Fixing compile errors

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

@@ -24,8 +24,7 @@ import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
 import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._
 import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._
 
-import scala.concurrent.ExecutionContext.Implicits.global
-import scala.concurrent.Await
+import scala.concurrent.{ Await, Future }
 import scala.concurrent.duration.Duration
 
 class BammetricsReport(val parent: Configurable) extends ReportBuilderExtension {
@@ -43,12 +42,12 @@ object BammetricsReport extends ReportBuilder {
   val reportName = "Bam Metrics"
 
   /** Root page for single BamMetrcis report */
-  def indexPage = {
-    val bamMetricsPage = this.bamMetricsPage(summary, sampleId, libId)
+  def indexPage: Future[ReportPage] = Future {
+    val bamMetricsPage = Await.result(this.bamMetricsPage(summary, sampleId, libId), Duration.Inf)
     ReportPage(bamMetricsPage.subPages ::: List(
-      "Versions" -> ReportPage(List(), List("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
-      )), Map()),
-      "Files" -> ReportPage(List(), List(), Map())
+      "Versions" -> Future(ReportPage(List(), List("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
+      )), Map())),
+      "Files" -> Future(ReportPage(List(), List(), Map()))
     ), List(
       "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp")
     ) ::: bamMetricsPage.sections,
@@ -60,7 +59,7 @@ object BammetricsReport extends ReportBuilder {
   def bamMetricsPage(summary: SummaryDb,
                      sampleId: Option[Int],
                      libId: Option[Int],
-                     metricsTag: String = "bammetrics") = {
+                     metricsTag: String = "bammetrics"): Future[ReportPage] = Future {
 
     //val pipelineId: Int = summary.getPipelineId(runId, metricsTag).map(_.get)
 
@@ -85,10 +84,10 @@ object BammetricsReport extends ReportBuilder {
 
     ReportPage(
       if (targets.isEmpty) List()
-      else List("Targets" -> ReportPage(
+      else List("Targets" -> Future(ReportPage(
         List(),
         targets.map(t => t -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp", Map("target" -> Some(t)))),
-        Map())),
+        Map()))),
       List(
         "Summary" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
         "Mapping Quality" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp", Map("showPlot" -> true)),

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

@@ -24,11 +24,10 @@ import org.broadinstitute.gatk.utils.commandline.Input
 import org.fusesource.scalate.TemplateEngine
 
 import scala.collection.mutable
-import scala.concurrent.{ Await, Future }
+import scala.concurrent.{ Await, ExecutionContextExecutor, Future }
 import scala.concurrent.duration.Duration
 import scala.language.postfixOps
 import scala.language.implicitConversions
-import scala.concurrent.ExecutionContext.Implicits.global
 
 /**
  * This trait is meant to make an extension for a report object
@@ -74,8 +73,9 @@ trait ReportBuilderExtension extends ToolCommandFunction {
 
 trait ReportBuilder extends ToolCommand {
 
+  implicit lazy val global: ExecutionContextExecutor = scala.concurrent.ExecutionContext.global
   implicit def toOption[T](x: T): Option[T] = Option(x)
-  //  implicit def autoWait[T](x: Future[T]): T = Await.result(x, Duration.Inf)
+  implicit def autoWait[T](x: Future[T]): T = Await.result(x, Duration.Inf)
 
   case class Args(summaryDbFile: File = null,
                   outputDir: File = null,

gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleReport.scala

@@ -19,7 +19,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._
 import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.{ LibraryId, SampleId }
 
-import scala.concurrent.Await
+import scala.concurrent.{ Await, Future }
 import scala.concurrent.duration.Duration
 
 class GearsSingleReport(val parent: Configurable) extends ReportBuilderExtension {
@@ -31,7 +31,7 @@ object GearsSingleReport extends ReportBuilder {
   override def extFiles = super.extFiles ++ List("js/gears.js", "js/krona-2.0.js", "img/krona/loading.gif", "img/krona/hidden.png", "img/krona/favicon.ico")
     .map(x => ExtFile("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + x, x))
 
