Added scala docs to report code

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

@@ -6,17 +6,24 @@ import nl.lumc.sasc.biopet.core.report.{ ReportBuilder, ReportPage, ReportSectio
 import nl.lumc.sasc.biopet.core.summary.{ SummaryValue, Summary }
 import nl.lumc.sasc.biopet.extensions.rscript.{ XYPlot, StackedBarPlot }
 
+//TODO: Add basic report to BamMetrics as single pipeline
+
 /**
  * Created by pjvan_thof on 3/30/15.
  */
 object BammetricsReport extends ReportBuilder {
-  // FIXME: Not yet finished
 
+  /** Name of report */
   val reportName = "Bam Metrics"
 
+  /** Root page for single BamMetrcis report */
   def indexPage = ReportPage(List(), List(), Map())
 
-  def bamMetricsPage(summary: Summary, sampleId: Option[String], libId: Option[String]) = {
+  /** Generates a page with alignment stats */
+  def bamMetricsPage(summary: Summary,
+                     sampleId: Option[String],
+                     libId: Option[String],
+                     metricsTag: String = "bammetrics") = {
     val targets = (
       summary.getLibraryValue(sampleId, libId, "bammetrics", "settings", "amplicon_name"),
       summary.getLibraryValue(sampleId, libId, "bammetrics", "settings", "roi_name")
@@ -35,10 +42,18 @@ object BammetricsReport extends ReportBuilder {
         "Summary" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
         "Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp", Map("showPlot" -> true))
       ),
-      Map()
+      Map("metricsTag" -> metricsTag)
     )
   }
 
+  /**
+   * Generate a stackbar plot for alignment stats
+   * @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 alignmentSummaryPlot(outputDir: File,
                            prefix: String,
                            summary: Summary,
@@ -94,6 +109,14 @@ object BammetricsReport extends ReportBuilder {
     plot.runLocal()
   }
 
+  /**
+   * Generate a line plot for insertsize
+   * @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 insertSizePlot(outputDir: File,
                      prefix: String,
                      summary: Summary,
@@ -174,6 +197,14 @@ object BammetricsReport extends ReportBuilder {
     plot.runLocal()
   }
 
+  /**
+   * Generate a line plot for wgs coverage
+   * @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 wgsHistogramPlot(outputDir: File,
                        prefix: String,
                        summary: Summary,

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

@@ -4,22 +4,28 @@ package nl.lumc.sasc.biopet.core.report
  * Created by pjvan_thof on 3/30/15.
  */
 trait MultisampleReportBuilder extends ReportBuilder {
+
+  /** Method to generate a single sample page */
   def samplePage(sampleId: String, args: Map[String, Any]): ReportPage
 
+  /** Default list of samples, can be override */
   def samplesSections: List[(String, ReportSection)] = {
     List(
       ("Samples", ReportSection("/nl/lumc/sasc/biopet/core/report/samplesList.ssp"))
     )
   }
 
+  /** Method to generate a single library page */
   def libraryPage(sampleId: String, libraryId: String, args: Map[String, Any]): ReportPage
 
+  /** Default list of libraries, can be override */
   def libririesSections: List[(String, ReportSection)] = {
     List(
       ("Libraries", ReportSection("/nl/lumc/sasc/biopet/core/report/librariesList.ssp"))
     )
   }
 
+  /** Generate the samples page including a single sample page for each sample in the summary */
   def generateSamplesPage(args: Map[String, Any]): ReportPage = {
     val samplePages = summary.samples
       .map(sampleId => (sampleId -> samplePage(sampleId, args ++ Map("sampleId" -> Some(sampleId)))))
@@ -27,6 +33,7 @@ trait MultisampleReportBuilder extends ReportBuilder {
     ReportPage(samplePages, 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) => x.toString

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

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.core.report
 
 import java.io._
 
-import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, ToolCommand }
 import nl.lumc.sasc.biopet.core.summary.Summary
 import org.broadinstitute.gatk.utils.commandline.Input
 import org.fusesource.scalate.{ TemplateSource, TemplateEngine }
@@ -13,13 +13,16 @@ import nl.lumc.sasc.biopet.utils.IoUtils
  */
 trait ReportBuilderExtension extends ToolCommandFuntion {
 
