Adding stats to db

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala

@@ -26,9 +26,9 @@ import org.broadinstitute.gatk.utils.commandline.{Input, Output}
 
 import scala.collection.mutable
 import scala.io.Source
-
 import scala.concurrent.Await
 import scala.concurrent.duration.Duration
+import scala.concurrent.ExecutionContext.Implicits.global
 
 /**
  * This will collect and write the summary
@@ -87,7 +87,25 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
   def run(): Unit = {
     val db = SummaryDb.openSqliteSummary(qscript.summaryDbFile)
 
-    //TODO: Add stats
+    val pipelineId = Await.result(db.getPipelines(name = Some(qscript.summaryName), runId = Some(qscript.summaryRunId)).map(_.head.id), Duration.Inf)
+
+    for (((name, sampleName, libName), summarizables) <-qscript.summarizables) {
+      require(summarizables.nonEmpty)
+      val stats = ConfigUtils.anyToJson(if (summarizables.size == 1) summarizables.head.summaryStats
+      else {
+        val s = summarizables.map(_.summaryStats)
+        s.tail.foldLeft(Map("stats" -> s.head))((a,b) =>
+          ConfigUtils.mergeMaps(a, Map("stats" -> b), summarizables.head.resolveSummaryConflict))("stats")
+      })
+      val moduleId = db.getModules(name = Some(name), runId = Some(qscript.summaryRunId), pipelineId = Some(pipelineId))
+        .map(_.head.id)
+      val sampleId = sampleName.map(name => db.getSamples(runId = Some(qscript.summaryRunId), name = Some(name)).map(_.head.id))
+      val libId = libName.map(name => db.getLibraries(runId = Some(qscript.summaryRunId), name = Some(name),
+        sampleId = sampleId.map(Await.result(_, Duration.Inf))).map(_.head.id))
+      db.createOrUpdateStat(qscript.summaryRunId, pipelineId, Some(Await.result(moduleId, Duration.Inf)),
+        sampleId.map(Await.result(_, Duration.Inf)), libId.map(Await.result(_, Duration.Inf)), stats.nospaces)
+
+    }
 
     //TODO: Add Files
 

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/SummaryDb.scala

@@ -145,8 +145,16 @@ class SummaryDb(db: Database) extends Closeable {
     db.run(stats.forceInsert(Stat(runId, pipelineId, moduleId, sampleId, libId, content)))
   }
 
-  def getStats(runId: Option[Int] = None, pipelineId: Option[Int] = None, moduleId: Option[Option[Int]] = None,
-               sampleId: Option[Option[Int]] = None, libId: Option[Option[Int]] = None) = {
+  def createOrUpdateStat(runId: Int, pipelineId: Int, moduleId: Option[Int] = None,
+                         sampleId: Option[Int] = None, libId: Option[Int] = None, content: String) = {
+    val filter = statsFilter(Some(runId), Some(pipelineId), Some(moduleId), Some(sampleId), Some(libId))
+    val r = Await.result(db.run(filter.size.result), Duration.Inf)
+    if (r == 0) createStat(runId, pipelineId, moduleId, sampleId, libId, content)
+    else db.run(filter.map(_.content).update(content))
+  }
+
+  private def statsFilter(runId: Option[Int] = None, pipelineId: Option[Int] = None, moduleId: Option[Option[Int]] = None,
+                           sampleId: Option[Option[Int]] = None, libId: Option[Option[Int]] = None) = {
     val l: List[Option[Query[Stats, Stats#TableElementType, Seq] => Query[Stats, Stats#TableElementType, Seq]]] = List(
       runId.map(x => y => y.filter(_.runId === x)),
       pipelineId.map(x => y => y.filter(_.pipelineId === x)),
@@ -154,9 +162,12 @@ class SummaryDb(db: Database) extends Closeable {
       sampleId.map(x => y => (if (x.isDefined) y.filter(_.sampleId === x) else y.filter(_.sampleId.isEmpty))),
       libId.map(x => y => (if (x.isDefined) y.filter(_.libraryId === x) else y.filter(_.libraryId.isEmpty)))
     )
-    val q = l.flatten.foldLeft(stats.subquery)((a,b) => b(a))
+    l.flatten.foldLeft(stats.subquery)((a,b) => b(a))
+  }
 
-    db.run(q.result)
+  def getStats(runId: Option[Int] = None, pipelineId: Option[Int] = None, moduleId: Option[Option[Int]] = None,
+               sampleId: Option[Option[Int]] = None, libId: Option[Option[Int]] = None) = {
+    db.run(statsFilter(runId, pipelineId, moduleId, sampleId, libId).result)
   }
 
   def getStat(runId: Int, pipelineId: Int, moduleId: Option[Int] = None,