0" cellpadding="0" cellspacing="0" class="info_table" width="100%"> + <colgroup> + <col/> + <col width="100%"/> + </colgroup> + <tr><td class="label">Normal Coverage:</td><td class="value"><xsl:value-of select="//samples/sample/models/model/@normal-haploid-coverage"/>X</td></tr> + <tr><td class="label">Tumor Coverage:</td><td class="value"><xsl:value-of select="//samples/sample/models/model/@tumor-haploid-coverage"/>X</td></tr> + </table> + </td> + </tr> + </table> + <hr style="margin-bottom: 0;"/> + <h2 class="report_section" style="margin-bottom: 0; margin-top: 0">Circos Graph   <a id="ZTbutton" href="javascript: void(0);" style="font-size: 85%; font-weight: normal;">[toggle zoom]</a></h2> + <p id="ZTthumbnail"> + <img> + <xsl:attribute name="id">zoomImage</xsl:attribute> + <xsl:attribute name="src"><xsl:value-of select="//individual/circos-images/@small"/></xsl:attribute> + <xsl:attribute name="width">920</xsl:attribute> + <xsl:attribute name="height">920</xsl:attribute> + </img> + </p> + <h2 class="report_section" style="margin-bottom: 0">Tier 1 SNPs +<!-- <form class="status_selector"> + <input type="hidden" name="table" value="tier_1_snps"/> + <table cellpadding="0" cellspacing="0"> + <tr> + <td class="table_lbl">Show:</td> + <xsl:for-each select="set:distinct(//variants/snps/snp/@validation-status)"> + <td class="cb"> + <input type="checkbox"><xsl:attribute name="value"><xsl:value-of select="."/></xsl:attribute></input> + </td> + <td class="lbl"> + <xsl:value-of select="."/> + </td> + </xsl:for-each> + </tr> + </table> + </form> +--> + + </h2> + <table id="tier_1_snps" class="list tablesorter" width="100%" cellspacing="0" cellpadding="0" border="0" style="margin-top: 0;"> + <xsl:choose> + <xsl:when test="count(//variants/snps/snp) > 0"> + + <thead> + <tr> + <th>validation status</th> + <th>chromosome</th> + <th class="last">start</th> + <th class="last">reference</th> + <th class="last">variant</th> + <th class="last">gene</th> + <th class="last">amino acid change</th> + <th class="last">trv type</th> + </tr> + </thead> + <tbody> + <xsl:for-each select="//variants/snps/snp"> + <xsl:sort select="@validation-status" data-type="text" order="ascending"/> + <xsl:sort select="@chromosome" data-type="number" order="ascending"/> + <tr> + <td class="validation_status"><xsl:value-of select="@validation-status"/></td> + <td><xsl:value-of select="@chromosome"/></td> + <td class="last"> + <xsl:variable name="start" select="@start"/><xsl:value-of select="format-number($start, '#,##0')"/> + </td> + <td class="last"><xsl:value-of select="@reference-allele"/></td> + <td class="last"><xsl:value-of select="@variant-allele"/></td> + <td class="last"><xsl:value-of select="@gene"/></td> + <td class="last"><xsl:value-of select="@amino-acid-change"/></td> + <td class="last"><xsl:value-of select="@trv-type"/></td> + </tr> + </xsl:for-each> + </tbody> + </xsl:when> + <xsl:otherwise> + <tr><td><span class="note">None found.</span></td></tr> + </xsl:otherwise> + </xsl:choose> + </table> + + <h2 class="report_section" style="margin-bottom: 0">Tier 1 Insertions</h2> + <table id="tier_1_insertions" class="list tablesorter" width="100%" cellspacing="0" cellpadding="0" border="0" style="margin-top: 0;"> + <xsl:choose> + <xsl:when test="count(//variants/insertions/insertion) > 0"> + <thead> + <tr> + <th>validation status</th> + <th>chromosome</th> + <th class="last">start</th> + <th class="last">stop</th> + <th class="last">variant</th> + <th class="last">gene</th> + <th class="last">amino acid change</th> + <th class="last">trv type</th> + </tr> + </thead> + <tbody> + <xsl:for-each