Prevent double adding

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala

@@ -32,6 +32,8 @@ trait Summarizable {
   /** Can be used to add additional Summarizable, this is executed at the start of WriteSummary*/
   def addToQscriptSummary(qscript: SummaryQScript) {}
 
+  private[summary] var addToQscriptSummaryDone = false
+
   /**
    * This function is used to merge value that are found at the same path in the map. Default there will throw a exception at conflicting values.
    * @param v1 Value of new map

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala

@@ -55,32 +55,6 @@ trait SummaryQScript extends BiopetQScript { qscript: QScript =>
     case _                 => throw new IllegalStateException("Root should be a SummaryQScript")
   }
 
-  /**
-   * Add a module to summary for this pipeline
-   *
-   * Auto detect sample and library from pipeline
-   *
-   * @param summarizable summarizable to add to summary for this pipeline
-   * @param name Name of module
-   */
-  def addSummarizable(summarizable: Summarizable, name: String): Unit = {
-    this match {
-      case tag: SampleLibraryTag => addSummarizable(summarizable, name, tag.sampleId, tag.libId)
-      case _                     => addSummarizable(summarizable, name, None, None)
-    }
-  }
-
-  /**
-   * Add a module to summary for this pipeline
-   *
-   * @param summarizable summarizable to add to summary for this pipeline
-   * @param name Name of module
-   * @param sampleId Id of sample
-   */
-  def addSummarizable(summarizable: Summarizable, name: String, sampleId: Option[String]): Unit = {
-    addSummarizable(summarizable, name, sampleId, None)
-  }
-
   /**
    * Add a module to summary for this pipeline
    *
@@ -88,10 +62,19 @@ trait SummaryQScript extends BiopetQScript { qscript: QScript =>
    * @param name Name of module
    * @param sampleId Id of sample
    * @param libraryId Id of libary
+   * @param forceSingle If true it replaces summarizable instead of adding to it
    */
-  def addSummarizable(summarizable: Summarizable, name: String, sampleId: Option[String], libraryId: Option[String]): Unit = {
-    if (libraryId.isDefined) require(sampleId.isDefined) // Library always require a sample
-    summarizables += (name, sampleId, libraryId) -> (summarizable :: summarizables.getOrElse((name, sampleId, libraryId), Nil))
+  def addSummarizable(summarizable: Summarizable, name: String,
+                      sampleId: Option[String] = None,
+                      libraryId: Option[String] = None,
+                      forceSingle: Boolean = false): Unit = {
+    val (sId, lId) = this match {
+      case tag: SampleLibraryTag => (tag.sampleId, tag.libId)
+      case _                     => (sampleId, libraryId)
+    }
+    if (lId.isDefined) require(sId.isDefined) // Library always require a sample
+    if (forceSingle) summarizables = summarizables.filterNot(_._1 == (name, sId, lId))
+    summarizables += (name, sId, lId) -> (summarizable :: summarizables.getOrElse((name, sId, lId), Nil))
   }
 
   /** Add an other qscript to merge in output summary */

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala

@@ -53,7 +53,10 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
   }
 
   def init(): Unit = {
-    qscript.summarizables.foreach(_._2.foreach(_.addToQscriptSummary(qscript)))
+    qscript.summarizables.foreach(_._2.foreach { s =>
+      if (!s.addToQscriptSummaryDone) s.addToQscriptSummary(qscript)
+      s.addToQscriptSummaryDone = true
+    })
 
     val db = SummaryDb.openSqliteSummary(qscript.summaryDbFile)
     if (qscript == root) { // This initialize the database

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala

@@ -98,18 +98,18 @@ class CollectMultipleMetrics(val parent: Configurable) extends Picard with Summa
       .foreach { p =>
         p match {
           case _ if p == Programs.CollectAlignmentSummaryMetrics.toString =>
-            qscript.addSummarizable(summarizable(() => Picard.getMetrics(new File(outputName + ".alignment_summary_metrics"), groupBy = Some("CATEGORY"))), p)
+            qscript.addSummarizable(summarizable(() => Picard.getMetrics(new File(outputName + ".alignment_summary_metrics"), groupBy = Some("CATEGORY"))), p, forceSingle = true)
           case _ if p == Programs.CollectInsertSizeMetrics.toString =>
             qscript.addSummarizable(summarizable(() => Map(
               "metrics" -> Picard.getMetrics(new File(outputName + ".insert_size_metrics")),
               "histogram" -> Picard.getHistogram(new File(outputName + ".insert_size_metrics"))
-            )), p)
+            )), p, forceSingle = true)
           case _ if p == Programs.QualityScoreDistribution.toString =>
-            qscript.addSummarizable(summarizable(() => Picard.getHistogram(new File(outputName + ".quality_distribution_metrics"))), p)
+            qscript.addSummarizable(summarizable(() => Picard.getHistogram(new File(outputName + ".quality_distribution_metrics"))), p, forceSingle = true)
           case _ if p == Programs.MeanQualityByCycle.toString =>
-            qscript.addSummarizable(summarizable(() => Picard.getHistogram(new File(outputName + ".quality_by_cycle_metrics"))), p)
+            qscript.addSummarizable(summarizable(() => Picard.getHistogram(new File(outputName + ".quality_by_cycle_metrics"))), p, forceSingle = true)
           case _ if p == Programs.CollectBaseDistributionByCycle.toString =>
-            qscript.addSummarizable(summarizable(() => Picard.getHistogram(new File(outputName + ".base_distribution_by_cycle_metrics"), tag = "METRICS CLASS")), p)
+            qscript.addSummarizable(summarizable(() => Picard.getHistogram(new File(outputName + ".base_distribution_by_cycle_metrics"), tag = "METRICS CLASS")), p, forceSingle = true)
           case _ => None
         }
       }

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

@@ -78,7 +78,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
         List("Reference" -> ReportPage(List(), List(
           "Reference" -> ReportSection("/nl/lumc/sasc/biopet/core/report/reference.ssp", Map("pipeline" -> pipelineName))
         ), Map()),
-          "Files" -> filesPage,
+          "Files" -> filesPage(),
           "Versions" -> ReportPage(List(), List("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
           )), Map())
         ),
@@ -112,7 +112,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
   }
 
   /** Files page, can be used general or at sample level */
-  def filesPage: ReportPage = {
+  def filesPage(sampleId: Option[Int] = None, libraryId: Option[Int] = None): ReportPage = {
     val flexiprepExecuted = Await.result(summary.getStatsSize(runId, Right("flexiprep"), Some(None), mustHaveLibrary = true), Duration.Inf) >= 1
 
     ReportPage(List(), Nil, Map())
@@ -140,7 +140,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
         "Krona Plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
         )), Map()))
       else Nil) ++
-      List("Files" -> filesPage
+      List("Files" -> filesPage()
       ), List(
       "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
         Map("showPlot" -> true)),