Fix style

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

@@ -14,12 +14,12 @@
  */
 package nl.lumc.sasc.biopet.pipelines.bammetrics
 
-import java.io.{File, PrintWriter}
+import java.io.{ File, PrintWriter }
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.report.{ReportBuilder, ReportBuilderExtension, ReportPage, ReportSection}
+import nl.lumc.sasc.biopet.core.report.{ ReportBuilder, ReportBuilderExtension, ReportPage, ReportSection }
 import nl.lumc.sasc.biopet.utils.ConfigUtils
-import nl.lumc.sasc.biopet.utils.rscript.{LinePlot, StackedBarPlot}
+import nl.lumc.sasc.biopet.utils.rscript.{ LinePlot, StackedBarPlot }
 import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
 
 import scala.concurrent.ExecutionContext.Implicits.global
@@ -69,10 +69,9 @@ object BammetricsReport extends ReportBuilder {
 
     val insertsizeMetrics = summary.getStatKeys(runId, Right(metricsTag), Some(Right("CollectInsertSizeMetrics")),
       sample = sampleId.map(Left(_)), library = libId.map(Left(_)), Map("metrics" -> List("metrics")))
-        .exists(_._2.isDefined)
+      .exists(_._2.isDefined)
 
-
-    val targetSettings = summary.getSettingKeys(runId, Right(metricsTag),None, sample = sampleId.map(Left(_)), library = libId.map(Left(_)),
+    val targetSettings = summary.getSettingKeys(runId, Right(metricsTag), None, sample = sampleId.map(Left(_)), library = libId.map(Left(_)),
       Map("amplicon_name" -> List("amplicon_name"), "roi_name" -> List("roi_name")))
     val targets = (
       targetSettings("amplicon_name"),
@@ -136,9 +135,9 @@ object BammetricsReport extends ReportBuilder {
       summary.getStatsForLibraries(runId, Right("bammetrics"), Some(Right("bamstats")),
         sampleId = sampleId, keyValues = statsPaths).map(x => (x._1._1, Some(x._1._2)) -> x._2)
     } else summary.getStatsForSamples(runId, Right("bammetrics"), Some(Right("bamstats")),
-       sample = sampleId.map(Left(_)), keyValues = statsPaths).map(x => (x._1, None) -> x._2)
+      sample = sampleId.map(Left(_)), keyValues = statsPaths).map(x => (x._1, None) -> x._2)
 
-    for (((s,l),result) <- results) {
+    for (((s, l), result) <- results) {
       val sampleName: String = summary.getSampleName(s).map(_.get)
       val libName: Option[String] = l.flatMap(x => Await.result(summary.getLibraryName(x), Duration.Inf))
       val sb = new StringBuffer()
@@ -168,20 +167,20 @@ object BammetricsReport extends ReportBuilder {
   }
 
   def writePlotFromSummary(outputDir: File,
-           prefix: String,
-           summary: SummaryDb,
-           libraryLevel: Boolean = false,
-           sampleId: Option[Int] = None,
-           libraryId: Option[Int] = None,
-           statsPaths: Map[String, List[String]],
-           xKey: String,
-           yKey: String,
-           pipeline: Either[Int,String],
-           module: Option[Either[Int,String]],
-           xlabel: Option[String] = None,
-           ylabel: Option[String] = None,
-           title: Option[String] = None,
-           removeZero: Boolean = true): Unit = {
+                           prefix: String,
+                           summary: SummaryDb,
+                           libraryLevel: Boolean = false,
+                           sampleId: Option[Int] = None,
+                           libraryId: Option[Int] = None,
+                           statsPaths: Map[String, List[String]],
+                           xKey: String,
+                           yKey: String,
+                           pipeline: Either[Int, String],
+                           module: Option[Either[Int, String]],
+                           xlabel: Option[String] = None,
+                           ylabel: Option[String] = None,
+                           title: Option[String] = None,
+                           removeZero: Boolean = true): Unit = {
     val tsvFile = new File(outputDir, prefix + ".tsv")
     val pngFile = new File(outputDir, prefix + ".png")
 
@@ -191,14 +190,15 @@ object BammetricsReport extends ReportBuilder {
     } else summary.getStatsForSamples(runId, pipeline, module, sample = sampleId.map(Left(_)), keyValues = statsPaths)
       .map(x => (x._1, None) -> x._2.map(x => x._1 -> x._2.map(ConfigUtils.any2list(_).toArray)))
 
