Switch to krona plots

38e13cdd · Peter van 't Hof · dceac7c8 · 38e13cdd · 38e13cdd · 38e13cdd
Commit 38e13cdd authored Dec 24, 2015 by Peter van 't Hof
--- 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
+#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>
--- 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>

--- 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
+#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>
--- 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"),

--- 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
    )