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

public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp

@@ -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>

public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/biopet.css

-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;
-}

public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap-theme.min.css

+/*!
+ * Bootstrap v3.3.4 (http://getbootstrap.com)
+ * Copyright 2011-2015 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
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GradientType=0);background-repeat:repeat-x}.panel-info>.panel-heading{background-image:-webkit-linear-gradient(top,#d9edf7 0,#c4e3f3 100%);background-image:-o-linear-gradient(top,#d9edf7 0,#c4e3f3 100%);background-image:-webkit-gradient(linear,left top,left bottom,from(#d9edf7),to(#c4e3f3));background-image:linear-gradient(to bottom,#d9edf7 0,#c4e3f3 100%);filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffd9edf7', endColorstr='#ffc4e3f3', GradientType=0);background-repeat:repeat-x}.panel-warning>.panel-heading{background-image:-webkit-linear-gradient(top,#fcf8e3 0,#faf2cc 100%);background-image:-o-linear-gradient(top,#fcf8e3 0,#faf2cc 100%);background-image:-webkit-gradient(linear,left top,left bottom,from(#fcf8e3),to(#faf2cc));background-image:linear-gradient(to bottom,#fcf8e3 0,#faf2cc 100%);filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fffcf8e3', endColorstr='#fffaf2cc', GradientType=0);background-repeat:repeat-x}.panel-danger>.panel-heading{background-image:-webkit-linear-gradient(top,#f2dede 0,#ebcccc 100%);background-image:-o-linear-gradient(top,#f2dede 0,#ebcccc 100%);background-image:-webkit-gradient(linear,left top,left bottom,from(#f2dede),to(#ebcccc));background-image:linear-gradient(to bottom,#f2dede 0,#ebcccc 100%);filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff2dede', endColorstr='#ffebcccc', GradientType=0);background-repeat:repeat-x}.well{background-image:-webkit-linear-gradient(top,#e8e8e8 0,#f5f5f5 100%);background-image:-o-linear-gradient(top,#e8e8e8 0,#f5f5f5 100%);background-image:-webkit-gradient(linear,left top,left bottom,from(#e8e8e8),to(#f5f5f5));background-image:linear-gradient(to bottom,#e8e8e8 0,#f5f5f5 100%);filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffe8e8e8', endColorstr='#fff5f5f5', GradientType=0);background-repeat:repeat-x;border-color:#dcdcdc;-webkit-box-shadow:inset 0 1px 3px rgba(0,0,0,.05),0 1px 0 rgba(255,255,255,.1);box-shadow:inset 0 1px 3px rgba(0,0,0,.05),0 1px 0 rgba(255,255,255,.1)}
\ No newline at end of file

public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap_dashboard.css

+/*
+ * 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

public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/sortable-theme-bootstrap.css

+/* 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

public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/sortable.min.js

+/*! 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

public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/main.ssp

@@ -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">

public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/samplesList.ssp

@@ -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>

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala

 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()
         }
       }
     }

public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp

@@ -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>

public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp

@@ -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>

public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp

@@ -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