Fixing gearssingle report

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

@@ -27,12 +27,22 @@
     }
 }#
 <%
-    val summaries = summary.getStatsForSamples(runId, summaryModuleTag, summaryStatsTag, sampleId.map(SummaryDb.SampleId),
+    val summaries = if (libId.isDefined) summary.getStatsForLibraries(runId, summaryModuleTag, summaryStatsTag, sampleId,
+      Map("all" -> Nil)
+    ).filter(_._1._2 == libId.get).map(x => x._1._1 -> x._2)
+    else summary.getStatsForSamples(runId, summaryModuleTag, summaryStatsTag, sampleId.map(SummaryDb.SampleId),
       Map("all" -> Nil)
     )
 
     val totalReads = centrifugeTag.map { tag =>
-      summary.getStatsForSamples(runId, summaryModuleTag, ModuleName(tag), sampleId.map(SummaryDb.SampleId),
+    if (libId.isDefined) {
+        val stats = summary.getStatsForLibraries(runId, summaryModuleTag, ModuleName(tag), sampleId,
+            Map("total" -> List("metrics", "Read"))
+        ).filter(_._1._2 == libId.get).head
+        val lib = allLibraries.filter(_.id == stats._1._2).head
+        val sample = allSamples.filter(_.id == stats._1._1).head
+        Map(s"${sample.name}" -> stats._2("total").map(_.toString.toLong).getOrElse(0L))
+    } else 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))
     }

gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsKraken.scala

@@ -124,7 +124,7 @@ object GearsKraken {
     val taxs: mutable.Map[String, Any] = mutable.Map()
 
     def addTax(map: Map[String, Any], path: List[String] = Nil): Unit = {
-      val name = map("name").toString
+      val name = map.get("name").getOrElse("noName").toString
       val x = path.foldLeft(taxs)((a, b) => if (a.contains(b)) a(b).asInstanceOf[mutable.Map[String, Any]] else {
         a += b -> mutable.Map[String, Any]()
         a(b).asInstanceOf[mutable.Map[String, Any]]
@@ -132,13 +132,13 @@ object GearsKraken {
 
       if (!x.contains(name)) x += name -> mutable.Map[String, Any]()
 
-      map("children").asInstanceOf[List[Any]].foreach(x => addTax(x.asInstanceOf[Map[String, Any]], path ::: name :: Nil))
+      map.get("children").getOrElse(List()).asInstanceOf[List[Any]].foreach(x => addTax(x.asInstanceOf[Map[String, Any]], path ::: name :: Nil))
     }
 
-    summaries.foreach { x => addTax(x._2("classified").asInstanceOf[Map[String, Any]]) }
+    summaries.foreach { x => addTax(x._2.get("classified").getOrElse(Map()).asInstanceOf[Map[String, Any]]) }
 
     def getValue(sample: String, path: List[String], key: String) = {
-      path.foldLeft(summaries(sample)("classified").asInstanceOf[Map[String, Any]]) { (b, a) =>
+      path.foldLeft(summaries(sample).get("classified").getOrElse(Map()).asInstanceOf[Map[String, Any]]) { (b, a) =>
         b.getOrElse("children", List[Map[String, Any]]())
           .asInstanceOf[List[Map[String, Any]]]
           .find(_.getOrElse("name", "") == a).getOrElse(Map[String, Any]())