Commit acf21ee3 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Report update, sorting order (display)

parent c736d0cb
......@@ -15,7 +15,7 @@
buffer.append("<ul class=\"dropdown-menu\">")
}
for (subPage <- page.subPages) {
for (subPage <- page.subPages.sortBy(_._1)) {
val href: String = {
if (path.isEmpty) rootPath + subPage._1 + "/index.html"
else rootPath + path.mkString("","/","/") + subPage._1 + "/index.html"
......
......@@ -5,7 +5,7 @@
<%@ var pipeline: String %>
#{
val contigs = summary.getValue(pipeline, "settings", "reference", "contigs").get.asInstanceOf[Map[String, Map[String, Any]]]
val contigs = summary.getValue(pipeline, "settings", "reference", "contigs").getOrElse(Map.empty).asInstanceOf[Map[String, Map[String, Any]]]
}#
<table class="table">
......
......@@ -2,6 +2,7 @@
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %>
<%@ var rootPath: String %>
<%@ var pipeline: String %>
<table class="table">
<tbody>
......@@ -9,7 +10,7 @@
<tr><th>Version</th><td>${summary.getValue("meta", "pipeline_version")}</td></tr>
<tr><th>Last commit hash</th><td>${summary.getValue("meta", "last_commit_hash")}</td></tr>
<tr><th>Output directory</th><td>${summary.getValue("meta", "output_dir")}</td></tr>
<tr><th>Reference</th><td>${summary.getValue("shiva", "settings", "reference", "species")} - ${summary.getValue("shiva", "settings", "reference", "name")}</td></tr>
<tr><th>Reference</th><td>${summary.getValue(pipeline, "settings", "reference", "species")} - ${summary.getValue(pipeline, "settings", "reference", "name")}</td></tr>
<tr><th>Number of samples</th><td>${summary.samples.size}</td></tr>
</tbody>
</table>
......@@ -18,7 +19,7 @@
<div class="col-md-1"></div>
<div class="col-md-6">
<p>
In this web document you can find your <em>Shiva</em> pipeline report.
In this web document you can find your <em>${pipeline}</em> pipeline report.
Different categories of data can be found in the left-side menu.
Statistics per sample and library can be accessed through the top-level menu.
Some statistics for target regions can be found in the regions tab.
......
......@@ -56,7 +56,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
"QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp",
Map("showPlot" -> true, "showTable" -> false))
),
pageArgs
pageArgs ++ Map("pipeline" -> pipelineName)
)
}
......
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