Switching to Future.successful

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

@@ -51,8 +51,8 @@ object GearsReport extends MultisampleReportBuilder {
     val qiimeClosesOtuTable = summary.getFile(runId, "gears", key = "qiime_closed_otu_table")
     val qiimeOpenOtuTable = summary.getFile(runId, "gears", key = "qiime_open_otu_table")
 
-    val centrifugePage = (if (centrifugeExecuted) Some("Centriguge analysis" -> Future(ReportPage(List("Non-unique" ->
-      Future(ReportPage(List(), List("All mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
+    val centrifugePage = (if (centrifugeExecuted) Some("Centriguge analysis" -> Future.successful(ReportPage(List("Non-unique" ->
+      Future.successful(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",
@@ -60,17 +60,17 @@ object GearsReport extends MultisampleReportBuilder {
       )), Map("summaryModuleTag" -> "gearscentrifuge", "centrifugeTag" -> Some("centrifuge")))))
     else None)
 
-    val krakenPage = (if (krakenExecuted) Some("Kraken analysis" -> Future(ReportPage(List(), List(
-      "Krona plot" -> Future(ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
+    val krakenPage = (if (krakenExecuted) Some("Kraken analysis" -> Future.successful(ReportPage(List(), List(
+      "Krona plot" -> Future.successful(ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
       ))), Map())))
     else None)
 
-    val qiimeClosedPage = (if (qiimeClosesOtuTable.isDefined) Some("Qiime closed reference analysis" -> Future(ReportPage(List(), List(
-      "Krona plot" -> Future(ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
+    val qiimeClosedPage = (if (qiimeClosesOtuTable.isDefined) Some("Qiime closed reference analysis" -> Future.successful(ReportPage(List(), List(
+      "Krona plot" -> Future.successful(ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
       ))), Map("biomFile" -> new File(run.outputDir + File.separator + qiimeClosesOtuTable.get.path)))))
     else None)
 
-    val qiimeOpenPage = (if (qiimeOpenOtuTable.isDefined) Some("Qiime open reference analysis" -> Future(ReportPage(List(), List(
+    val qiimeOpenPage = (if (qiimeOpenOtuTable.isDefined) Some("Qiime open reference analysis" -> Future.successful(ReportPage(List(), List(
       "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
       )), Map("biomFile" -> new File(run.outputDir + File.separator + qiimeOpenOtuTable.get.path)))))
     else None)
@@ -99,20 +99,20 @@ object GearsReport extends MultisampleReportBuilder {
     val qiimeClosesOtuTable = Await.result(summary.getFile(runId, "gearssingle", NoModule, sampleId, NoLibrary, "qiime_closed_otu_table"), Duration.Inf)
     val qiimeOpenOtuTable = Await.result(summary.getFile(runId, "gearssingle", NoModule, sampleId, NoLibrary, "qiime_open_otu_table"), Duration.Inf)
 
-    ReportPage((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",
+    ReportPage((if (centrifugeExecuted) List("Centriguge analysis" -> Future.successful(ReportPage(List(
+      "Non-unique" -> Future.successful(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("Kraken analysis" -> Future(ReportPage(List(), List(
+    else Nil) ::: (if (krakenExecuted) List("Kraken analysis" -> Future.successful(ReportPage(List(), List(
       "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
       )), Map())))
-    else Nil) ::: (if (qiimeClosesOtuTable.isDefined) List("Qiime closed reference analysis" -> Future(ReportPage(List(), List(
+    else Nil) ::: (if (qiimeClosesOtuTable.isDefined) List("Qiime closed reference analysis" -> Future.successful(ReportPage(List(), List(
       "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
       )), Map("biomFile" -> new File(run.outputDir + File.separator + qiimeClosesOtuTable.get.path)))))
-    else Nil) ::: (if (qiimeOpenOtuTable.isDefined) List("Qiime open reference analysis" -> Future(ReportPage(List(), List(
+    else Nil) ::: (if (qiimeOpenOtuTable.isDefined) List("Qiime open reference analysis" -> Future.successful(ReportPage(List(), List(
       "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
       )), Map("biomFile" -> new File(run.outputDir + File.separator + qiimeOpenOtuTable.get.path)))))
     else Nil) ::: List(
@@ -136,20 +136,20 @@ object GearsReport extends MultisampleReportBuilder {
 