+  /** Report builder object */
   val builder: ReportBuilder
 
   @Input(required = true)
   var summaryFile: File = _
 
+  /** OutputDir for the report  */
   var outputDir: File = _
 
+  /** Arguments that are passed on the commandline */
   var args: Map[String, String] = Map()
 
   override def beforeGraph: Unit = {
@@ -28,6 +31,7 @@ trait ReportBuilderExtension extends ToolCommandFuntion {
     javaMainClass = builder.getClass.getName.takeWhile(_ != '$')
   }
 
+  /** Command to generate the report */
   override def commandLine: String = {
     super.commandLine +
       required("--summary", summaryFile) +
@@ -52,15 +56,19 @@ trait ReportBuilder extends ToolCommand {
     }
   }
 
+  /** summary object internaly */
   private var setSummary: Summary = _
 
+  /** Retrival of summary, read only */
   final def summary = setSummary
 
+  /** default args that are passed to all page withing the report */
   def pageArgs: Map[String, Any] = Map()
 
   private var done = 0
   private var total = 0
 
+  /** Main function to for building the report */
   def main(args: Array[String]): Unit = {
     logger.info("Start")
 
@@ -95,7 +103,7 @@ trait ReportBuilder extends ToolCommand {
     logger.info("Parsing summary")
     setSummary = new Summary(cmdArgs.summary)
 
-    total = countPages(indexPage)
+    total = ReportBuilder.countPages(indexPage)
     logger.info(total + " pages to be generated")
 
     logger.info("Generate pages")
@@ -106,14 +114,21 @@ trait ReportBuilder extends ToolCommand {
     logger.info(jobs + " Done")
   }
 
+  /** This must be implemented, this will be the root page of the report */
   def indexPage: ReportPage
 
+  /** This must be implemented, this will because the title of the report */
   def reportName: String
 
-  def countPages(page: ReportPage): Int = {
-    page.subPages.map(x => countPages(x._2)).fold(1)(_ + _)
-  }
-
+  /**
+   * This method will render the page and the subpages recursivly
+   * @param summary The summary object
+   * @param page Page to render
+   * @param outputDir Root output dir of the report
+   * @param path Path from root to current page
+   * @param args Args to add to this sub page, are args from current page are passed automaticly
+   * @return Number of pages including all subpages that are rendered
+   */
   def generatePage(summary: Summary,
                    page: ReportPage,
                    outputDir: File,
@@ -151,10 +166,17 @@ trait ReportBuilder extends ToolCommand {
 
 object ReportBuilder {
 
+  /** Single template render engine, this will have a cache for all compile templates */
   protected val engine = new TemplateEngine()
 
+  /** Cache of temp file for templates from the classpath / jar */
   private var templateCache: Map[String, File] = Map()
 
+  /** This will give the total number of pages including all nested pages */
+  def countPages(page: ReportPage): Int = {
+    page.subPages.map(x => countPages(x._2)).fold(1)(_ + _)
+  }
+
   /**
    * This method will render a template that is located in the classpath / jar
    * @param location location in the classpath / jar

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportPage.scala

@@ -2,6 +2,10 @@ package nl.lumc.sasc.biopet.core.report
 
 /**
  * Created by pjvan_thof on 3/27/15.
+ *
+ * @param subPages Subpages for this page
+ * @param sections Sections for this page
+ * @param args Arguments for this page, this arguments get passed to all section and subpages
  */
 case class ReportPage(subPages: List[(String, ReportPage)],
                       sections: List[(String, ReportSection)],

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportSection.scala

@@ -2,15 +2,18 @@ package nl.lumc.sasc.biopet.core.report
 
 /**
  * Created by pjvan_thof on 4/8/15.
+ *
+ * @param location Location inside the classpath / jar
+ * @param args arguments only for current section, this is not passed to other sub pages
  */
 case class ReportSection(location: String,
-                         args: Map[String, Any] = Map(),
-                         intro: Option[String] = None) {
-
-  def render(args: Map[String, Any]): String = {
-    (intro match {
-      case Some(template) => ReportBuilder.renderTemplate(location, args ++ this.args)
-      case _              => ""
-    }) + ReportBuilder.renderTemplate(location, args ++ this.args)
+                         args: Map[String, Any] = Map()) {
+  /**
+   * This method will render this section
+   * @param args Possible to give more arguments
+   * @return Rendered result for this section
+   */
+  def render(args: Map[String, Any] = Map()): String = {
+    ReportBuilder.renderTemplate(location, args ++ this.args)
   }
 }

public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala

@@ -6,21 +6,27 @@ import nl.lumc.sasc.biopet.core.report.{ ReportSection, ReportPage, ReportBuilde
 import nl.lumc.sasc.biopet.core.summary.{ SummaryValue, Summary }
 import nl.lumc.sasc.biopet.extensions.rscript.StackedBarPlot
 
