Fixed compile issues

bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp

@@ -43,7 +43,7 @@
 #end
 
 #if (showPlot)
-    #{ BammetricsReport.insertSizePlot(outputDir, "insertsize", summary, !sampleLevel, sampleId = sampleId, libId = libId) }#
+    #{ BammetricsReport.insertSizePlot(outputDir, "insertsize", summary, !sampleLevel, sampleId = sampleId, libraryId = libId) }#
 
     <div class="panel-body">
     <img src="insertsize.png" class="img-responsive" />

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

@@ -19,6 +19,9 @@ import nl.lumc.sasc.biopet.core.report._
 import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
 import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
 
+import scala.concurrent.Await
+import scala.concurrent.duration.Duration
+
 class MappingReport(val parent: Configurable) extends ReportBuilderExtension {
   def builder = MappingReport
 }
@@ -35,12 +38,17 @@ object MappingReport 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 krakenExecuted = summary.getValue(sampleId, libId, "gears", "stats", "krakenreport").isDefined
+  summary.getStatsSize(runId, Right("gears"), Some(Right("krakenreport")),
+    sample = sampleId.map(Left(_)), library = libId.map(Left(_)))
+  def krakenExecuted: Boolean = Await.result(summary.getStatsSize(runId, Right("gears"), Some(Right("krakenreport")),
+    sample = sampleId.map(Left(_)), library = libId.map(Left(_))), Duration.Inf) >= 1
 
   /** Root page for single BamMetrcis report */
   def indexPage = {
-    val skipFlexiprep = summary.getValue(sampleId, libId, "mapping", "settings", "skip_flexiprep").getOrElse(false) == true
-    val bamMetricsPage = if (summary.getValue(sampleId, libId, "mapping", "settings", "skip_metrics").getOrElse(false) != true) {
+    val mappingSettings = summary.getSettingKeys(runId, Right("mapping"), None, sample = sampleId.map(Left(_)), library = libId.map(Left(_)),
+      keyValues = Map("skip_flexiprep" -> List("skip_flexiprep"), "skip_metrics" -> List("skip_metrics")))
+    val skipFlexiprep = mappingSettings.get("skip_flexiprep").flatten.getOrElse(false) == true
+    val bamMetricsPage = if (mappingSettings.get("skip_metrics").flatten.getOrElse(false) == true) {
       Some(BammetricsReport.bamMetricsPage(summary, sampleId, libId))
     } else None
     ReportPage((if (skipFlexiprep) Nil else List("QC" -> FlexiprepReport.flexiprepPage)) :::

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

@@ -14,11 +14,14 @@
  */
 package nl.lumc.sasc.biopet.pipelines.mapping
 
-import nl.lumc.sasc.biopet.core.report.{ ReportBuilderExtension, ReportSection, ReportPage, MultisampleReportBuilder }
+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
 
+import scala.concurrent.Await
+import scala.concurrent.duration.Duration
+
 /**
  * Created by pjvanthof on 11/01/16.
  */
@@ -45,15 +48,20 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
   /** Root page for the carp report */
   def indexPage = {
 
