Commit 281e30b5 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Update the tables with sortable indication and pull all online resources to jar for offline usage.

parent ad3013df
......@@ -35,7 +35,7 @@
<!-- Table -->
<table class="table sortable-theme-bootstrap" data-sortable>
<thead><tr>
<th>Sample</th>
<th data-sorted="true" data-sorted-direction="ascending">Sample</th>
#if (!sampleLevel) <th>Library</th> #end
<th>Total</th>
<th>Mapped</th>
......
header {
background-color:black;
color:white;
text-align:center;
padding:5px;
}
nav {
line-height:30px;
background-color:#eeeeee;
width:100%;
padding:5px;
}
nav ul ul {
display: none;
}
nav ul li:hover > ul {
display: block;
}
nav ul {
background: #efefef;
background: linear-gradient(top, #efefef 0%, #bbbbbb 100%);
background: -moz-linear-gradient(top, #efefef 0%, #bbbbbb 100%);
background: -webkit-linear-gradient(top, #efefef 0%,#bbbbbb 100%);
box-shadow: 0px 0px 9px rgba(0,0,0,0.15);
padding: 0 20px;
border-radius: 10px;
list-style: none;
position: relative;
display: inline-table;
}
nav ul:after {
content: ""; clear: both; display: block;
}
nav ul li {
float: left;
}
nav ul li:hover {
background: #4b545f;
background: linear-gradient(top, #4f5964 0%, #5f6975 40%);
background: -moz-linear-gradient(top, #4f5964 0%, #5f6975 40%);
background: -webkit-linear-gradient(top, #4f5964 0%,#5f6975 40%);
}
nav ul li:hover a {
color: #fff;
}
nav ul li a {
display: block; padding: 2px 10px;
color: #757575; text-decoration: none;
}
nav ul ul {
background: #5f6975; border-radius: 0px; padding: 0;
position: absolute; top: 100%;
}
nav ul ul li {
float: none;
border-top: 1px solid #6b727c;
border-bottom: 1px solid #575f6a;
position: relative;
}
nav ul ul li a {
padding: 5px 15px;
color: #fff;
}
nav ul ul li a:hover {
background: #4b545f;
}
nav ul ul ul {
position: absolute; left: 100%; top:0;
}
#main {
float: left;
padding: 15px;
}
#index {
left: 0;
float: left;
line-height:30px;
background-color:#eeeeee;
padding:5px;
}
footer {
background-color:black;
color:white;
clear:both;
text-align:center;
padding:5px;
}
table, td, th {
border: 1px solid green;
border-collapse: collapse;
padding: 2px;
}
th {
background-color: green;
border: 1px solid white;
color: white;
}
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* Copyright 2011-2015 Twitter, Inc.
* Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
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/*
* Base structure
*/
/* Move down content because we have a fixed navbar that is 50px tall */
body {
padding-top: 50px;
}
/*
* Global add-ons
*/
.sub-header {
padding-bottom: 10px;
border-bottom: 1px solid #eee;
}
/*
* Top navigation
* Hide default border to remove 1px line.
*/
.navbar-fixed-top {
border: 0;
}
/*
* Sidebar
*/
/* Hide for mobile, show later */
.sidebar {
display: none;
}
@media (min-width: 768px) {
.sidebar {
position: fixed;
top: 51px;
bottom: 0;
left: 0;
z-index: 1000;
display: block;
padding: 20px;
overflow-x: hidden;
overflow-y: auto; /* Scrollable contents if viewport is shorter than content. */
background-color: #f5f5f5;
border-right: 1px solid #eee;
}
}
/* Sidebar navigation */
.nav-sidebar {
margin-right: -21px; /* 20px padding + 1px border */
margin-bottom: 20px;
margin-left: -20px;
}
.nav-sidebar > li > a {
padding-right: 20px;
padding-left: 20px;
}
.nav-sidebar > .active > a,
.nav-sidebar > .active > a:hover,
.nav-sidebar > .active > a:focus {
color: #fff;
background-color: #428bca;
}
/*
* Main content
*/
.main {
padding: 20px;
}
@media (min-width: 768px) {
.main {
padding-right: 40px;
padding-left: 40px;
}
}
.main .page-header {
margin-top: 0;
}
/*
* Placeholder dashboard ideas
*/
.placeholders {
margin-bottom: 30px;
text-align: center;
}
.placeholders h4 {
margin-bottom: 0;
}
.placeholder {
margin-bottom: 20px;
}
.placeholder img {
display: inline-block;
border-radius: 50%;
}
\ No newline at end of file
/* line 2, ../sass/_sortable.sass */
table[data-sortable] {
border-collapse: collapse;
border-spacing: 0;
}
/* line 6, ../sass/_sortable.sass */
table[data-sortable] th {
vertical-align: bottom;
font-weight: bold;
}
/* line 10, ../sass/_sortable.sass */
table[data-sortable] th, table[data-sortable] td {
text-align: left;
padding: 10px;
}
/* line 14, ../sass/_sortable.sass */
table[data-sortable] th:not([data-sortable="false"]) {
