Updated some comments

bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala

@@ -44,27 +44,24 @@ object BammetricsReport extends ReportBuilder {
   def pipelineName = "bammetrics"
 
   /** Root page for single BamMetrcis report */
-  def indexPage: Future[ReportPage] = Future {
-    val bamMetricsPage = Await.result(this.bamMetricsPage(summary, sampleId, libId), Duration.Inf)
-    ReportPage(bamMetricsPage.subPages ::: List(
-      "Versions" -> Future(ReportPage(List(), List("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
-      )), Map())),
-      "Files" -> filesPage(sampleId, libId)
-    ), List(
-      "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp")
-    ) ::: bamMetricsPage.sections,
-      Map()
-    )
-  }
+  def indexPage: Future[ReportPage] =
+    bamMetricsPage(summary, sampleId, libId).map { bamMetricsPage =>
+      ReportPage(bamMetricsPage.subPages ::: List(
+        "Versions" -> Future(ReportPage(List(), List("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
+        )), Map())),
+        "Files" -> filesPage(sampleId, libId)
+      ), List(
+        "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp")
+      ) ::: bamMetricsPage.sections,
+        Map()
+      )
+    }
 
   /** Generates a page with alignment stats */
   def bamMetricsPage(summary: SummaryDb,
                      sampleId: Option[Int],
                      libId: Option[Int],
                      metricsTag: String = "bammetrics"): Future[ReportPage] = Future {
-
-    //val pipelineId: Int = summary.getPipelineId(runId, metricsTag).map(_.get)
-
     val wgsExecuted = summary.getStatsSize(runId, metricsTag, "wgs", sample = sampleId.map(SampleId), library = libId.map(LibraryId)) >= 1
     val rnaExecuted = summary.getStatsSize(runId, metricsTag, "rna", sample = sampleId.map(SampleId), library = libId.map(LibraryId)) >= 1
 
@@ -86,7 +83,7 @@ object BammetricsReport extends ReportBuilder {
 
     ReportPage(
       if (targets.isEmpty) List()
-      else List("Targets" -> Future(ReportPage(
+      else List("Targets" -> Future.successful(ReportPage(
         List(),
         targets.map(t => t -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp", Map("target" -> Some(t)))),
         Map()))),

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilder.scala

@@ -41,28 +41,28 @@ trait MultisampleReportBuilder extends ReportBuilder {
   }
 
   /** Generate the samples page including a single sample page for each sample in the summary */
-  def generateSamplesPage(args: Map[String, Any]): Future[ReportPage] = Future {
-    val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
-    val samplePages = samples.map(_.id)
-      .map(sampleId => sampleId -> samplePage(sampleId, args ++ Map("sampleId" -> Some(sampleId)))
-        .map(x => x.copy(subPages = x.subPages ::: "Files" -> filesPage(sampleId, None) :: Nil)))
-      .toList
-    ReportPage(samplePages.map(x => samples.find(_.id == x._1).get.name -> x._2), samplesSections, args)
-  }
+  def generateSamplesPage(args: Map[String, Any]): Future[ReportPage] =
+    summary.getSamples(runId = Some(runId)).map { samples =>
+      val samplePages = samples.map(_.id)
+        .map(sampleId => sampleId -> samplePage(sampleId, args ++ Map("sampleId" -> Some(sampleId)))
+          .map(x => x.copy(subPages = x.subPages ::: "Files" -> filesPage(sampleId, None) :: Nil)))
+        .toList
+      ReportPage(samplePages.map(x => samples.find(_.id == x._1).get.name -> x._2), samplesSections, args)
+    }
 
   /** Generate the libraries page for a single sample with a subpage for eacht library */
-  def generateLibraryPage(args: Map[String, Any]): Future[ReportPage] = Future {
+  def generateLibraryPage(args: Map[String, Any]): Future[ReportPage] = {
     val sampleId = args("sampleId") match {
       case Some(x: Int) => x
       case None         => throw new IllegalStateException("Sample not found")
     }
 
-    val libraries = Await.result(summary.getLibraries(runId = Some(runId), sampleId = Some(sampleId)), Duration.Inf)
-
-    val libPages = libraries.map(_.id)
-      .map(libId => libId -> libraryPage(sampleId, libId, args ++ Map("libId" -> Some(libId)))
-        .map(x => x.copy(subPages = x.subPages ::: "Files" -> filesPage(sampleId, libId) :: Nil)))
-      .toList
-    ReportPage(libPages.map(x => libraries.find(_.id == x._1).get.name -> x._2), librariesSections, args)
+    summary.getLibraries(runId = Some(runId), sampleId = Some(sampleId)).map { libraries =>
+      val libPages = libraries.map(_.id)
+        .map(libId => libId -> libraryPage(sampleId, libId, args ++ Map("libId" -> Some(libId)))
+          .map(x => x.copy(subPages = x.subPages ::: "Files" -> filesPage(sampleId, libId) :: Nil)))
+        .toList
+      ReportPage(libPages.map(x => libraries.find(_.id == x._1).get.name -> x._2), librariesSections, args)
+    }
   }
 }

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala

@@ -313,12 +313,14 @@ trait ReportBuilder extends ToolCommand {
           case (moduleId, files) =>
             val moduleName: Future[String] = moduleId match {
               case Some(id) => summary.getModuleName(pipelineId, id).map(_.getOrElse("Pipeline"))
-              case _        => Future("Pipeline")
+              case _        => Future.successful("Pipeline")
             }
             moduleName.map(_ -> ReportSection("/nl/lumc/sasc/biopet/core/report/files.ssp", Map("files" -> files)))
         }
         val moduleSectionsSorted = moduleSections.find(_._1 == "Pipeline") ++ moduleSections.filter(_._1 != "Pipeline")
-        summary.getPipelineName(pipelineId = pipelineId).map(_.get -> Future(ReportPage(Nil, Await.result(Future.sequence(moduleSectionsSorted), Duration.Inf).toList, Map())))
+        summary.getPipelineName(pipelineId = pipelineId)
+          .map(_.get -> Future.sequence(moduleSectionsSorted)
+            .map(sections => ReportPage(Nil, sections.toList, Map())))
     })
 
     val pipelineFiles = summary.getPipelineId(runId, pipelineName)

flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala

@@ -42,11 +42,10 @@ object FlexiprepReport extends ReportBuilder {
   override def pageArgs = Map("multisample" -> false)
 
   /** Index page for a flexiprep report */
-  def indexPage: Future[ReportPage] = Future {
-    val flexiprepPage = this.flexiprepPage
+  def indexPage: Future[ReportPage] = this.flexiprepPage.map { flexiprepPage =>
     ReportPage(Nil, List(
       "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFront.ssp")
-    ) ::: Await.result(flexiprepPage, Duration.Inf).sections,
+    ) ::: flexiprepPage.sections,
       Map()
     )
   }