-    val krakenExecuted = summary.getSampleValues("gearskraken", "stats", "krakenreport").values.forall(_.isDefined)
-    val centrifugeExecuted = summary.getSampleValues("gearscentrifuge", "stats", "centrifuge_report").values.forall(_.isDefined)
-    val wgsExecuted = summary.getSampleValues("bammetrics", "stats", "wgs").values.exists(_.isDefined)
-    val rnaExecuted = summary.getSampleValues("bammetrics", "stats", "rna").values.exists(_.isDefined)
-    val insertsizeExecuted = summary.getSampleValues("bammetrics", "stats", "CollectInsertSizeMetrics", "metrics").values.exists(_ != Some(None))
-    val mappingExecuted = summary.getLibraryValues("mapping").exists(_._2.isDefined)
-    val pairedFound = !mappingExecuted || summary.getLibraryValues("mapping", "settings", "paired").exists(_._2 == Some(true))
-    val flexiprepExecuted = summary.getLibraryValues("flexiprep")
-      .exists { case ((sample, lib), value) => value.isDefined }
+    val krakenExecuted = Await.result(summary.getStatsSize(runId, Right("gearskraken"), Some(Right("krakenreport")),
+      library = Some(None), mustHaveSample = true), Duration.Inf) >= 1
+    val centrifugeExecuted = Await.result(summary.getStatsSize(runId, Right("gearscentrifuge"), Some(Right("centrifuge_report")),
+      library = Some(None), mustHaveSample = true), Duration.Inf) >= 1
+    val wgsExecuted = Await.result(summary.getStatsSize(runId, Right("bammetrics"), Some(Right("wgs")),
+      library = Some(None), mustHaveSample = true), Duration.Inf) >= 1
+    val rnaExecuted = Await.result(summary.getStatsSize(runId, Right("bammetrics"), Some(Right("rna")),
+      library = Some(None), mustHaveSample = true), Duration.Inf) >= 1
+    val insertsizeExecuted = Await.result(summary.getStatsSize(runId, Right("bammetrics"), Some(Right("CollectInsertSizeMetrics")),
+      library = Some(None), mustHaveSample = true), Duration.Inf) >= 1
+    val mappingExecuted = Await.result(summary.getStatsSize(runId, Right("mapping"), Some(None), mustHaveLibrary = true), Duration.Inf) >= 1
+    val pairedFound = !mappingExecuted || summary.getSettingsForLibraries(runId, Right("mapping"), None, keyValues = Map("paired" -> List("paired")))
+      .exists(_._2.exists(_._2 == Some(true)))
+    val flexiprepExecuted = Await.result(summary.getStatsSize(runId, Right("flexiprep"), Some(None), mustHaveLibrary = true), Duration.Inf) >= 1
 
     ReportPage(
       List("Samples" -> generateSamplesPage(pageArgs)) ++
@@ -105,8 +113,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
 
   /** Files page, can be used general or at sample level */
   def filesPage: ReportPage = {
-    val flexiprepExecuted = summary.getLibraryValues("flexiprep")
-      .exists { case ((sample, lib), value) => value.isDefined }
+    val flexiprepExecuted = Await.result(summary.getStatsSize(runId, Right("flexiprep"), Some(None), mustHaveLibrary = true), Duration.Inf) >= 1
 
     ReportPage(List(), (if (flexiprepExecuted) List(
       "Input fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepInputfiles.ssp"),
@@ -118,11 +125,13 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
   }
 
   /** Single sample page */
-  def samplePage(sampleId: String, args: Map[String, Any]): ReportPage = {
-    val krakenExecuted = summary.getValue(Some(sampleId), None, "gearskraken", "stats", "krakenreport").isDefined
-    val centrifugeExecuted = summary.getValue(Some(sampleId), None, "gearscentrifuge", "stats", "centrifuge_report").isDefined
-    val flexiprepExecuted = summary.getLibraryValues("flexiprep")
-      .exists { case ((sample, lib), value) => sample == sampleId && value.isDefined }
+  def samplePage(sampleId: Int, args: Map[String, Any]): ReportPage = {
+    val krakenExecuted = Await.result(summary.getStatsSize(runId, Right("gearskraken"), Some(Right("krakenreport")),
+      library = Some(None), sample = Some(Left(sampleId))), Duration.Inf) >= 1
+    val centrifugeExecuted = Await.result(summary.getStatsSize(runId, Right("gearscentrifuge"), Some(Right("centrifuge_report")),
+      library = Some(None), sample = Some(Left(sampleId)), mustHaveSample = true), Duration.Inf) >= 1
+    val flexiprepExecuted = Await.result(summary.getStatsSize(runId, Right("flexiprep"), Some(None),
+      sample = Some(Left(sampleId)), mustHaveLibrary = true), Duration.Inf) >= 1
 
     ReportPage(List(
       "Libraries" -> generateLibraryPage(args),
@@ -149,10 +158,13 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
   }
 