-  def indexPage = {
+  def indexPage: Future[ReportPage] = Future {
     val sampleName = sampleId.flatMap(x => Await.result(summary.getSampleName(x), Duration.Inf))
     val libraryName = libId.flatMap(x => Await.result(summary.getLibraryName(x), Duration.Inf))
 
@@ -40,8 +40,8 @@ object GearsSingleReport extends ReportBuilder {
 
     ReportPage(
       List(
-        "Versions" -> ReportPage(List(),
-          List(("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"))), Map())
+        "Versions" -> Future(ReportPage(List(),
+          List(("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"))), Map()))
       ),
       List("Gears intro" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsSingleFront.ssp")) ++
         (if (krakenExecuted) List("Kraken analysis" ->

mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala

@@ -21,7 +21,7 @@ import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
 import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._
 import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._
 
-import scala.concurrent.Await
+import scala.concurrent.{ Await, Future }
 import scala.concurrent.duration.Duration
 
 class MappingReport(val parent: Configurable) extends ReportBuilderExtension {
@@ -44,7 +44,7 @@ object MappingReport extends ReportBuilder {
     sample = sampleId.map(SampleId), library = libId.map(LibraryId)), Duration.Inf) >= 1
 
   /** Root page for single BamMetrcis report */
-  def indexPage = {
+  def indexPage: Future[ReportPage] = Future {
     val mappingSettings = summary.getSettingKeys(runId, "mapping", NoModule,
       sample = sampleId.map(SampleId).getOrElse(NoSample), library = libId.map(LibraryId).getOrElse(NoLibrary),
       keyValues = Map("skip_flexiprep" -> List("skip_flexiprep"), "skip_metrics" -> List("skip_metrics")))
@@ -54,13 +54,13 @@ object MappingReport extends ReportBuilder {
     } else None
     ReportPage((if (skipFlexiprep) Nil else List("QC" -> FlexiprepReport.flexiprepPage)) :::
       bamMetricsPage.map(_.subPages).getOrElse(Nil) ::: List(
-        "Versions" -> ReportPage(List(), List("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
-        )), Map()),
-        "Files" -> ReportPage(List(), Nil, Map())
+        "Versions" -> Future(ReportPage(List(), List("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
+        )), Map())),
+        "Files" -> Future(ReportPage(List(), Nil, Map()))
       ) :::
-        (if (krakenExecuted) List("Gears - Metagenomics" -> ReportPage(List(), List(
+        (if (krakenExecuted) List("Gears - Metagenomics" -> Future(ReportPage(List(), List(
           "Sunburst analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp"
-          )), Map()))
+          )), Map())))
         else Nil), List(
       "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/mappingFront.ssp")
     ) ::: bamMetricsPage.map(_.sections).getOrElse(Nil),

mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala

@@ -49,7 +49,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
     .map(x => ExtFile("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + x, x))
 
   /** Root page for the carp report */
-  def indexPage = {
+  def indexPage: Future[ReportPage] = Future {
 
     val krakenExecuted = Await.result(summary.getStatsSize(runId, "gearskraken", "krakenreport",
       library = NoLibrary, mustHaveSample = true), Duration.Inf) >= 1
@@ -67,22 +67,23 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
 
