Change gentrap report to multisample mapping report

public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapReport.scala

@@ -15,10 +15,9 @@
  */
 package nl.lumc.sasc.biopet.pipelines.gentrap
 
+import nl.lumc.sasc.biopet.core.report.{ReportBuilderExtension, ReportSection}
+import nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingReportTrait
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.report.{ ReportBuilderExtension, ReportSection, ReportPage, MultisampleReportBuilder }
-import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
-import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
 
 /**
  * Class to generate report for [[Gentrap]]
@@ -29,68 +28,9 @@ class GentrapReport(val root: Configurable) extends ReportBuilderExtension {
   def builder = GentrapReport
 }
 
-object GentrapReport extends MultisampleReportBuilder {
+object GentrapReport extends MultisampleMappingReportTrait {
 
-  /** Root page for the carp report */
-  def indexPage = {
-    //Source.fromInputStream(getClass.getResourceAsStream("/nl/lumc/sasc/biopet/pipelines/carp/carpFont.ssp")).foreach(print(_))
-    ReportPage(
-      List("Samples" -> generateSamplesPage(pageArgs)) ++
-        Map("Files" -> filesPage,
-          "Versions" -> ReportPage(List(), List("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
-          )), Map())
-        ),
-      List(
-        "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gentrap/gentrapFront.ssp"),
-        "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
-          Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)
-        ),
-        "Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp",
-          Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)),
-        "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp",
-          Map("showPlot" -> true, "showTable" -> false)),
-        "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp",
-          Map("showPlot" -> true, "showTable" -> false))
-      ),
-      pageArgs
-    )
-  }
-
-  /** Files page, can be used general or at sample level */
-  def filesPage: ReportPage = ReportPage(List(), List(
-    "Input fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepInputfiles.ssp"),
-    "After QC fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepOutputfiles.ssp"),
-    "Bam files per lib" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp", Map("sampleLevel" -> false)) //,
-  //"Preprocessed bam files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp",
-  //  Map("pipelineName" -> "shiva", "fileTag" -> "preProcessBam"))
-  ), Map())
-
-  /** Single sample page */
-  def samplePage(sampleId: String, args: Map[String, Any]): ReportPage = {
-    ReportPage(List(
-      "Libraries" -> generateLibraryPage(args),
-      "Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), None),
-      "Files" -> filesPage
-    ), List(
-      "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
-        if (summary.libraries(sampleId).size > 1) Map("showPlot" -> true) else Map()),
-      "Preprocessing" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp", Map("sampleLevel" -> true)),
-      "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
-      "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
-    ), args)
-  }
-
-  /** Library page */
-  def libraryPage(sampleId: String, libId: String, args: Map[String, Any]): ReportPage = {
-    ReportPage(List(
-      "Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), Some(libId)),
-      "QC" -> FlexiprepReport.flexiprepPage
-    ), List(
-      "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
-      "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
-      "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
-    ), args)
-  }
+  override def frontSection = ReportSection("/nl/lumc/sasc/biopet/pipelines/gentrap/gentrapFront.ssp")
 
   /** Name of the report */
   def reportName = "Gentrap Report"

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

@@ -15,15 +15,13 @@
  */
 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.core.report._
-import nl.lumc.sasc.biopet.utils.summary.{ Summary, SummaryValue }
 import nl.lumc.sasc.biopet.utils.rscript.StackedBarPlot
-import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
-import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
+import nl.lumc.sasc.biopet.utils.summary.{Summary, SummaryValue}
 
 /**
  * With this extension the report is executed within a pipeline