-    val tables: Array[Map[String, Array[Any]]] = results.map { case ((sample,library), map) =>
+    val tables: Array[Map[String, Array[Any]]] = results.map {
+      case ((sample, library), map) =>
         val sampleName = Await.result(summary.getSampleName(sample), Duration.Inf)
           .getOrElse(throw new IllegalStateException("Sample must be there"))
         val libraryName = library.flatMap(l => Await.result(summary.getLibraryName(l), Duration.Inf))
-      Map(
-        yKey -> map(yKey).getOrElse(Array()),
-        (sampleName + libraryName.map("-" + _)getOrElse("")) -> map(xKey).getOrElse(Array())
-      )
+        Map(
+          yKey -> map(yKey).getOrElse(Array()),
+          (sampleName + libraryName.map("-" + _) getOrElse ("")) -> map(xKey).getOrElse(Array())
+        )
     }.toArray
 
     writeTableToTsv(tsvFile, mergeTables(tables, yKey), yKey)
@@ -230,7 +230,7 @@ object BammetricsReport extends ReportBuilder {
       "count" -> List("histogram", "All_Reads.fr_count")
     )
 
-    writePlotFromSummary(outputDir, prefix, summary, libraryLevel, sampleId, libraryId,statsPaths,
+    writePlotFromSummary(outputDir, prefix, summary, libraryLevel, sampleId, libraryId, statsPaths,
       "insert_size", "count", Right("bammetrics"), Some(Right("CollectInsertSizeMetrics")),
       "Insert size", "Reads", "Insert size")
   }

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

@@ -50,14 +50,14 @@ trait MultisampleReportBuilder extends ReportBuilder {
     val samplePages = samples.map(_.id)
       .map(sampleId => sampleId -> samplePage(sampleId, args ++ Map("sampleId" -> Some(sampleId))))
       .toList
-    ReportPage(samplePages.map(x => samples.find(_.name == x._1).get.name -> x._2), samplesSections, args)
+    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]): ReportPage = {
     val sampleId = args("sampleId") match {
       case Some(x: Int) => x
-      case None    => throw new IllegalStateException("Sample not found")
+      case None         => throw new IllegalStateException("Sample not found")
     }
 
     val libraries = Await.result(summary.getLibraries(runId = Some(runId), sampleId = Some(sampleId)), Duration.Inf)
@@ -65,6 +65,6 @@ trait MultisampleReportBuilder extends ReportBuilder {
     val libPages = libraries.map(_.id)
       .map(libId => libId -> libraryPage(sampleId, libId, args ++ Map("libId" -> Some(libId))))
       .toList
-    ReportPage(libPages.map(x => libraries.find(_.name == x._1).get.name -> x._2), librariesSections, args)
+    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

@@ -17,15 +17,15 @@ package nl.lumc.sasc.biopet.core.report
 import java.io._
 
 import nl.lumc.sasc.biopet.core.ToolCommandFunction
-import nl.lumc.sasc.biopet.utils.summary.db.Schema.{Library, Sample}
+import nl.lumc.sasc.biopet.utils.summary.db.Schema.{ Library, Sample }
 import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
-import nl.lumc.sasc.biopet.utils.{IoUtils, Logging, ToolCommand}
+import nl.lumc.sasc.biopet.utils.{ IoUtils, Logging, ToolCommand }
 import org.broadinstitute.gatk.utils.commandline.Input
 import nl.lumc.sasc.biopet.utils.tryToParseNumber
-import org.fusesource.scalate.{TemplateEngine, TemplateSource}
+import org.fusesource.scalate.{ TemplateEngine, TemplateSource }
 
 import scala.collection.mutable
-import scala.concurrent.{Await, Future}
+import scala.concurrent.{ Await, Future }
 import scala.concurrent.duration.Duration
 import scala.language.postfixOps
 
@@ -73,8 +73,8 @@ trait ReportBuilderExtension extends ToolCommandFunction {
 
 trait ReportBuilder extends ToolCommand {
 
-  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 toOption[T](x: T): Option[T] = Option(x)
+  implicit def autoWait[T](x: Future[T]): T = Await.result(x, Duration.Inf)
 
   case class Args(summaryDbFile: File = null,
                   outputDir: File = null,

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/implicits/Either.scala

 package nl.lumc.sasc.biopet.utils.implicits
 
 /**
-  * Created by pjvanthof on 20/02/2017.
-  */
+ * Created by pjvanthof on 20/02/2017.
+ */
 object Either {
-  implicit def optionEitherLeft[T](x: Option[Either[T,_]]): Option[Option[T]] = {
+  implicit def optionEitherLeft[T](x: Option[Either[T, _]]): Option[Option[T]] = {
     x match {
-      case Some(i:Either[T, _]) if i.isLeft => Some(i.left.toOption)
-      case _ => None
+      case Some(i: Either[T, _]) if i.isLeft => Some(i.left.toOption)
+      case _                                 => None
     }
   }
 