   /** Library page */
-  def libraryPage(sampleId: String, libId: String, args: Map[String, Any]): ReportPage = {
-    val krakenExecuted = summary.getValue(Some(sampleId), Some(libId), "gearskraken", "stats", "krakenreport").isDefined
-    val centrifugeExecuted = summary.getValue(Some(sampleId), Some(libId), "gearscentrifuge", "stats", "centrifuge_report").isDefined
-    val flexiprepExecuted = summary.getValue(Some(sampleId), Some(libId), "flexiprep").isDefined
+  def libraryPage(sampleId: Int, libId: Int, args: Map[String, Any]): ReportPage = {
+    val krakenExecuted = Await.result(summary.getStatsSize(runId, Right("gearskraken"), Some(Right("krakenreport")),
+      library = Some(Left(libId)), sample = Some(Left(sampleId))), Duration.Inf) >= 1
+    val centrifugeExecuted = Await.result(summary.getStatsSize(runId, Right("gearscentrifuge"), Some(Right("centrifuge_report")),
+      library = Some(Left(libId)), sample = Some(Left(sampleId)), mustHaveSample = true), Duration.Inf) >= 1
+    val flexiprepExecuted = Await.result(summary.getStatsSize(runId, Right("flexiprep"), Some(None), library = Some(Left(libId)),
+      sample = Some(Left(sampleId)), mustHaveLibrary = true), Duration.Inf) >= 1
 
     ReportPage(
       ("Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), Some(libId))) ::

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

@@ -14,13 +14,17 @@
  */
 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.{ Summary, SummaryValue }
+import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
+import nl.lumc.sasc.biopet.utils.summary.{Summary, SummaryValue}
+
+import scala.concurrent.Await
+import scala.concurrent.duration.Duration
 
 /**
  * With this extension the report is executed within a pipeline
@@ -37,7 +41,8 @@ object ShivaReport extends ShivaReportTrait
 /** Trait for report generation for Shiva pipeline, this can be extended */
 trait ShivaReportTrait extends MultisampleMappingReportTrait {
 
-  def variantcallingExecuted = summary.getValue("shiva", "settings", "multisample_variantcalling") match {
+  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
   }
@@ -60,8 +65,8 @@ trait ShivaReportTrait extends MultisampleMappingReportTrait {
 
   /** Generate a page with all target coverage stats */
   def regionsPage: Option[(String, ReportPage)] = {
-    val roi = summary.getValue("shiva", "settings", "regions_of_interest")
-    val amplicon = summary.getValue("shiva", "settings", "amplicon_bed")
+    val roi = summary.getSetting(runId, Right("shiva")).get("regions_of_interest")
+    val amplicon = summary.getSetting(runId, Right("shiva")).get("amplicon_bed")
 
     var regionPages: Map[String, ReportPage] = Map()
 
@@ -108,7 +113,7 @@ trait ShivaReportTrait extends MultisampleMappingReportTrait {
   }
 
   /** Single sample page */
-  override def samplePage(sampleId: String, args: Map[String, Any]): ReportPage = {
+  override def samplePage(sampleId: Int, args: Map[String, Any]): ReportPage = {
     val variantcallingSection = if (variantcallingExecuted) List("Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp")) else Nil
     val oldPage = super.samplePage(sampleId, args)
     oldPage.copy(sections = variantcallingSection ++ oldPage.sections)
@@ -123,51 +128,37 @@ trait ShivaReportTrait extends MultisampleMappingReportTrait {
    * @param outputDir OutputDir for the tsv and png file
    * @param prefix Prefix of the tsv and png file
    * @param summary Summary class
-   * @param libraryLevel Default false, when set true plot will be based on library stats instead of sample stats
    * @param sampleId Default it selects all sampples, when sample is giving it limits to selected sample
    */
   def variantSummaryPlot(outputDir: File,
                          prefix: String,
-                         summary: Summary,
-                         libraryLevel: Boolean = false,
-                         sampleId: Option[String] = None,
+                         summary: SummaryDb,
+                         sampleId: Option[Int] = None,
                          caller: String = "final",
                          target: Option[String] = None): Unit = {
     val tsvFile = new File(outputDir, prefix + ".tsv")
     val pngFile = new File(outputDir, prefix + ".png")
     val tsvWriter = new PrintWriter(tsvFile)
-    if (libraryLevel) tsvWriter.print("Library") else tsvWriter.print("Sample")
-    tsvWriter.println("\tHomVar\tHet\tHomRef\tNoCall")
-
-    def getLine(summary: Summary, sample: String, summarySample: Option[String], lib: Option[String] = None): String = {
-      val path = target match {
-        case Some(t) => List("shivavariantcalling", "stats", s"multisample-vcfstats-$caller-$t", "genotype", sample)
-        case _       => List("shivavariantcalling", "stats", s"multisample-vcfstats-$caller", "total", "genotype", "general", sample)
-      }
-      val homVar = new SummaryValue(path :+ "HomVar", summary, summarySample, lib).value.getOrElse(0).toString.toLong
-      val homRef = new SummaryValue(path :+ "HomRef", summary, summarySample, lib).value.getOrElse(0).toString.toLong
-      val noCall = new SummaryValue(path :+ "NoCall", summary, summarySample, lib).value.getOrElse(0).toString.toLong
-      val het = new SummaryValue(path :+ "Het", summary, summarySample, lib).value.getOrElse(0).toString.toLong
-      val sb = new StringBuffer()
-      if (lib.isDefined) sb.append(sample + "-" + lib.get + "\t") else sb.append(sample + "\t")
-      sb.append(homVar + "\t")
-      sb.append(het + "\t")
-      sb.append(homRef + "\t")
-      sb.append(noCall)
-      sb.toString
+    tsvWriter.print("Sample")
+    val field = List("HomVar", "Het", "HomRef", "NoCall")
+    tsvWriter.println(s"\t${field.mkString("\t")}")
+
+    val samples = Await.result(summary.getSamples(runId = runId, sampleId = sampleId), Duration.Inf)
+    val statsPaths = {
+      (for (sample <- Await.result(summary.getSamples(runId = runId), Duration.Inf)) yield {
+        field.map(f => s"${sample.name};HomVar" -> List("total", "genotype", "general", sample.name, f)).toMap
+      }).fold(Map())(_ ++ _)
+    }
+
+    val moduleName = target match {
+      case Some(t) => s"multisample-vcfstats-$caller-$t"
+      case _       => s"multisample-vcfstats-$caller"
     }
 