     ReportPage(
       (if (flexiprepExecuted) List("QC" -> FlexiprepReport.flexiprepPage) 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",
+      ) ::: (if (centrifugeExecuted) List("Centriguge analysis" -> Future.successful(ReportPage(List(
+        "Non-unique" -> Future.successful(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("Kraken analysis" -> Future(ReportPage(List(), List(
+      else Nil) ::: (if (krakenExecuted) List("Kraken analysis" -> Future.successful(ReportPage(List(), List(
         "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
         )), Map())))
-      else Nil) ::: (if (qiimeClosesOtuTable.isDefined) List("Qiime closed reference analysis" -> Future(ReportPage(List(), List(
+      else Nil) ::: (if (qiimeClosesOtuTable.isDefined) List("Qiime closed reference analysis" -> Future.successful(ReportPage(List(), List(
         "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
         )), Map("biomFile" -> new File(qiimeClosesOtuTable.get.path)))))
-      else Nil) ::: (if (qiimeOpenOtuTable.isDefined) List("Qiime open reference analysis" -> Future(ReportPage(List(), List(
+      else Nil) ::: (if (qiimeOpenOtuTable.isDefined) List("Qiime open reference analysis" -> Future.successful(ReportPage(List(), List(
         "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
         )), Map("biomFile" -> new File(qiimeOpenOtuTable.get.path)))))
       else Nil), List(

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

@@ -34,6 +34,7 @@ object GearsSingleReport extends ReportBuilder {
     .map(x => ExtFile("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + x, x))
 
   def indexPage: Future[ReportPage] = Future {
+    sampleId.map
     val sampleName = sampleId.flatMap(x => Await.result(summary.getSampleName(x), Duration.Inf))
     val libraryName = libId.flatMap(x => Await.result(summary.getLibraryName(x), Duration.Inf))
 

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

@@ -56,7 +56,7 @@ object MappingReport extends ReportBuilder {
     } else None
     ReportPage((if (skipFlexiprep) Nil else List("QC" -> FlexiprepReport.flexiprepPage)) :::
       bamMetricsPage.map(_.subPages).getOrElse(Nil) :::
-      (if (krakenExecuted) List("Gears - Metagenomics" -> Future(ReportPage(List(), List(
+      (if (krakenExecuted) List("Gears - Metagenomics" -> Future.successful(ReportPage(List(), List(
         "Sunburst analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp"
         )), Map())))
       else Nil), List(

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

@@ -66,18 +66,18 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
 
     ReportPage(
       List("Samples" -> generateSamplesPage(pageArgs)) ++
-        (if (krakenExecuted) List("Dustbin analysis - Kraken" -> Future(ReportPage(List(), List(
+        (if (krakenExecuted) List("Dustbin analysis - Kraken" -> Future.successful(ReportPage(List(), List(
           "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
           )), 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",
+        else Nil) ++ (if (centrifugeExecuted) List("Centriguge analysis" -> Future.successful(ReportPage(List(
+          "Non-unique" -> Future.successful(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) ++
-        List("Reference" -> Future(ReportPage(List(), List(
+        List("Reference" -> Future.successful(ReportPage(List(), List(
           "Reference" -> ReportSection("/nl/lumc/sasc/biopet/core/report/reference.ssp", Map("pipeline" -> pipelineName))
         ), Map()))
         ),
@@ -122,14 +122,14 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
     ReportPage(List(
       "Libraries" -> generateLibraryPage(args),
       "Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), None)) ++
-      (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",
+      (if (centrifugeExecuted) List("Centriguge analysis" -> Future.successful(ReportPage(List(
+        "Non-unique" -> Future.successful(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" -> Future(ReportPage(List(), List(
+      else Nil) ::: (if (krakenExecuted) List("Dustbin analysis" -> Future.successful(ReportPage(List(), List(
         "Krona Plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
         )), Map())))
       else Nil), List(
@@ -154,14 +154,14 @@ 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" -> Future(ReportPage(List(
-          "Non-unique" -> Future(ReportPage(List(), List("All mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
+        (if (centrifugeExecuted) List("Centriguge analysis" -> Future.successful(ReportPage(List(
+          "Non-unique" -> Future.successful(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" -> Future(ReportPage(List(), List(
+        else Nil) ::: (if (krakenExecuted) List("Dustbin analysis" -> Future.successful(ReportPage(List(), List(
           "Krona Plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
           )), Map())))
         else Nil),