Fixing capture of failures

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

@@ -224,10 +224,11 @@ trait ReportBuilder extends ToolCommand {
 
     def wait(futures: List[Future[Any]]): Unit = {
       try {
-        Await.ready(Future.sequence(futures), Duration.fromNanos(30000000000L))
+        Await.result(Future.sequence(futures), Duration.fromNanos(30000000000L))
       } catch {
         case e: TimeoutException =>
       }
+      val dones = futures.filter(_.isCompleted)
       val notDone = futures.filter(!_.isCompleted)
       done += futures.size - notDone.size
       if (notDone.nonEmpty) {
@@ -236,8 +237,11 @@ trait ReportBuilder extends ToolCommand {
       }
     }
 
+    //jobsFutures.foreach(f => f.onFailure{ case e => throw new RuntimeException(e) })
+
     wait(jobsFutures)
-    Await.ready(baseFilesFuture, Duration.Inf)
+    Await.result(Future.sequence(jobsFutures), Duration.Inf)
+    Await.result(baseFilesFuture, Duration.Inf)
 
     logger.info(s"Done, $done pages generated")
   }
@@ -262,7 +266,7 @@ trait ReportBuilder extends ToolCommand {
                    pageFuture: Future[ReportPage],
                    outputDir: File,
                    path: List[String] = Nil,
-                   args: Map[String, Any] = Map()): List[Future[_]] = {
+                   args: Map[String, Any] = Map()): List[Future[ReportPage]] = {
     val pageOutputDir = new File(outputDir, path.mkString(File.separator))
 
     def pageArgs(page: ReportPage) = {
@@ -301,6 +305,7 @@ trait ReportBuilder extends ToolCommand {
       writer.close()
       logger.info(s"Done rendering: $file")
 
+      page
     }
 
     renderFuture :: Await.result(subPageJobs, Duration.Inf)

carp/src/main/resources/nl/lumc/sasc/biopet/pipelines/carp/carpFront.ssp

 #import(nl.lumc.sasc.biopet.utils.summary.db.Schema.Run)
 #import(nl.lumc.sasc.biopet.utils.summary.db.Schema.Sample)
 <%@ var run: Run %>
-<%@ var allSamples: List[Sample] %>
+<%@ var allSamples: Seq[Sample] %>
 <table class="table">
 <tbody>
     <tr><th>Pipeline</th><td>Carp</td></tr>

flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp

@@ -19,8 +19,8 @@
 <%@ var showTable: Boolean = true %>
 <%@ var showIntro: Boolean = true %>
 <%@ var multisample: Boolean = true %>
-<%@ var allSamples: List[Sample] %>
-<%@ var allLibraries: List[Library] %>
+<%@ var allSamples: Seq[Sample] %>
+<%@ var allLibraries: Seq[Library] %>
 #{
     val samples = sampleId.map(id => allSamples.filter(_.id == id)).getOrElse(allSamples)
     val libraries = libId.map(id => allLibraries.filter(_.id == id)).getOrElse(allLibraries)

flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFront.ssp

@@ -4,8 +4,8 @@
 <%@ var sampleId: Option[Int] %>
 <%@ var libId: Option[Int] %>
 <%@ var run: Run %>
-<%@ var allSamples: List[Sample] %>
-<%@ var allLibraries: List[Library] %>
+<%@ var allSamples: Seq[Sample] %>
+<%@ var allLibraries: Seq[Library] %>
 <table class="table">
 <tbody>
     <tr><th>Pipeline</th><td>Flexiprep</td></tr>

flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp

@@ -18,8 +18,8 @@
 <%@ var showTable: Boolean = true %>
 <%@ var showIntro: Boolean = true %>
 <%@ var multisample: Boolean = true %>
-<%@ var allSamples: List[Sample] %>
-<%@ var allLibraries: List[Library] %>
+<%@ var allSamples: Seq[Sample] %>
+<%@ var allLibraries: Seq[Library] %>
 #{
     val samples = sampleId.map(id => allSamples.filter(_.id == id)).getOrElse(allSamples)
     val libraries = libId.map(id => allLibraries.filter(_.id == id)).getOrElse(allLibraries)

gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsFront.ssp

 #import(nl.lumc.sasc.biopet.utils.summary.db.Schema.Run)
 #import(nl.lumc.sasc.biopet.utils.summary.db.Schema.Sample)
 <%@ var run: Run %>
-<%@ var allSamples: List[Sample] %>
+<%@ var allSamples: Seq[Sample] %>
 <table class="table">
 <tbody>
     <tr><th>Pipeline</th><td>Gears</td></tr>

gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/gentrapFront.ssp

 #import(nl.lumc.sasc.biopet.utils.summary.db.Schema.Run)
 #import(nl.lumc.sasc.biopet.utils.summary.db.Schema.Sample)
 <%@ var run: Run %>
-<%@ var allSamples: List[Sample] %>
+<%@ var allSamples: Seq[Sample] %>
 <table class="table">
 <tbody>
     <tr><th>Pipeline</th><td>Gentrap</td></tr>

mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/mappingFront.ssp

@@ -5,8 +5,6 @@
 #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
 #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
 #import(nl.lumc.sasc.biopet.core.report.ReportPage)
-#import(scala.concurrent.Await)
-#import(scala.concurrent.duration.Duration)
 <%@ var summary: SummaryDb %>
 <%@ var rootPath: String %>
 <%@ var runId: Int %>

mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/multisampleMappingFront.ssp

@@ -11,7 +11,7 @@
 <%@ var pipeline: String %>
 <%@ var runId: Int %>
 <%@ var run: Run %>
-<%@ var allSamples: List[Sample] %>
+<%@ var allSamples: Seq[Sample] %>
 #{
     val samples = allSamples
     val settings = summary.getSettingKeys(runId, pipeline,

shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp

@@ -19,7 +19,7 @@
 <%@ var target: Option[String] = None %>
 <%@ var caller: String = "final" %>
 <%@ var runId: Int %>
-<%@ var allSamples: List[Sample] %>
+<%@ var allSamples: Seq[Sample] %>
 #{
     val fields = List("Hom", "HomVar", "Het", "HomRef", "NoCall", "Variant", "Total")
 

shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp

 #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
 #import(nl.lumc.sasc.biopet.utils.summary.db.Schema.Run)
+#import(nl.lumc.sasc.biopet.utils.summary.db.Schema.Sample)
 #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
 #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
 #import(nl.lumc.sasc.biopet.core.report.ReportPage)
@@ -8,8 +9,8 @@
 <%@ var summary: SummaryDb %>
 <%@ var runId: Int %>
 <%@ var run: Run %>
+<%@ var allSamples: Seq[Sample] %>
 #{
-    val samples = Await.result(summary.getSamples(Some(runId)), Duration.Inf)
     val settings = summary.getSettingKeys(runId, run.name,
     keyValues = Map(
         "contigs" -> List("reference", "contigs"),
@@ -33,7 +34,7 @@
         <td>${settings.get("variantcallers")}</td>
     </tr>
     <tr><th>Reference</th><td>${settings.get("species")} - ${settings.get("name")}</td></tr>
-    <tr><th>Number of samples</th><td>${samples.size}</td></tr>
+    <tr><th>Number of samples</th><td>${allSamples.size}</td></tr>
     <tr><th>Annotation</th><td>${settings.get("annotation")}</td></tr>
     <tr><th>Multisample variantcalling</th><td>${settings.get("multisample_variantcalling")}</td></tr>
     <tr><th>Sv calling</th><td>${settings.get("sv_calling")}</td></tr>