-  implicit def optionEitherRight[T](x: Option[Either[_,T]]): Option[Option[T]] = {
+  implicit def optionEitherRight[T](x: Option[Either[_, T]]): Option[Option[T]] = {
     x match {
-      case Some(i:Either[_,T]) if i.isRight => Some(i.right.toOption)
-      case _ => None
+      case Some(i: Either[_, T]) if i.isRight => Some(i.right.toOption)
+      case _                                  => None
     }
   }
 
-  implicit def eitherLeft[T](x: Either[T,_]): Option[T] = {
+  implicit def eitherLeft[T](x: Either[T, _]): Option[T] = {
     x match {
       case Left(x) => Some(x)
-      case _ => None
+      case _       => None
     }
   }
 
-  implicit def eitherRight[T](x: Either[_,T]): Option[T] = {
+  implicit def eitherRight[T](x: Either[_, T]): Option[T] = {
     x match {
       case Right(x) => Some(x)
-      case _ => None
+      case _        => None
     }
   }
 
-  implicit def left[T](x:T): Left[T, _] = Left(x)
-  implicit def right[T](x:T): Right[_, T] = Right(x)
-  implicit def left[T](x:Option[T]): Option[Left[T, _]] = x.map(Left(_))
-  implicit def right[T](x:Option[T]): Option[Right[_, T]] = x.map(Right(_))
+  implicit def left[T](x: T): Left[T, _] = Left(x)
+  implicit def right[T](x: T): Right[_, T] = Right(x)
+  implicit def left[T](x: Option[T]): Option[Left[T, _]] = x.map(Left(_))
+  implicit def right[T](x: Option[T]): Option[Right[_, T]] = x.map(Right(_))
 
 }

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

@@ -15,7 +15,7 @@
 package nl.lumc.sasc.biopet.pipelines.gears
 
 import nl.lumc.sasc.biopet.utils.implicits.Either._
-import nl.lumc.sasc.biopet.core.report.{MultisampleReportBuilder, ReportBuilderExtension, ReportPage, ReportSection}
+import nl.lumc.sasc.biopet.core.report.{ MultisampleReportBuilder, ReportBuilderExtension, ReportPage, ReportSection }
 import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
 import nl.lumc.sasc.biopet.utils.config.Configurable
 
@@ -86,7 +86,6 @@ object GearsReport extends MultisampleReportBuilder {
     val qiimeClosesOtuTable = Await.result(summary.getFile(runId, "gears", None, sampleName, None, key = "qiime_closed_otu_table"), Duration.Inf)
     val qiimeOpenOtuTable = Await.result(summary.getFile(runId, "gears", None, sampleName, None, key = "qiime_open_otu_table"), Duration.Inf)
 
-
     ReportPage((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(
@@ -121,7 +120,6 @@ object GearsReport extends MultisampleReportBuilder {
     val qiimeClosesOtuTable = Await.result(summary.getFile(runId, "gears", None, sName, lName, key = "qiime_closed_otu_table"), Duration.Inf)
     val qiimeOpenOtuTable = Await.result(summary.getFile(runId, "gears", None, sName, lName, key = "qiime_open_otu_table"), Duration.Inf)
 
-
     ReportPage(
       (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",

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

@@ -14,7 +14,7 @@
  */
 package nl.lumc.sasc.biopet.pipelines.mapping
 
-import nl.lumc.sasc.biopet.core.report.{MultisampleReportBuilder, ReportBuilderExtension, ReportPage, ReportSection}
+import nl.lumc.sasc.biopet.core.report.{ MultisampleReportBuilder, ReportBuilderExtension, ReportPage, ReportSection }
 import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
 import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
 import nl.lumc.sasc.biopet.utils.config.Configurable

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

@@ -14,14 +14,14 @@
  */
 package nl.lumc.sasc.biopet.pipelines.shiva
 
-import java.io.{File, PrintWriter}
+import java.io.{ File, PrintWriter }
 
 import nl.lumc.sasc.biopet.core.report._
 import nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingReportTrait
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.utils.rscript.StackedBarPlot
 import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
-import nl.lumc.sasc.biopet.utils.summary.{Summary, SummaryValue}
+import nl.lumc.sasc.biopet.utils.summary.{ Summary, SummaryValue }
 
 import scala.concurrent.Await
 import scala.concurrent.duration.Duration
@@ -43,9 +43,9 @@ trait ShivaReportTrait extends MultisampleMappingReportTrait {
 
   def variantcallingExecuted = summary.getSettingKeys(runId, Right("shiva"), None, keyValues = Map("multisample_variantcalling" -> List("multisample_variantcalling"))).get("multisample_variantcalling")
     .flatten match {
-    case Some(true) => true
-    case _          => false
-  }
+      case Some(true) => true
+      case _          => false
+    }
 
   override def frontSection = ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp")