rna- and wgs histogram defutured

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

@@ -89,7 +89,7 @@
                 #if (libs.head != libId) <tr> #end
                         #if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
                         #{
-                    val results: Map[String, Option[Any]] = insertSizeTableResults(sample.id, libId)
+                            val results: Map[String, Option[Any]] = insertSizeTableResults(sample.id, libId)
                         }#
                         #for (field <- fields)
                             <td>${results(field)}</td>

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

@@ -20,6 +20,8 @@
 <%@ var runId: Int %>
 <%@ var allSamples: Seq[Sample] %>
 <%@ var allLibraries: Seq[Library] %>
+<%@ var rnaHistogramPlotTables: Option[Array[Map[String, Array[Any]]]] %>
+<%@ var rnaHistogramTableResults: Map[(Int, Int), Map[String, Option[Any]]] %>
 #{
     val samples = sampleId match {
     case Some(id) => allSamples.filter(_.id == id).toList
@@ -39,7 +41,7 @@
 #end
 
 #if (showPlot)
-    #{ BammetricsReport.rnaHistogramPlot(outputDir, "rna", summary, !sampleLevel, sampleId = sampleId, libraryId = libId) }#
+    #{ BammetricsReport.rnaHistogramPlot(outputDir, "rna", rnaHistogramPlotTables.getOrElse(Array(Map("x" -> Array(""))))) }#
 
     <div class="panel-body">
         <img src="rna.png" class="img-responsive" />
@@ -79,8 +81,7 @@
                 #if (libs.head != libId) <tr> #end
                     #if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
                     #{
-                        val statsPaths = fields.map(x => x -> List("metrics", x.toUpperCase)).toMap
-                        val results = summary.getStatKeys(runId, "bammetrics", "rna", sample = sample.id, library = libId.map(LibraryId).getOrElse(NoLibrary), keyValues = statsPaths)
+                          val results = rnaHistogramTableResults(sample.id, libId)
                     }#
                     #for (field <- fields)
                         <td>${results(field)}</td>

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

@@ -19,6 +19,8 @@
 <%@ var fields: List[String] = List("mean_coverage", "pct_5x", "pct_10x", "pct_15x", "pct_20x", "pct_25x", "pct_30x", "pct_40x", "pct_50x", "pct_60x", "pct_70x", "pct_80x", "pct_90x", "pct_100x")%>
 <%@ var allSamples: Seq[Sample] %>
 <%@ var allLibraries: Seq[Library] %>
+<%@ var wgsHistogramPlotTables: Option[Array[Map[String, Array[Any]]]] %>
+<%@ var wgsHistogramTableResults: Map[(Int, Int), Map[String, Option[Any]]] %>
 #{
     val samples = sampleId match {
     case Some(id) => allSamples.filter(_.id == id).toList
@@ -38,7 +40,7 @@
 #end
 
 #if (showPlot)
-    #{ BammetricsReport.wgsHistogramPlot(outputDir, "wgs", summary, !sampleLevel, sampleId = sampleId, libraryId = libId) }#
+    #{ BammetricsReport.wgsHistogramPlot(outputDir, "rna", wgsHistogramPlotTables.getOrElse(Array(Map("x" -> Array(""))))) }#
 
     <div class="panel-body">
     <img src="wgs.png" class="img-responsive" />
@@ -78,9 +80,8 @@
                 #if (libs.head != libId) <tr> #end
                     #if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
                     #{
-                        val statsPaths = fields.map(x => x -> List("metrics", x.toUpperCase)).toMap
-                        val results = summary.getStatKeys(runId, "bammetrics", "wgs", sample = sample.id, library = libId.map(LibraryId).getOrElse(NoLibrary), keyValues = statsPaths)
-                    }#
+                        val results = wgsHistogramTableResults(sample.id, libId)
+                     }#
                     #for (field <- fields)
                         <td>${results(field)}</td>
                     #end

bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReportPage.scala

@@ -144,5 +144,71 @@ object BammetricsReportPage {
       "libId" -> libId
     )
   }
+  def rnaHistogramValues(summary: SummaryDb,
+                       runId: Int,
+                       allSamples: Seq[Sample],
+                       allLibraries: Seq[Library],
+                       sampleId: Option[Int],
+                       libId: Option[Int],
+                       fields: List[String] = List("PF_ALIGNED_BASES", "MEDIAN_5PRIME_BIAS", "MEDIAN_3PRIME_BIAS", "MEDIAN_5PRIME_TO_3PRIME_BIAS"),
+                       sampleLevel: Boolean = false,
+                       showPlot: Boolean = false,
+                       showIntro: Boolean = true,
+                       showTable: Boolean = true): Map[String, Any] = {
+
+    val samples = sampleId match {
+      case Some(id) => allSamples.filter(_.id == id).toList
+      case _ => allSamples.toList
+    }
+    val rnaHistogramPlotTables: Option[Array[Map[String, Array[Any]]]] =
+      if (showPlot)
+        Some(BammetricsReport.rnaHistogramPlotTables(summary, !sampleLevel, sampleId, libId))
+      else None
+
+    val statsPaths = fields.map(x => x -> List("metrics", x.toUpperCase)).toMap
+    val rnaHistogramTableResults = summary.getStatsForLibraries(runId, "bammetrics", "rna", sampleId, statsPaths)
+    Map(
+      "rnaHistogramPlotTables" -> rnaHistogramPlotTables,
+      "rnaHistogramTableResults" -> rnaHistogramTableResults,
+      "showIntro" -> showIntro,
+      "showTable" -> showTable,
+      "showPlot" -> showPlot,
+      "sampleId" -> sampleId,
+      "libId" -> libId
+    )
+  }
+  def wgsHistogramValues(summary: SummaryDb,
+                         runId: Int,
+                         allSamples: Seq[Sample],
+                         allLibraries: Seq[Library],
+                         sampleId: Option[Int],
+                         libId: Option[Int],
+                         fields: List[String] = List("mean_coverage", "pct_5x", "pct_10x", "pct_15x", "pct_20x", "pct_25x", "pct_30x", "pct_40x", "pct_50x", "pct_60x", "pct_70x", "pct_80x", "pct_90x", "pct_100x"),
+                         sampleLevel: Boolean = false,
+                         showPlot: Boolean = false,
+                         showIntro: Boolean = true,
+                         showTable: Boolean = true): Map[String, Any] = {
+
+    val samples = sampleId match {
+      case Some(id) => allSamples.filter(_.id == id).toList
+      case _ => allSamples.toList
+    }
+    val wgsHistogramPlotTables: Option[Array[Map[String, Array[Any]]]] =
+      if (showPlot)
+        Some(BammetricsReport.wgsHistogramPlotTables(summary, !sampleLevel, sampleId, libId))
+      else None
+
+    val statsPaths = fields.map(x => x -> List("metrics", x.toUpperCase)).toMap
+    val wgsHistogramTableResults = summary.getStatsForLibraries(runId, "bammetrics", "wgs", sampleId, statsPaths)
+    Map(
+      "wgsHistogramPlotTables" -> wgsHistogramPlotTables,
+      "wgsHistogramTableResults" -> wgsHistogramTableResults,
+      "showIntro" -> showIntro,
+      "showTable" -> showTable,
+      "showPlot" -> showPlot,
+      "sampleId" -> sampleId,
+      "libId" -> libId
+    )
+  }
 }