Fixing krona plots for centrifuge and kraken

gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp

 #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
+#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
 #import(nl.lumc.sasc.biopet.utils.summary.db.Schema.Library)
 #import(nl.lumc.sasc.biopet.utils.summary.db.Schema.Sample)
 #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
@@ -30,14 +31,15 @@
       Map("all" -> Nil)
     )
 
-    val totalReads = if (sampleId.isEmpty) {
-        centrifugeTag.map {tag => summary.getSampleValues(summaryModuleTag, "stats", tag, "metrics", "Read").map(x => x._1 -> x._2.getOrElse(0L).toString.toLong) }
-    } else centrifugeTag.flatMap(tag => summary.getValue(sampleId, libId, summaryModuleTag, "stats", tag, "metrics", "Read"))
-      .map(value => Map(sampleId.get -> value.toString.toLong))
+    val totalReads = centrifugeTag.map { tag =>
+      summary.getStatsForSamples(runId, summaryModuleTag, ModuleName(tag), sampleId.map(SummaryDb.SampleId),
+        Map("total" -> List("metrics", "Read"))
+        ).map(x => allSamples.find(_.id == x._1).head.name -> x._2("total").map(_.toString.toLong).getOrElse(0L))
+    }
 
     val tempFile = File.createTempFile("krona.", ".xml")
     tempFile.deleteOnExit()
-    GearsKraken.convertKrakenSummariesToKronaXml(summaries, tempFile, totalReads)
+    GearsKraken.convertKrakenSummariesToKronaXml(summaries.map(x => allSamples.find(_.id == x._1).head.name -> x._2("all").map(_.asInstanceOf[Map[String, Any]]).getOrElse(Map())), tempFile, totalReads)
 
     val output = ReportBuilder.renderTemplate("/nl/lumc/sasc/biopet/core/report/krona.ssp",
     args ++ Map("kronaXml" -> tempFile))