Colapse all summaries into 1 connector

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala

@@ -272,7 +272,6 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
         if (!libNamesOld.contains(libName)) Await.result(db.createLibrary(libName, summaryRunId, sampleId, libraryTags), Duration.Inf)
       }
     }
-    db.close()
   }
 }
 

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

@@ -20,6 +20,8 @@ import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.extensions.{CheckChecksum, Md5sum}
 import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
 import org.broadinstitute.gatk.queue.QScript
+import org.broadinstitute.gatk.queue.engine.JobRunInfo
+import org.broadinstitute.gatk.queue.function.QFunction
 
 import scala.collection.mutable
 import scala.concurrent.Await
@@ -198,6 +200,10 @@ trait SummaryQScript extends BiopetQScript { qscript: QScript =>
 
     addedJobs = true
   }
+
+  override def onExecutionDone(jobs: Map[QFunction, JobRunInfo], success: Boolean) = {
+    SummaryDb.closeAll()
+  }
 }
 
 object SummaryQScript {

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

@@ -75,7 +75,7 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
     }
     val pipelineId = Await.result(db.createPipeline(qscript.summaryName, qscript.summaryRunId), Duration.Inf)
     qscript.summarizables.map(x => Await.result(db.createModule(x._1._1, qscript.summaryRunId, pipelineId), Duration.Inf))
-    db.close()
+
     for (q <- qscript.summaryQScripts)
       deps :+= q.summaryFile
     for ((_, l) <- qscript.summarizables; s <- l) {
@@ -179,8 +179,6 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
 
     }
 
-    db.close()
-
     ///////////////// OLD //////////////////
     for (((name, sampleId, libraryId), summarizables) <- qscript.summarizables; summarizable <- summarizables) {
       summarizable.addToQscriptSummary(qscript, name)

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

@@ -286,11 +286,20 @@ class SummaryDb(db: Database) extends Closeable {
 }
 
 object SummaryDb {
+  private var summaryConnections = Map[File, SummaryDb]()
+
+  def closeAll(): Unit = {
+    summaryConnections.foreach(_._2.close())
+  }
+
   def openSqliteSummary(file: File): SummaryDb = {
-    val exist = file.exists()
-    val db = Database.forURL(s"jdbc:sqlite:${file.getAbsolutePath}", driver = "org.sqlite.JDBC")
-    val s = new SummaryDb(db)
-    if (!exist) s.createTables()
-    s
+    if (!summaryConnections.contains(file)) {
+      val exist = file.exists()
+      val db = Database.forURL(s"jdbc:sqlite:${file.getAbsolutePath}", driver = "org.sqlite.JDBC")
+      val s = new SummaryDb(db)
+      if (!exist) s.createTables()
+      summaryConnections += file -> s
+    }
+    summaryConnections(file)
   }
 }
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