Move generic pages to multisamplemapping

public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpReport.scala

@@ -15,6 +15,7 @@
  */
 package nl.lumc.sasc.biopet.pipelines.carp
 
+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
@@ -29,71 +30,7 @@ class CarpReport(val root: Configurable) extends ReportBuilderExtension {
   def builder = CarpReport
 }
 
-object CarpReport extends MultisampleReportBuilder {
-
-  /** 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/carp/carpFront.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)),
-        "Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.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()),
-      "Merged" -> 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)
-  }
-
+object CarpReport extends MultisampleMappingReportTrait {
   /** Name of the report */
   def reportName = "Carp Report"
 }
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public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala

+package nl.lumc.sasc.biopet.pipelines.mapping
+
+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
+import nl.lumc.sasc.biopet.utils.config.Configurable
+
+/**
+  * Created by pjvanthof on 11/01/16.
+  */
+class MultisampleMappingReport(val root: Configurable) extends ReportBuilderExtension {
+  def builder = MultisampleMappingReport
+}
+
+object MultisampleMappingReport extends MultisampleMappingReportTrait {
+  /** Name of the report */
+  def reportName = "Mapping Report"
+}
+
+trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
+  /** 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/carp/carpFront.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)),
+        "Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.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()),
+      "Merged" -> 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)
+  }
+}
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