Defutured covstats.ssp

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

@@ -7,6 +7,7 @@
 #import(scala.concurrent.Await)
 #import(scala.concurrent.duration.Duration)
 #import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
+#import(nl.lumc.sasc.biopet.utils.summary.db.Schema)
 #import(java.io.File)
 <%@ var summary: SummaryDb %>
 <%@ var sampleId: Option[Int] %>
@@ -16,17 +17,15 @@
 <%@ var target: Option[String] %>
 <%@ var runId: Int %>
 <%@ var fields: List[String] = List("mean", "median", "max", "horizontal", "frac_min_10x", "frac_min_20x", "frac_min_30x", "frac_min_40x", "frac_min_50x") %>
+<%@ var plotFile: Option[Schema.File] %>
+<%@ var values: Map[String, Option[Any]] %>
 #{
     val moduleName = target.get + "_cov_stats"
 
-    val statsPaths = fields.map(x => x -> List("coverage", "_all", x)).toMap
-    val plotFile = Await.result(summary.getFile(runId, PipelineName(metricsTag), ModuleName(moduleName), sampleId.map(SampleId).get, libId.map(LibraryId).getOrElse(NoLibrary), "plot"), Duration.Inf)
     val originalPlot = new File(plotFile.get.path)
     val plot = new File(outputDir, target.get + "_cov_stats.png")
 
-    val values = summary.getStatKeys(runId, PipelineName(metricsTag), ModuleName(moduleName), sampleId.map(SampleId).get, libId.map(LibraryId).getOrElse(NoLibrary), statsPaths)
-
-    if (originalPlot.exists()) IoUtils.copyFile(originalPlot, plot)
+     if (originalPlot.exists()) IoUtils.copyFile(originalPlot, plot)
 }#
 <img src="${plot.getName}">
 

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

@@ -85,6 +85,7 @@
                     #for (field <- fields)
                         <td>${results(field)}</td>
                     #end
+                    #end
                 </tr>
             #end
         #end

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

@@ -23,13 +23,11 @@ import nl.lumc.sasc.biopet.core.report.{
   ReportPage,
   ReportSection
 }
-import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport.mappingQualityPlotTables
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import nl.lumc.sasc.biopet.utils.rscript.{LinePlot, StackedBarPlot}
 import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
 import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._
 import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._
-import nl.lumc.sasc.biopet.utils.summary.db.Schema._
 
 import scala.collection.mutable.ArrayBuffer
 import scala.concurrent.{Await, Future}
@@ -71,11 +69,20 @@ object BammetricsReport extends ReportBuilder {
       )
     }
 
+  /** Generates values for bamMetricsPage */
+  def bamMetricsPageValues(summary: SummaryDb,
+                           sampleId: Option[Int],
+                           libId: Option[Int],
+                           metricsTag: String = "bammetrics"): Map[String, Any] = {
+    Map("" -> "")
+  }
+
   /** Generates a page with alignment stats */
   def bamMetricsPage(summary: SummaryDb,
                      sampleId: Option[Int],
                      libId: Option[Int],
-                     metricsTag: String = "bammetrics"): Future[ReportPage] = Future {
+                     metricsTag: String = "bammetrics"): Future[ReportPage] = {
+
     val wgsExecuted = summary.getStatsSize(runId,
                                            metricsTag,
                                            "wgs",
@@ -115,45 +122,55 @@ object BammetricsReport extends ReportBuilder {
       case _ => Nil
     }
 
