Adding pipeline and modules during init

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

@@ -28,6 +28,9 @@ import scala.collection.mutable
 import scala.io.Source
 import slick.driver.H2Driver.api._
 
+import scala.concurrent.Await
+import scala.concurrent.duration.Duration
+
 /**
  * This will collect and write the summary
  *
@@ -59,10 +62,11 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
         case s: MultiSampleQScript => s.initSummaryDb
         case _ => qscript.summaryRunId
       }
-      val db = SummaryDb.openSqliteSummary(qscript.summaryDbFile)
-
-      db.close()
     }
+    val db = SummaryDb.openSqliteSummary(qscript.summaryDbFile)
+    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) {

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

@@ -62,7 +62,7 @@ object SummaryToSqlite extends ToolCommand {
 
     println(Await.result(summary.getLibraries(), Duration.Inf))
 
-    val pipelineId = Await.result(summary.createPipeline("pipelineName", runId), Duration.Inf)
+    val pipelineId = Await.result(summary.forceCreatePipeline("pipelineName", runId), Duration.Inf)
 
     println(Await.result(summary.getPipelines(), Duration.Inf))
 

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

@@ -91,11 +91,19 @@ class SummaryDb(db: Database) extends Closeable {
       .map(_.headOption.flatten.map(ConfigUtils.jsonTextToMap))
   }
 
-  def createPipeline(name: String, runId: Int): Future[Int] = {
+  def forceCreatePipeline(name: String, runId: Int): Future[Int] = {
     val id = Await.result(db.run(pipelines.size.result), Duration.Inf)
     db.run(pipelines.forceInsert(Pipeline(id, name, runId))).map(_ => id)
   }
 
+  def createPipeline(name: String, runId: Int): Future[Int] = {
+    getPipelines(name = Some(name), runId = Some(runId))
+      .flatMap{ case m =>
+        if (m.isEmpty) forceCreatePipeline(name, runId)
+        else Future(m.head.id)
+      }
+  }
+
   def getPipelines(pipelineId: Option[Int] = None, name: Option[String] = None, runId: Option[Int] = None) = {
     val q = pipelines.filter { lib =>
       List(
@@ -104,14 +112,22 @@ class SummaryDb(db: Database) extends Closeable {
         name.map(lib.name === _)
       ).collect({ case Some(criteria) => criteria }).reduceLeftOption(_ && _).getOrElse(true: Rep[Boolean])
     }
-    db.run(q.map(x => (x.id, x.name, x.runId)).result)
+    db.run(q.result)
   }
 
-  def createModule(name: String, runId: Int, pipelineId: Int): Future[Int] = {
+  def forceCreateModule(name: String, runId: Int, pipelineId: Int): Future[Int] = {
     val id = Await.result(db.run(modules.size.result), Duration.Inf)
     db.run(modules.forceInsert(Module(id, name, runId, pipelineId))).map(_ => id)
   }
 
+  def createModule(name: String, runId: Int, pipelineId: Int): Future[Int] = {
+    getModules(name = Some(name), runId = Some(runId), pipelineId = Some(pipelineId))
+      .flatMap{ case m =>
+        if (m.isEmpty) forceCreateModule(name, runId, pipelineId)
+        else Future(m.head.id)
+      }
+  }
+
   def getModules(moduleId: Option[Int] = None, name: Option[String] = None, runId: Option[Int] = None, pipelineId: Option[Int] = None) = {
     val q = modules.filter { lib =>
       List(
@@ -121,7 +137,7 @@ class SummaryDb(db: Database) extends Closeable {
         name.map(lib.name === _)
       ).collect({ case Some(criteria) => criteria }).reduceLeftOption(_ && _).getOrElse(true: Rep[Boolean])
     }
-    db.run(q.map(x => (x.id, x.name, x.runId)).result)
+    db.run(q.result)
   }
 
   def createStat(runId: Int, pipelineId: Int, moduleId: Option[Int] = None,