Remove close method

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

@@ -17,9 +17,9 @@ package nl.lumc.sasc.biopet.core
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.MultiSampleQScript.Gender
-import nl.lumc.sasc.biopet.core.summary.{Summarizable, SummaryQScript}
+import nl.lumc.sasc.biopet.core.summary.{ Summarizable, SummaryQScript }
 import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
-import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
+import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
 import org.broadinstitute.gatk.queue.QScript
 
 import scala.concurrent.Await

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

@@ -14,10 +14,10 @@
  */
 package nl.lumc.sasc.biopet.core.summary
 
-import java.io.{File, PrintWriter}
+import java.io.{ File, PrintWriter }
 
 import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.core.extensions.{CheckChecksum, Md5sum}
+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
@@ -200,10 +200,6 @@ 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

@@ -14,15 +14,15 @@
  */
 package nl.lumc.sasc.biopet.core.summary
 
-import java.io.{File, PrintWriter}
+import java.io.{ File, PrintWriter }
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import nl.lumc.sasc.biopet.LastCommitHash
 import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
-import org.broadinstitute.gatk.queue.function.{InProcessFunction, QFunction}
-import org.broadinstitute.gatk.utils.commandline.{Input, Output}
+import org.broadinstitute.gatk.queue.function.{ InProcessFunction, QFunction }
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 import scala.collection.mutable
 import scala.io.Source
@@ -60,17 +60,18 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
     if (qscript == root) { // This initialize the database
       qscript match {
         case s: MultiSampleQScript => s.initSummaryDb
-        case t:SampleLibraryTag => t.sampleId.foreach { case sampleName =>
-          val sampleId = Await.result(db.getSamples(name = Some(sampleName), runId = Some(qscript.summaryRunId)).map(_.headOption.map(_.id)), Duration.Inf).getOrElse {
-            Await.result(db.createSample(sampleName, qscript.summaryRunId), Duration.Inf)
-          }
-          t.libId.foreach {libName =>
-            val libId = Await.result(db.getSamples(name = Some(libName), runId = Some(qscript.summaryRunId), sampleId = Some(sampleId)).map(_.headOption.map(_.id)), Duration.Inf).getOrElse {
-              Await.result(db.createLibrary(libName, qscript.summaryRunId, sampleId), Duration.Inf)
+        case t: SampleLibraryTag => t.sampleId.foreach {
+          case sampleName =>
+            val sampleId = Await.result(db.getSamples(name = Some(sampleName), runId = Some(qscript.summaryRunId)).map(_.headOption.map(_.id)), Duration.Inf).getOrElse {
+              Await.result(db.createSample(sampleName, qscript.summaryRunId), Duration.Inf)
+            }
+            t.libId.foreach { libName =>
+              val libId = Await.result(db.getSamples(name = Some(libName), runId = Some(qscript.summaryRunId), sampleId = Some(sampleId)).map(_.headOption.map(_.id)), Duration.Inf).getOrElse {
+                Await.result(db.createLibrary(libName, qscript.summaryRunId, sampleId), Duration.Inf)
+              }
             }
-          }
         }
-        case _                     => qscript.summaryRunId
+        case _ => qscript.summaryRunId
       }
     }
     val pipelineId = Await.result(db.createPipeline(qscript.summaryName, qscript.summaryRunId), Duration.Inf)
@@ -163,10 +164,12 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
         db.createOrUpdateSetting(qscript.summaryRunId, pipelineId, None, None, None, ConfigUtils.mapToJson(q.summarySettings).nospaces)
     }
 
-    for ((name, f) <- qscript.functions.flatMap(_ match {
-      case c:Configurable with Version => Some(c)
-      case _ => None
-    }).groupBy(_.configNamespace)) yield {
+    for (
+      (name, f) <- qscript.functions.flatMap(_ match {
+        case c: Configurable with Version => Some(c)
+        case _                            => None
+      }).groupBy(_.configNamespace)
+    ) yield {
       f match {
         case f: BiopetJavaCommandLineFunction with Version =>
           db.createOrUpdateExecutable(qscript.summaryRunId, name, f.getVersion, f.getJavaVersion, javaMd5 = BiopetCommandLineFunction.executableMd5Cache.get(f.executable), jarPath = Some(f.jarFile.getAbsolutePath))