-webkit-user-select: none;
-moz-user-select: none;
-ms-user-select: none;
-o-user-select: none;
user-select: none;
-webkit-tap-highlight-color: rgba(0, 0, 0, 0);
-webkit-touch-callout: none;
cursor: pointer;
}
/* line 26, ../sass/_sortable.sass */
table[data-sortable] th:after {
content: "";
visibility: hidden;
display: inline-block;
vertical-align: inherit;
height: 0;
width: 0;
border-width: 5px;
border-style: solid;
border-color: transparent;
margin-right: 1px;
margin-left: 10px;
float: right;
}
/* line 40, ../sass/_sortable.sass */
table[data-sortable] th[data-sorted="true"]:after {
visibility: visible;
}
/* line 43, ../sass/_sortable.sass */
table[data-sortable] th[data-sorted-direction="descending"]:after {
border-top-color: inherit;
margin-top: 8px;
}
/* line 47, ../sass/_sortable.sass */
table[data-sortable] th[data-sorted-direction="ascending"]:after {
border-bottom-color: inherit;
margin-top: 3px;
}
/* line 5, ../sass/sortable-theme-bootstrap.sass */
table[data-sortable].sortable-theme-bootstrap {
font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;
font-size: 14px;
line-height: 20px;
color: #333333;
background: white;
}
/* line 12, ../sass/sortable-theme-bootstrap.sass */
table[data-sortable].sortable-theme-bootstrap thead th {
border-bottom: 2px solid #e0e0e0;
}
/* line 15, ../sass/sortable-theme-bootstrap.sass */
table[data-sortable].sortable-theme-bootstrap tbody td {
border-top: 1px solid #e0e0e0;
}
/* line 18, ../sass/sortable-theme-bootstrap.sass */
table[data-sortable].sortable-theme-bootstrap th[data-sorted="true"] {
color: #3a87ad;
background: #d9edf7;
border-bottom-color: #bce8f1;
}
/* line 23, ../sass/sortable-theme-bootstrap.sass */
table[data-sortable].sortable-theme-bootstrap th[data-sorted="true"][data-sorted-direction="descending"]:after {
border-top-color: #3a87ad;
}
/* line 26, ../sass/sortable-theme-bootstrap.sass */
table[data-sortable].sortable-theme-bootstrap th[data-sorted="true"][data-sorted-direction="ascending"]:after {
border-bottom-color: #3a87ad;
}
/* line 31, ../sass/sortable-theme-bootstrap.sass */
table[data-sortable].sortable-theme-bootstrap.sortable-theme-bootstrap-striped tbody > tr:nth-child(odd) > td {
background-color: #f9f9f9;
}
\ No newline at end of file
/*! sortable.js 0.5.0 */
(function(){var a,b,c,d,e,f;a="table[data-sortable]",c=/^-?[£$¤]?[\d,.]+%?$/,f=/^\s+|\s+$/g,e="ontouchstart"in document.documentElement,b=e?"touchstart":"click",d={init:function(){var b,c,e,f,g;for(c=document.querySelectorAll(a),g=[],e=0,f=c.length;f>e;e++)b=c[e],g.push(d.initTable(b));return g},initTable:function(a){var b,c,e,f,g;if(1===a.tHead.rows.length&&"true"!==a.getAttribute("data-sortable-initialized")){for(a.setAttribute("data-sortable-initialized","true"),e=a.querySelectorAll("th"),b=f=0,g=e.length;g>f;b=++f)c=e[b],"false"!==c.getAttribute("data-sortable")&&d.setupClickableTH(a,c,b);return a}},setupClickableTH:function(a,c,e){var f;return f=d.getColumnType(a,e),c.addEventListener(b,function(){var b,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u;for(j="true"===this.getAttribute("data-sorted"),k=this.getAttribute("data-sorted-direction"),b=j?"ascending"===k?"descending":"ascending":f.defaultSortDirection,m=this.parentNode.querySelectorAll("th"),n=0,q=m.length;q>n;n++)c=m[n],c.setAttribute("data-sorted","false"),c.removeAttribute("data-sorted-direction");for(this.setAttribute("data-sorted","true"),this.setAttribute("data-sorted-direction",b),l=a.tBodies[0],h=[],t=l.rows,o=0,r=t.length;r>o;o++)g=t[o],h.push([d.getNodeValue(g.cells[e]),g]);for(j?h.reverse():h.sort(f.compare),u=[],p=0,s=h.length;s>p;p++)i=h[p],u.push(l.appendChild(i[1]));return u})},getColumnType:function(a,b){var e,f,g,h,i;for(i=a.tBodies[0].rows,g=0,h=i.length;h>g;g++)if(e=i[g],f=d.getNodeValue(e.cells[b]),""!==f&&f.match(c))return d.types.numeric;return d.types.alpha},getNodeValue:function(a){return a?null!==a.getAttribute("data-value")?a.getAttribute("data-value"):"undefined"!=typeof a.innerText?a.innerText.replace(f,""):a.textContent.replace(f,""):""},types:{numeric:{defaultSortDirection:"descending",compare:function(a,b){var c,d;return c=parseFloat(a[0].replace(/[^0-9.-]/g,"")),d=parseFloat(b[0].replace(/[^0-9.-]/g,"")),isNaN(c)&&(c=0),isNaN(d)&&(d=0),d-c}},alpha:{defaultSortDirection:"ascending",compare:function(a,b){var c,d;return c=a[0].toLowerCase(),d=b[0].toLowerCase(),c===d?0:d>c?-1:1}}}},setTimeout(d.init,0),window.Sortable=d}).call(this);