select="//variants/insertions/insertion"> + <xsl:sort select="@validation-status" data-type="text" order="ascending"/> + <xsl:sort select="@chromosome" data-type="number" order="ascending"/> + <tr> + <td class="validation_status"><xsl:value-of select="@validation-status"/></td> + <td><xsl:value-of select="@chromosome"/></td> + <td class="last"> + <xsl:variable name="start" select="@start"/><xsl:value-of select="format-number($start, '#,##0')"/> + </td> + <td class="last"> + <xsl:variable name="stop" select="@stop"/><xsl:value-of select="format-number($stop, '#,##0')"/> + </td> + <td class="last"><xsl:value-of select="@variant-allele"/></td> + <td class="last"><xsl:value-of select="@gene"/></td> + <td class="last"><xsl:value-of select="@amino-acid-change"/></td> + <td class="last"><xsl:value-of select="@trv-type"/></td> + </tr> + </xsl:for-each> + </tbody> + </xsl:when> + <xsl:otherwise> + <tr><td><span class="note">None found.</span></td></tr> + </xsl:otherwise> + </xsl:choose> + </table> + + <h2 class="report_section" style="margin-bottom: 0">Tier 1 Deletions</h2> + <table id="tier_1_deletions" class="list tablesorter" width="100%" cellspacing="0" cellpadding="0" border="0" style="margin-top: 0;"> + <xsl:choose> + <xsl:when test="count(//variants/deletions/deletion) > 0"> + <thead> + <tr> + <th>validation status</th> + <th>chromosome</th> + <th class="last">start</th> + <th class="last">stop</th> + <th class="last">reference</th> + <th class="last">gene</th> + <th class="last">amino acid change</th> + <th class="last">trv type</th> + </tr> + </thead> + <tbody> + <xsl:for-each select="//variants/deletions/deletion"> + <xsl:sort select="@validation-status" data-type="text" order="ascending"/> + <xsl:sort select="@chromosome" data-type="number" order="ascending"/> + <tr> + <td class="validation_status"><xsl:value-of select="@validation-status"/></td> + <td><xsl:value-of select="@chromosome"/></td> + <td class="last"> + <xsl:variable name="start" select="@start"/><xsl:value-of select="format-number($start, '#,##0')"/> + </td> + <td class="last"> + <xsl:variable name="stop" select="@stop"/><xsl:value-of select="format-number($stop, '#,##0')"/> + </td> + <td class="last"><xsl:value-of select="@reference-allele"/></td> + <td class="last"><xsl:value-of select="@gene"/></td> + <td class="last"><xsl:value-of select="@amino-acid-change"/></td> + <td class="last"><xsl:value-of select="@trv-type"/></td> + </tr> + </xsl:for-each> + </tbody> + </xsl:when> + <xsl:otherwise> + <tr><td><span class="note">None found.</span></td></tr> + </xsl:otherwise> + </xsl:choose> + </table> + + <h2 class="report_section" style="margin-bottom: 0;">Structural Variations (translocations)</h2> + <table id="sv_translocations" class="list" width="100%" cellspacing="0" cellpadding="0" border="0" style="margin-top: 0;"> + <xsl:choose> + <xsl:when test="count(//structural-variants/translocations/translocation) > 0"> + <thead> + <tr> + <th>validation status</th> + <th class="last">chromosome</th> + <th class="last">position</th> + <th> </th> + <th class="last">chromosome</th> + <th class="last">position</th> + </tr> + </thead> + <tbody> + <xsl:for-each select="//structural-variants/translocations/translocation"> + <xsl:sort select="@validation-status" data-type="text" order="ascending"/> + <xsl:sort select="start/@chromosome" data-type="number" order="ascending"/> + <tr> + <td class="validation_status"><xsl:value-of select="@validation-status"/></td> + <td class="last"><xsl:value-of select="start/@chromosome"/></td> + <td class="last"> + <xsl:variable name="start_position" select="start/@position"/><xsl:value-of select="format-number($start_position, '#,##0')"/> + </td> + + <td class="last"><span style="font-size: 100%; font-weight: bold;">→</span></td> + + <td class="last"><xsl:value-of select="stop/@chromosome"/></td> + <td class="last"> + <xsl:variable name="stop_position" select="stop/@position"/><xsl:value-of select="format-number($stop_position, '#,##0')"/> + </td> + </tr> + </xsl:for-each> + </tbody> + </xsl:when> + <xsl:otherwise> + <tr><td><span class="note">None found.