+//TODO: add basic report to flexiprep as single pipeline
 /**
  * Created by pjvan_thof on 3/30/15.
  */
 object FlexiprepReport extends ReportBuilder {
   val reportName = "Flexiprep"
 
-  def indexPage = ReportPage(List(
-    "QC" -> flexiprepPage
-  ), List(
-    "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFront.ssp")
-  ),
-    Map()
-  )
+  /** Index page for a flexiprep report */
+  def indexPage = {
+    val flexiprepPage = this.flexiprepPage
+    ReportPage(List(
+      "QC" -> flexiprepPage
+    ), List(
+      "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFront.ssp")
+    ) ::: flexiprepPage.sections,
+      Map()
+    )
+  }
 
-  def flexiprepPage = ReportPage(
+  /** Generate a QC report page for 1 single library, sampleId and libId must be defined in the arguments */
+  def flexiprepPage: ReportPage = ReportPage(
     List(),
     List(
       "Read Summary" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
@@ -41,8 +47,14 @@ object FlexiprepReport extends ReportBuilder {
     name -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFastaqcPlot.ssp", Map("plot" -> tag))
   }
 
-  // FIXME: Not yet finished
-
+  /**
+   * Generated a stacked bar plot for reads QC
+   * @param outputDir OutputDir for plot
+   * @param prefix prefix for tsv and png file
+   * @param read Must give "R1" or "R2"
+   * @param summary Summary class
+   * @param sampleId Default selects all samples, when given plot is limits on given sample
+   */
   def readSummaryPlot(outputDir: File,
                       prefix: String,
                       read: String,
@@ -92,6 +104,14 @@ object FlexiprepReport extends ReportBuilder {
     plot.runLocal()
   }
 
+  /**
+   * Generated a stacked bar plot for bases QC
+   * @param outputDir OutputDir for plot
+   * @param prefix prefix for tsv and png file
+   * @param read Must give "R1" or "R2"
+   * @param summary Summary class
+   * @param sampleId Default selects all samples, when given plot is limits on given sample
+   */
   def baseSummaryPlot(outputDir: File,
                       prefix: String,
                       read: String,

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

@@ -18,10 +18,10 @@ class ShivaReport(val root: Configurable) extends ReportBuilderExtension {
   override val defaultCoreMemory = 3.0
 }
 
+/** Object for report generation for Shiva pipeline */
 object ShivaReport extends MultisampleReportBuilder {
 
-  // FIXME: Not yet finished
-
+  /** Root page for the shiva report */
   def indexPage = {
     val regions = regionsPage
     ReportPage(
@@ -52,7 +52,9 @@ object ShivaReport extends MultisampleReportBuilder {
     )
   }
 
-  def regionsPage = {
+  //TODO: Add variants per target
+  /** 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")
 
@@ -88,7 +90,8 @@ object ShivaReport extends MultisampleReportBuilder {
     else None
   }
 
-  def filesPage = ReportPage(List(), List(
+  /** 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)),
@@ -97,7 +100,8 @@ object ShivaReport extends MultisampleReportBuilder {
     "VCF files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/outputVcfFiles.ssp", Map("sampleId" -> None))
   ), Map())
 
-  def samplePage(sampleId: String, args: Map[String, Any]) = {
+  /** Single sample page */
+  def samplePage(sampleId: String, args: Map[String, Any]): ReportPage = {
     ReportPage(List(
       "Libraries" -> generateLibraryPage(args),
       "Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), None),
@@ -112,7 +116,8 @@ object ShivaReport extends MultisampleReportBuilder {
     ), args)
   }
 
-  def libraryPage(sampleId: String, libId: String, args: Map[String, Any]) = {
+  /** 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
@@ -123,8 +128,17 @@ object ShivaReport extends MultisampleReportBuilder {
     ), args)
   }
 
+  /** Name of the report */
   def reportName = "Shiva Report"
 
+  /**
+   * Generate a stackbar plot for found variants
+   * @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,