     ReportPage(
       List("Samples" -> generateSamplesPage(pageArgs)) ++
-        (if (krakenExecuted) List("Dustbin analysis - Kraken" -> ReportPage(List(), List(
+        (if (krakenExecuted) List("Dustbin analysis - Kraken" -> Future(ReportPage(List(), List(
           "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
-          )), Map()))
-        else Nil) ++ (if (centrifugeExecuted) List("Centriguge analysis" -> ReportPage(List("Non-unique" -> ReportPage(List(), List("All mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
-          Map("summaryStatsTag" -> "centrifuge_report")
-        )), Map())), List(
+          )), Map())))
+        else Nil) ++ (if (centrifugeExecuted) List("Centriguge analysis" -> Future(ReportPage(List(
+          "Non-unique" -> Future(ReportPage(List(), List("All mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
+            Map("summaryStatsTag" -> "centrifuge_report")
+          )), Map()))), List(
           "Unique mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
             Map("summaryStatsTag" -> "centrifuge_unique_report")
-          )), Map("summaryModuleTag" -> "gearscentrifuge", "centrifugeTag" -> Some("centrifuge"))))
+          )), Map("summaryModuleTag" -> "gearscentrifuge", "centrifugeTag" -> Some("centrifuge")))))
         else Nil) ++
-        List("Reference" -> ReportPage(List(), List(
+        List("Reference" -> Future(ReportPage(List(), List(
           "Reference" -> ReportSection("/nl/lumc/sasc/biopet/core/report/reference.ssp", Map("pipeline" -> pipelineName))
-        ), Map()),
-          "Files" -> Await.result(filesPage(), Duration.Inf),
-          "Versions" -> ReportPage(List(), List("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
-          )), Map())
+        ), Map())),
+          "Files" -> filesPage(),
+          "Versions" -> Future(ReportPage(List(), List("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
+          )), Map()))
         ),
       List(
         "Report" -> frontSection) ++
@@ -129,7 +130,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
             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 -> ReportPage(Nil, Await.result(Future.sequence(moduleSectionsSorted), Duration.Inf).toList, Map()))
+        summary.getPipelineName(pipelineId = pipelineId).map(_.get -> Future(ReportPage(Nil, Await.result(Future.sequence(moduleSectionsSorted), Duration.Inf).toList, Map())))
     })
 
     val pipelineFiles = summary.getPipelineId(runId, pipelineName).flatMap(pipelinelineId => dbFiles.map(x => x(pipelinelineId.get).filter(_.moduleId.isEmpty)))
@@ -140,7 +141,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
   }
 
   /** Single sample page */
-  def samplePage(sampleId: Int, args: Map[String, Any]): ReportPage = {
+  def samplePage(sampleId: Int, args: Map[String, Any]): Future[ReportPage] = Future {
     val krakenExecuted = Await.result(summary.getStatsSize(runId, "gearskraken", "krakenreport",
       library = NoLibrary, sample = sampleId), Duration.Inf) >= 1
     val centrifugeExecuted = Await.result(summary.getStatsSize(runId, "gearscentrifuge", "centrifuge_report",
@@ -151,17 +152,18 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
     ReportPage(List(
       "Libraries" -> generateLibraryPage(args),
       "Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), None)) ++
-      (if (centrifugeExecuted) List("Centriguge analysis" -> ReportPage(List("Non-unique" -> ReportPage(List(), List("All mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
-        Map("summaryStatsTag" -> "centrifuge_report", "centrifugeTag" -> Some("centrifuge"))
-      )), Map())), List(
+      (if (centrifugeExecuted) List("Centriguge analysis" -> Future(ReportPage(List(
+        "Non-unique" -> Future(ReportPage(List(), List("All mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
+          Map("summaryStatsTag" -> "centrifuge_report", "centrifugeTag" -> Some("centrifuge"))
+        )), Map()))), List(
         "Unique mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
           Map("summaryStatsTag" -> "centrifuge_unique_report")
-        )), Map("summaryModuleTag" -> "gearscentrifuge")))
-      else Nil) ::: (if (krakenExecuted) List("Dustbin analysis" -> ReportPage(List(), List(
+        )), Map("summaryModuleTag" -> "gearscentrifuge"))))
+      else Nil) ::: (if (krakenExecuted) List("Dustbin analysis" -> Future(ReportPage(List(), List(
         "Krona Plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
-        )), Map()))
+        )), Map())))
       else Nil) ++
-      List("Files" -> Await.result(filesPage(sampleId = sampleId), Duration.Inf)
+      List("Files" -> filesPage(sampleId = sampleId)
       ), List(
       "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
         Map("showPlot" -> true)),
@@ -173,7 +175,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
   }
 
