WIP

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.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._)
 #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 summary: SummaryDb %>
 <%@ var rootPath: String %>
-<%@ var sampleId: Option[String] = None %>
-<%@ var libId: Option[String] = None %>
+<%@ var sampleId: Option[Int] = None %>
+<%@ var libId: Option[Int] = None %>
 <%@ var args: Map[String, Any] %>
 <%@ var outputDir: File %>
 <%@ var centrifugeTag: Option[String] = None %>
 <%@ var summaryStatsTag: String = "krakenreport" %>
 <%@ var summaryModuleTag: String = "gearskraken" %>
+<%@ var runId: Int %>
+<%@ var allSamples: Seq[Sample] %>
+<%@ var allLibraries: Seq[Library] %>
+#{
+    val samples = sampleId match {
+    case Some(id) => allSamples.filter(_.id == id).toList
+    case _ => allSamples.toList
+    }
+}#
 <%
-    val summaries = if (sampleId.isEmpty) {
-        summary.getSampleValues(summaryModuleTag, "stats", summaryStatsTag).map(x => x._1 -> x._2.get.asInstanceOf[Map[String, Any]])
-    } else summary.getValue(sampleId, libId, summaryModuleTag, "stats", summaryStatsTag).map(sampleId.get -> _.asInstanceOf[Map[String, Any]]).toList.toMap
+    val summaries = summary.getStatsForSamples(runId, summaryModuleTag, summaryStatsTag, sampleId.map(SummaryDb.SampleId),
+      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) }