Added wait step for executable

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

@@ -121,8 +121,8 @@ trait SummaryQScript extends BiopetQScript { qscript: QScript =>
   private def createRun(): Int = {
     val db = SummaryDb.openSqliteSummary(summaryDbFile)
     val dir = root match {
-      case q:BiopetQScript => q.outputDir
-      case _ => throw new IllegalStateException("Root should be a BiopetQscript")
+      case q: BiopetQScript => q.outputDir
+      case _                => throw new IllegalStateException("Root should be a BiopetQscript")
     }
     val id = Await.result(db.createRun(summaryName, dir.getAbsolutePath), Duration.Inf)
     runIdFile.getParentFile.mkdir()

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

@@ -164,23 +164,16 @@ 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 {
-      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))
-        case f: BiopetCommandLineFunction with Version =>
-          db.createOrUpdateExecutable(qscript.summaryRunId, name, f.getVersion, Option(f.executable))
-        case f: Configurable with Version =>
-          db.createOrUpdateExecutable(qscript.summaryRunId, name, f.getVersion)
-        case _ => None
-      }
-
-    }
+    (for (f <- qscript.functions.par) yield f match {
+      case f: BiopetJavaCommandLineFunction with Version =>
+        Some(db.createOrUpdateExecutable(qscript.summaryRunId, f.configNamespace, f.getVersion, f.getJavaVersion,
+          javaMd5 = BiopetCommandLineFunction.executableMd5Cache.get(f.executable), jarPath = Some(f.jarFile.getAbsolutePath)))
+      case f: BiopetCommandLineFunction with Version =>
+        Some(db.createOrUpdateExecutable(qscript.summaryRunId, f.configNamespace, f.getVersion, Option(f.executable)))
+      case f: Configurable with Version =>
+        Some(db.createOrUpdateExecutable(qscript.summaryRunId, f.configNamespace, f.getVersion))
+      case _ => None
+    }).flatten.foreach(Await.ready(_, Duration.Inf))
 
     ///////////////// OLD //////////////////
     for (((name, sampleId, libraryId), summarizables) <- qscript.summarizables; summarizable <- summarizables) {

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

@@ -215,7 +215,7 @@ class SummaryDb(db: Database) extends Closeable {
 
   /** This return a [[Query]] for [[Settings]] */
   private def settingsFilter(runId: Option[Int] = None, pipelineId: Option[Int] = None, moduleId: Option[Option[Int]] = None,
-                     sampleId: Option[Option[Int]] = None, libId: Option[Option[Int]] = None) = {
+                             sampleId: Option[Option[Int]] = None, libId: Option[Option[Int]] = None) = {
     var f: Query[Settings, Settings#TableElementType, Seq] = settings
     runId.foreach(r => f = f.filter(_.runId === r))
     pipelineId.foreach(r => f = f.filter(_.pipelineId === r))
@@ -249,8 +249,8 @@ class SummaryDb(db: Database) extends Closeable {
 
   /** Return a [[Query]] for [[Files]] */
   private def filesFilter(runId: Option[Int] = None, pipelineId: Option[Int] = None, moduleId: Option[Option[Int]],
-                  sampleId: Option[Option[Int]] = None, libId: Option[Option[Int]] = None,
-                  key: Option[String] = None) = {
+                          sampleId: Option[Option[Int]] = None, libId: Option[Option[Int]] = None,
+                          key: Option[String] = None) = {
     var f: Query[Files, Files#TableElementType, Seq] = files
     runId.foreach(r => f = f.filter(_.runId === r))
     pipelineId.foreach(r => f = f.filter(_.pipelineId === r))