   /** Library page */
-  def libraryPage(sampleId: Int, libId: Int, args: Map[String, Any]): ReportPage = {
+  def libraryPage(sampleId: Int, libId: Int, args: Map[String, Any]): Future[ReportPage] = Future {
     val krakenExecuted = Await.result(summary.getStatsSize(runId, "gearskraken", "krakenreport",
       library = libId, sample = sampleId), Duration.Inf) >= 1
     val centrifugeExecuted = Await.result(summary.getStatsSize(runId, "gearscentrifuge", "centrifuge_report",
@@ -184,16 +186,17 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
     ReportPage(
       ("Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), Some(libId))) ::
         (if (flexiprepExecuted) List("QC" -> FlexiprepReport.flexiprepPage) else Nil) :::
-        (if (centrifugeExecuted) List("Centriguge analysis" -> ReportPage(List("Non-unique" -> ReportPage(List(), List("All mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
-          Map("summaryStatsTag" -> "centrifuge_report")
-        )), Map())), List(
+        (if (centrifugeExecuted) List("Centriguge analysis" -> Future(ReportPage(List(
+          "Non-unique" -> Future(ReportPage(List(), List("All mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
+            Map("summaryStatsTag" -> "centrifuge_report")
+          )), Map()))), List(
           "Unique mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
             Map("summaryStatsTag" -> "centrifuge_unique_report")
-          )), Map("summaryModuleTag" -> "gearscentrifuge", "centrifugeTag" -> Some("centrifuge"))))
-        else Nil) ::: (if (krakenExecuted) List("Dustbin analysis" -> ReportPage(List(), List(
+          )), Map("summaryModuleTag" -> "gearscentrifuge", "centrifugeTag" -> Some("centrifuge")))))
+        else Nil) ::: (if (krakenExecuted) List("Dustbin analysis" -> Future(ReportPage(List(), List(
           "Krona Plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
-          )), Map()))
-        else Nil) ::: List("Files" -> Await.result(filesPage(sampleId = sampleId, libraryId = libId), Duration.Inf)),
+          )), Map())))
+        else Nil) ::: List("Files" -> filesPage(sampleId = sampleId, libraryId = libId)),
       "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp") ::
         (if (flexiprepExecuted) List("QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
           "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp"))

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala

@@ -24,7 +24,7 @@ import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
 import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._
 import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.{ NoModule, NoSample, SampleId }
 
-import scala.concurrent.Await
+import scala.concurrent.{ Await, Future }
 import scala.concurrent.duration.Duration
 
 /**
@@ -57,15 +57,15 @@ trait ShivaReportTrait extends MultisampleMappingReportTrait {
   else Nil)
 
   /** Root page for the shiva report */
-  override def indexPage = {
+  override def indexPage: Future[ReportPage] = Future {
     val regions = regionsPage
-    val oldPage = super.indexPage
+    val oldPage = Await.result(super.indexPage, Duration.Inf)
 
     oldPage.copy(subPages = oldPage.subPages ++ regionsPage)
   }
 
   /** Generate a page with all target coverage stats */
-  def regionsPage: Option[(String, ReportPage)] = {
+  def regionsPage: Option[(String, Future[ReportPage])] = {
     val shivaSettings = Await.result(summary.getSetting(runId, "shiva"), Duration.Inf).get
     val roi = shivaSettings.get("regions_of_interest")
     val amplicon = shivaSettings.get("amplicon_bed")
@@ -91,24 +91,24 @@ trait ShivaReportTrait extends MultisampleMappingReportTrait {
       case _                =>
     }
 
-    if (regionPages.nonEmpty) Some("Regions" -> ReportPage(
-      regionPages.map(p => p._1 -> ReportPage(Nil,
+    if (regionPages.nonEmpty) Some("Regions" -> Future(ReportPage(
+      regionPages.map(p => p._1 -> Future(ReportPage(Nil,
         List(
           "Variants" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp", Map("showPlot" -> true)),
           "Coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp")
         ),
         Map("target" -> Some(p._1.stripSuffix(" (Amplicon)")))
-      )).toList.sortBy(_._1),
+      ))).toList.sortBy(_._1),
       List(),
-      Map())
+      Map()))
     )
     else None
   }
 
   /** Single sample page */
-  override def samplePage(sampleId: Int, args: Map[String, Any]): ReportPage = {
+  override def samplePage(sampleId: Int, args: Map[String, Any]): Future[ReportPage] = Future {
     val variantcallingSection = if (variantcallingExecuted) List("Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp")) else Nil
-    val oldPage = super.samplePage(sampleId, args)
+    val oldPage: ReportPage = super.samplePage(sampleId, args)
     oldPage.copy(sections = variantcallingSection ++ oldPage.sections)
   }