</span></td></tr> + </xsl:otherwise> + </xsl:choose> + </table> + + <h2 class="report_section" style="margin-bottom: 0;">Structural Variations (insertions)</h2> + <table id="sv_insertions" class="list" width="100%" cellspacing="0" cellpadding="0" border="0" style="margin-top: 0;"> + <tbody> + <xsl:choose> + <xsl:when test="count(//structural-variants/insertions/insertion) > 0"> + <thead> + <tr> + <th>validation status</th> + <th class="last">chromosome</th> + <th class="last">start</th> + <th class="last">stop</th> + <th class="last">size</th> + </tr> + </thead> + <xsl:for-each select="//structural-variants/insertions/insertion"> + <xsl:sort select="@validation-status" data-type="number" order="ascending"/> + <xsl:sort select="start/@chromosome" data-type="number" order="ascending"/> + <tr> + <td class="validation_status"><xsl:value-of select="@validation-status"/></td> + <td class="last"><xsl:value-of select="start/@chromosome"/></td> + <td class="last"> + <xsl:variable name="start_position" select="start/@position"/><xsl:value-of select="format-number($start_position, '#,##0')"/> + </td> + <td class="last"> + <xsl:variable name="stop_position" select="stop/@position"/><xsl:value-of select="format-number($stop_position, '#,##0')"/> + </td> + <xsl:variable name="size" select="@size"/><xsl:value-of select="format-number($size, '#,##0')"/> + + </tr> + </xsl:for-each> + </xsl:when> + <xsl:otherwise> + <tr><td><span class="note">None found.</span></td></tr> + </xsl:otherwise> + </xsl:choose> + </tbody> + </table> + + <h2 class="report_section" style="margin-bottom: 0;">Structural Variations (deletions)</h2> + <table id="sv_deletions" class="list" width="100%" cellspacing="0" cellpadding="0" border="0" style="margin-top: 0;"> + <xsl:choose> + <xsl:when test="count(//structural-variants/deletions/deletion) > 0"> + <thead> + <tr> + <th>validation status</th> + <th class="last">chromosome</th> + <th class="last">start</th> + <th class="last">stop</th> + <th class="last">size</th> + </tr> + </thead> + <tbody> + <xsl:for-each select="//structural-variants/deletions/deletion"> + <xsl:sort select="@validation-status" data-type="number" order="ascending"/> + <xsl:sort select="start/@chromosome" data-type="number" order="ascending"/> + <tr> + <td class="validation_status"><xsl:value-of select="@validation-status"/></td> + <td class="last"><xsl:value-of select="start/@chromosome"/></td> + <td class="last"> + <xsl:variable name="start_position" select="start/@position"/><xsl:value-of select="format-number($start_position, '#,##0')"/> + </td> + <td class="last"> + <xsl:variable name="stop_position" select="stop/@position"/><xsl:value-of select="format-number($stop_position, '#,##0')"/> + </td> + <td class="last"> + <xsl:variable name="size" select="@size"/><xsl:value-of select="format-number($size, '#,##0')"/> + </td> + </tr> + </xsl:for-each> + </tbody> + </xsl:when> + <xsl:otherwise> + <tr><td><span class="note">None found.</span></td></tr> + </xsl:otherwise> + </xsl:choose> + </table> + </div> + </div> + </div> + </body> + </html> + + </xsl:template> + +</xsl:stylesheet> |