\ No newline at end of file
......@@ -119,16 +119,16 @@
<!-- Bootstrap core JavaScript
================================================== -->
<!-- Placed at the end of the document so the pages load faster -->
<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.11.2/jquery.min.js"></script>
<script src="${rootPath}ext/js/jquery.min.js"></script>
<!-- Latest compiled and minified CSS -->
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css">
<link rel="stylesheet" href="${rootPath}ext/css/bootstrap.min.css">
<!-- Optional theme -->
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap-theme.min.css">
<link rel="stylesheet" href="${rootPath}ext/css/bootstrap-theme.min.css">
<!-- Latest compiled and minified JavaScript -->
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.js"></script>
<script src="${rootPath}ext/js/bootstrap.min.js"></script>
<link rel="stylesheet" type="text/css" href="${rootPath}ext/css/bootstrap_dashboard.css">
<link rel="stylesheet" type="text/css" href="${rootPath}ext/css/sortable-theme-bootstrap.css">
......
......@@ -3,7 +3,7 @@
<%@ var summary: Summary %>
<%@ var rootPath: String %>
<table class="table sortable-theme-bootstrap" data-sortable>
<thead><tr></tr><th>Sample</th></thead></tr>
<thead><tr></tr><th data-sorted="true" data-sorted-direction="ascending">Sample</th></thead></tr>
<tbody>
#for (sample <- summary.samples)
<tr><td><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td></tr>
......
package nl.lumc.sasc.biopet.core.report
import java.io.{ PrintWriter, File }
import java.io.{FileOutputStream, PrintWriter, File}
import java.net.URL
import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, ToolCommand }
import nl.lumc.sasc.biopet.core.summary.Summary
import org.apache.commons.io.IOUtils
import org.broadinstitute.gatk.utils.commandline.Input
import org.fusesource.scalate.{ TemplateSource, TemplateEngine }
......@@ -91,23 +92,20 @@ trait ReportBuilder extends ToolCommand {
logger.info(srcFile.getPath)
if (srcFile.isDirectory) {
var newPath: String = srcFile.getAbsolutePath.split(resourcePath).last
val newPath: String = srcFile.getAbsolutePath.split(resourcePath).last
val workDir = new File(externalDir, newPath)
workDir.mkdirs()
logger.info("Writing to " + workDir.getAbsolutePath)
for (f <- srcFile.listFiles()) {
var newFilePath: String = f.getAbsolutePath.split(resourcePath+ newPath).last
val resourceWriter = new PrintWriter( new File(workDir, newFilePath) )
val resourceSrcPath: File = new File( resourcePath, newPath+"/"+newFilePath )
val resourceSrcPath: String = new File( resourcePath, newPath+"/"+newFilePath ).getAbsolutePath
val is = getClass.getResourceAsStream(resourceSrcPath.getPath)
val os = new FileOutputStream(new File(workDir, newFilePath).getAbsolutePath)
Source.fromInputStream(
getClass.getResourceAsStream(
resourceSrcPath
)
).getLines().foreach(resourceWriter.println)
resourceWriter.close()
org.apache.commons.io.IOUtils.copy(is, os)
os.close()
}
}
}
......
......@@ -43,7 +43,7 @@
<table class="table sortable-theme-bootstrap" data-sortable>
<thead><tr>
<th>Sample</th>
<th data-sorted="true" data-sorted-direction="ascending">Sample</th>
<th colspan="2">Library</th>
<th>Before QC</th>
<th>Discarded</th>
......
......@@ -43,7 +43,7 @@
<!-- Table -->
<table class="table sortable-theme-bootstrap" data-sortable>
<thead><tr>
<th>Sample</th>
<th data-sorted="true" data-sorted-direction="ascending">Sample</th>
<th colspan="2">Library</th>
<th>Before QC</th>
<th>Clipping</th>
......
......@@ -30,12 +30,12 @@
<!-- Table -->
<table class="table sortable-theme-bootstrap" data-sortable>
<thead><tr><th>Sample</th>
<thead><tr><th data-sorted="true" data-sorted-direction="ascending">Sample</th>
#for (field <- fields) <th>${field}</th> #end
</tr></thead>
<tbody>
#for (sample <- samples.toList.sorted)
<tr><td data-sorted="true"><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
<tr><td><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
#for (field <- fields)
<td>${summary.getSampleValue(sample, "shivavariantcalling", "stats", "multisample-vcfstats-final", "genotype", field)}</td>
#end
......
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