-    if (libraryLevel) {
-      for (
-        sample <- summary.samples if sampleId.isEmpty || sample == sampleId.get;
-        lib <- summary.libraries(sample)
-      ) {
-        tsvWriter.println(getLine(summary, sample, sampleId, Some(lib)))
-      }
-    } else {
-      for (sample <- summary.samples if sampleId.isEmpty || sample == sampleId.get) {
-        tsvWriter.println(getLine(summary, sample, sampleId))
-      }
+    val results = summary.getStatKeys(runId, Right("shivavariantcalling"), Some(Right(moduleName)), sampleId.map(Left(_)), keyValues = statsPaths)
+
+    for (sample <- samples if sampleId.isEmpty || sample.id == sampleId.get) {
+      tsvWriter.println(sample.name + "\t" + field.map(f => results(s"${sample.name};$f").getOrElse("")).mkString("\t"))
     }
 
     tsvWriter.close()
@@ -176,9 +167,7 @@ trait ShivaReportTrait extends MultisampleMappingReportTrait {
     plot.input = tsvFile
     plot.output = pngFile
     plot.ylabel = Some("VCF records")
-    if (libraryLevel) {
-      plot.width = Some(200 + (summary.libraries.filter(s => sampleId.getOrElse(s._1) == s._1).foldLeft(0)(_ + _._2.size) * 10))
-    } else plot.width = Some(200 + (summary.samples.count(s => sampleId.getOrElse(s) == s) * 10))
+    plot.width = Some(200 + (samples.count(s => sampleId.getOrElse(s) == s) * 10))
     plot.runLocal()
   }
 }

tinycap/src/main/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapReport.scala

@@ -33,17 +33,5 @@ object TinyCapReport extends MultisampleMappingReportTrait {
   /** Front section for the report */
   override def frontSection: ReportSection = ReportSection("/nl/lumc/sasc/biopet/pipelines/tinycap/tinycapFront.ssp")
 
-  override def additionalSections = List(
-    "Fragments per gene" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gentrap/measure_plotreport.ssp",
-      Map("pipelineName" -> pipelineName,
-        "plotName" -> "fragmentspergene",
-        "plotPath" -> summary.getValue("fragmentspergene", "files", "pipeline", "fragments_per_gene_heatmap", "path")
-      )),
-    "Fragments per microRNA" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gentrap/measure_plotreport.ssp",
-      Map("pipelineName" -> pipelineName,
-        "plotName" -> "fragmentspersmallrna",
-        "plotPath" -> summary.getValue("fragmentspersmallrna", "files", "pipeline", "fragments_per_smallrna_heatmap", "path")))
-  )
-
   override def pipelineName = "tinycap"
 }