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SummaryToSqlite.scala

@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.tools
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
-import nl.lumc.sasc.biopet.utils.{ConfigUtils, ToolCommand}
+import nl.lumc.sasc.biopet.utils.{ ConfigUtils, ToolCommand }
 import slick.driver.H2Driver.api._
 
 import scala.concurrent.Await

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

@@ -8,7 +8,7 @@ import slick.driver.H2Driver.api._
 
 import scala.concurrent.ExecutionContext.Implicits.global
 import scala.concurrent.duration.Duration
-import scala.concurrent.{Await, Future}
+import scala.concurrent.{ Await, Future }
 
 /**
  * Created by pjvanthof on 05/02/2017.
@@ -209,7 +209,7 @@ class SummaryDb(db: Database) extends Closeable {
   }
 
   def createOrUpdateSetting(runId: Int, pipelineId: Int, moduleId: Option[Int] = None,
-                         sampleId: Option[Int] = None, libId: Option[Int] = None, content: String) = {
+                            sampleId: Option[Int] = None, libId: Option[Int] = None, content: String) = {
     val filter = settingsFilter(Some(runId), Some(pipelineId), Some(moduleId), Some(sampleId), Some(libId))
     val r = Await.result(db.run(filter.size.result), Duration.Inf)
     if (r == 0) createSetting(runId, pipelineId, moduleId, sampleId, libId, content)
@@ -256,13 +256,13 @@ class SummaryDb(db: Database) extends Closeable {
 
   def createFile(runId: Int, pipelineId: Int, moduleId: Option[Int] = None,
                  sampleId: Option[Int] = None, libId: Option[Int] = None,
-                 key:String, path: String, md5: String, link: Boolean = false, size: Long) = {
+                 key: String, path: String, md5: String, link: Boolean = false, size: Long) = {
     db.run(files.forceInsert(Schema.File(runId, pipelineId, moduleId, sampleId, libId, key, path, md5, link, size)))
   }
 
   def createOrUpdateFile(runId: Int, pipelineId: Int, moduleId: Option[Int] = None,
                          sampleId: Option[Int] = None, libId: Option[Int] = None,
-                         key:String, path: String, md5: String, link: Boolean = false, size: Long) = {
+                         key: String, path: String, md5: String, link: Boolean = false, size: Long) = {
     val filter = filesFilter(Some(runId), Some(pipelineId), Some(moduleId), Some(sampleId), Some(libId), Some(key))
     val r = Await.result(db.run(filter.size.result), Duration.Inf)
     if (r == 0) createFile(runId, pipelineId, moduleId, sampleId, libId, key, path, md5, link, size)

biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/summary/db/SummaryDbTest.scala

@@ -10,8 +10,8 @@ import scala.concurrent.Await
 import scala.concurrent.duration.Duration
 
 /**
-  * Created by pjvanthof on 14/02/2017.
-  */
+ * Created by pjvanthof on 14/02/2017.
+ */
 class SummaryDbTest extends TestNGSuite with Matchers {
 
   @Test
@@ -23,9 +23,9 @@ class SummaryDbTest extends TestNGSuite with Matchers {
 
     Await.result(db.createOrUpdateSetting(0, 0, None, None, None, """{"content": "test" }"""), Duration.Inf)
     val bla = Await.result(db.getSettings(Some(0)), Duration.Inf)
-    Await.result(db.getSetting(0,0, None, None, None), Duration.Inf) shouldBe Some(Map("content" -> "test"))
+    Await.result(db.getSetting(0, 0, None, None, None), Duration.Inf) shouldBe Some(Map("content" -> "test"))
     Await.result(db.createOrUpdateSetting(0, 0, None, None, None, """{"content": "test2" }"""), Duration.Inf)
-    Await.result(db.getSetting(0,0, None, None, None), Duration.Inf) shouldBe Some(Map("content" -> "test2"))
+    Await.result(db.getSetting(0, 0, None, None, None), Duration.Inf) shouldBe Some(Map("content" -> "test2"))
     db.close()
   }