-    ReportPage(
-      if (targets.isEmpty) List()
-      else
+    val covstatsPlotValuesArray = ArrayBuffer[(String, Map[String,Any])]()
+      for (t <- targets) {
+        covstatsPlotValuesArray += Tuple2(t,BammetricsReportPage.covstatsPlotValues(summary, runId, sampleId, libId, Some(t)))
+      }
+
+    val covstatsPlotValuesList = covstatsPlotValuesArray.toList
+
+
+    Future {
+      ReportPage(
+        if (targets.isEmpty) List()
+        else
+          List(
+            "Targets" -> Future.successful(
+              ReportPage(
+                List(),
+                covstatsPlotValuesList.map(covstats =>
+                  covstats._1 -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp",
+                    covstats._2)),
+                Map()))),
         List(
-          "Targets" -> Future.successful(
-            ReportPage(
-              List(),
-              targets.map(t =>
-                t -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp",
-                                   Map("target" -> Some(t)))),
-              Map()))),
-      List(
-        "Summary" -> ReportSection(
-          "/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
-        "Mapping Quality" -> ReportSection(
-          "/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp",
-          Map("showPlot" -> true)),
-        "Clipping" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/clipping.ssp",
-                                    Map("showPlot" -> true))
-      ) ++
-        (if (insertsizeMetrics)
-           List(
-             "Insert Size" -> ReportSection(
-               "/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp",
-               Map("showPlot" -> true)))
-         else Nil) ++ (if (wgsExecuted)
-                         List(
-                           "Whole genome coverage" -> ReportSection(
-                             "/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp",
-                             Map("showPlot" -> true)))
-                       else Nil) ++
-        (if (rnaExecuted)
-           List(
-             "Rna coverage" -> ReportSection(
-               "/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp",
-               Map("showPlot" -> true)))
-         else Nil),
-      Map("metricsTag" -> metricsTag)
-    )
+          "Summary" -> ReportSection(
+            "/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
+          "Mapping Quality" -> ReportSection(
+            "/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp",
+            Map("showPlot" -> true)),
+          "Clipping" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/clipping.ssp",
+                                      Map("showPlot" -> true))
+        ) ++
+          (if (insertsizeMetrics)
+             List(
+               "Insert Size" -> ReportSection(
+                 "/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp",
+                 Map("showPlot" -> true)))
+           else Nil) ++ (if (wgsExecuted)
+                           List(
+                             "Whole genome coverage" -> ReportSection(
+                               "/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp",
+                               Map("showPlot" -> true)))
+                         else Nil) ++
+          (if (rnaExecuted)
+             List(
+               "Rna coverage" -> ReportSection(
+                 "/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp",
+                 Map("showPlot" -> true)))
+           else Nil),
+        Map("metricsTag" -> metricsTag)
+      )
+    }
   }
 
   /**
@@ -541,4 +558,4 @@ object BammetricsReport extends ReportBuilder {
     }
     writer.close()
   }
-}
\ No newline at end of file
+}

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

@@ -2,10 +2,14 @@ package nl.lumc.sasc.biopet.pipelines.bammetrics
 
 import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport.mappingQualityPlotTables
 import nl.lumc.sasc.biopet.utils.summary.db.Schema.{Library, Sample}
-import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
+import nl.lumc.sasc.biopet.utils.summary.db.{Schema, SummaryDb}
 import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._
 import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._
 
+import scala.concurrent.Await
+import scala.concurrent.duration.Duration
+import java.io.File
+
 object BammetricsReportPage {
   def alignmentSummaryValues(summary: SummaryDb,
                              runId: Int,
@@ -99,7 +103,8 @@ object BammetricsReportPage {
       else None
 
     val statsPaths = fields.map(x => x -> List("clipping", "general", x)).toMap
-    val clippingTableResults = summary.getStatsForLibraries(runId, "bammetrics", "bamstats", sampleId, statsPaths)
+    val clippingTableResults =
+      summary.getStatsForLibraries(runId, "bammetrics", "bamstats", sampleId, statsPaths)
     Map(
       "clippingPlotTables" -> clippingPlotTables,
       "clippingTableResults" -> clippingTableResults,
@@ -117,7 +122,8 @@ object BammetricsReportPage {
                        allLibraries: Seq[Library],
                        sampleId: Option[Int],
                        libId: Option[Int],
-                       fields: List[String] = List("mean_insert_size", "standard_deviation", "median_insert_size"),
+                       fields: List[String] =
+                         List("mean_insert_size", "standard_deviation", "median_insert_size"),
                        sampleLevel: Boolean = false,
                        showPlot: Boolean = false,
                        showIntro: Boolean = true,
@@ -133,7 +139,11 @@ object BammetricsReportPage {
       else None
 
