From 38e13cdd75f229b121e74ce612a555c8df8cc2ae Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 24 Dec 2015 17:04:27 +0100
Subject: [PATCH] Switch to krona plots
---
.../nl/lumc/sasc/biopet/core/report/krona.ssp | 24 ++++++++++++++
.../nl/lumc/sasc/biopet/core/report/main.ssp | 2 +-
.../biopet/pipelines/gears/krakenKrona.ssp | 33 +++++++++++++++++++
.../biopet/pipelines/gears/GearsReport.scala | 4 +--
.../pipelines/gears/GearsSingleReport.scala | 4 +--
5 files changed, 62 insertions(+), 5 deletions(-)
create mode 100644 public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/krona.ssp
create mode 100644 public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp
diff --git a/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/krona.ssp b/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/krona.ssp
new file mode 100644
index 000000000..8c5f1e5d0
--- /dev/null
+++ b/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/krona.ssp
@@ -0,0 +1,24 @@
+#import(java.io.File)
+#import(scala.io.Source)
+<%@ var rootPath: String %>
+<%@ var kronaXml: File %>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+<meta charset="utf-8"/>
+<link rel="shortcut icon" href="${rootPath}ext/img/krona/favicon.ico"/>
+<!--<script id="notfound">window.onload=function(){document.body.innerHTML="Could not get resources from \"http://krona.sourceforge.net\"."}</script>-->
+<script src="${rootPath}ext/js/krona-2.0.js"></script>
+</head>
+<body>
+<img id="hiddenImage" src="${rootPath}ext/img/krona/hidden.png" style="display:none"/>
+<img id="loadingImage" src="${rootPath}ext/img/krona/loading.gif" style="display:none"/>
+<noscript>Javascript must be enabled to view this page.</noscript>
+<div style="display:none">
+<%
+ val reader = Source.fromFile(kronaXml)
+ val xml = reader.getLines().mkString("\n")
+ reader.close()
+%>
+${unescape(xml)}
+</div></body></html>
diff --git a/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/main.ssp b/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/main.ssp
index 7102c5ef7..356ddc00e 100644
--- a/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/main.ssp
+++ b/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/main.ssp
@@ -148,7 +148,7 @@
${name}
</h3>
</div>
- ${unescape(section.render(args))}
+ ${unescape(section.render(args ++ Map("args" -> args)))}
</div>
#end
</div>
diff --git a/public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp b/public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp
new file mode 100644
index 000000000..a57d62ebb
--- /dev/null
+++ b/public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp
@@ -0,0 +1,33 @@
+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
+#import(nl.lumc.sasc.biopet.core.report.ReportPage)
+#import(nl.lumc.sasc.biopet.core.report.ReportBuilder)
+#import(nl.lumc.sasc.biopet.pipelines.gears.GearsKraken)
+#import(java.io.File)
+#import(java.io.PrintWriter)
+<%@ var summary: Summary %>
+<%@ var rootPath: String %>
+<%@ var sampleId: Option[String] = None %>
+<%@ var libId: Option[String] = None %>
+<%@ var args: Map[String, Any] %>
+<%@ var outputDir: File %>
+
+<%
+ val bla = if (sampleId.isEmpty && libId.isEmpty) {
+ summary.getSampleValues("gearskraken", "stats", "krakenreport").map(x => x._1 -> x._2.get.asInstanceOf[Map[String, Any]])
+ } else summary.getValue(sampleId, libId, "gearskraken", "stats", "krakenreport").map(sampleId.get -> _.asInstanceOf[Map[String, Any]]).toList.toMap
+
+ val tempFile = File.createTempFile("krona.", ".xml")
+ tempFile.deleteOnExit()
+ GearsKraken.convertKrakenSummariesToKronaXml(bla, tempFile)
+
+ val output = ReportBuilder.renderTemplate("/nl/lumc/sasc/biopet/core/report/krona.ssp",
+ args ++ Map("kronaXml" -> tempFile))
+
+
+ val file = new File(outputDir, "kraken_krona.html")
+ val writer = new PrintWriter(file)
+ writer.println(output)
+ writer.close()
+%>
+
+<iframe src="kraken_krona.html" style="width:100%;height:80vh;border:none;"></iframe>
diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
index 622a481d0..ff4397af5 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
+++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
@@ -16,7 +16,7 @@ object GearsReport extends MultisampleReportBuilder {
def reportName = "Gears Report"
- override def extFiles = super.extFiles ++ List("js/gears.js")
+ override def extFiles = super.extFiles ++ List("js/gears.js", "js/krona-2.0.js", "img/krona/loading.gif", "img/krona/hidden.png", "img/krona/favicon.ico")
.map(x => ExtFile("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + x, x))
def indexPage = {
@@ -54,7 +54,7 @@ object GearsReport extends MultisampleReportBuilder {
ReportPage(
if (krakenExecuted) List("Gears - Metagenomics" -> ReportPage(List(), List(
- "Sunburst analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp"
+ "Kraken analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)), Map()))
else Nil, List(
"QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleReport.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleReport.scala
index 5ceb961b0..2532afb51 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleReport.scala
+++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleReport.scala
@@ -27,7 +27,7 @@ object GearsSingleReport extends ReportBuilder {
// TODO: Add dustbin analysis (aggregated)
// TODO: Add alignment stats per sample for the dustbin analysis
- override def extFiles = super.extFiles ++ List("js/gears.js")
+ override def extFiles = super.extFiles ++ List("js/gears.js", "js/krona-2.0.js", "img/krona/loading.gif", "img/krona/hidden.png", "img/krona/favicon.ico")
.map(x => ExtFile("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + x, x))
def indexPage = {
@@ -39,7 +39,7 @@ object GearsSingleReport extends ReportBuilder {
),
List(
"Gears intro" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsSingleFront.ssp"),
- "Sunburst analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp")
+ "Kraken analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp")
),
pageArgs
)
--
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