     val statsPaths = fields.map(x => x -> List("metrics", x.toUpperCase)).toMap
-    val insertSizeTableResults = summary.getStatsForLibraries(runId, "bammetrics", "CollectInsertSizeMetrics", sampleId, statsPaths)
+    val insertSizeTableResults = summary.getStatsForLibraries(runId,
+                                                              "bammetrics",
+                                                              "CollectInsertSizeMetrics",
+                                                              sampleId,
+                                                              statsPaths)
     Map(
       "insertSizePlotTables" -> insertSizePlotTables,
       "insertSizeTableResults" -> insertSizeTableResults,
@@ -145,16 +155,19 @@ object BammetricsReportPage {
     )
   }
   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] = {
+                         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
@@ -166,7 +179,8 @@ object BammetricsReportPage {
       else None
 
     val statsPaths = fields.map(x => x -> List("metrics", x.toUpperCase)).toMap
-    val rnaHistogramTableResults = summary.getStatsForLibraries(runId, "bammetrics", "rna", sampleId, statsPaths)
+    val rnaHistogramTableResults =
+      summary.getStatsForLibraries(runId, "bammetrics", "rna", sampleId, statsPaths)
     Map(
       "rnaHistogramPlotTables" -> rnaHistogramPlotTables,
       "rnaHistogramTableResults" -> rnaHistogramTableResults,
@@ -183,7 +197,20 @@ object BammetricsReportPage {
                          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"),
+                         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,
@@ -199,7 +226,8 @@ object BammetricsReportPage {
       else None
 
     val statsPaths = fields.map(x => x -> List("metrics", x.toUpperCase)).toMap
-    val wgsHistogramTableResults = summary.getStatsForLibraries(runId, "bammetrics", "wgs", sampleId, statsPaths)
+    val wgsHistogramTableResults =
+      summary.getStatsForLibraries(runId, "bammetrics", "wgs", sampleId, statsPaths)
     Map(
       "wgsHistogramPlotTables" -> wgsHistogramPlotTables,
       "wgsHistogramTableResults" -> wgsHistogramTableResults,
@@ -210,5 +238,41 @@ object BammetricsReportPage {
       "libId" -> libId
     )
   }
+  def covstatsPlotValues(summary: SummaryDb,
+                         runId: Int,
+                         sampleId: Option[Int],
+                         libId: Option[Int],
+                         target: Option[String],
+                         metricsTag: String = "bammetrics",
+                         fields: List[String] = List("mean",
+                                                     "median",
+                                                     "max",
+                                                     "horizontal",
+                                                     "frac_min_10x",
+                                                     "frac_min_20x",
+                                                     "frac_min_30x",
+                                                     "frac_min_40x",
+                                                     "frac_min_50x")): Map[String, Any] = {
+    val moduleName = target.get + "_cov_stats"
+    val plotFile: Option[Schema.File] = Await.result(
+      summary.getFile(runId,
+                      PipelineName(metricsTag),
+                      ModuleName(moduleName),
+                      sampleId.map(SampleId).get,
+                      libId.map(LibraryId).getOrElse(NoLibrary),
+                      "plot"),
+      Duration.Inf
+    )
+    val statsPaths = fields.map(x => x -> List("coverage", "_all", x)).toMap
+    val values: Map[String, Option[Any]] = summary.getStatKeys(
+      runId,
+      PipelineName(metricsTag),
+      ModuleName(moduleName),
+      sampleId.map(SampleId).get,
+      libId.map(LibraryId).getOrElse(NoLibrary),
+      statsPaths)
+    Map("plotFile" -> plotFile, "values" -> values,
+    "target" -> target,
+    "metricsTag" -> metricsTag)
+  }
 }
-

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

@@ -53,36 +53,36 @@ object FlexiprepReport extends ReportBuilder {
   /** Index page for a flexiprep report */
   def indexPage: Future[ReportPage] = {
     val flexiprepPageSummaries = this.flexiprepPageSummaries(summary, sampleId.get, libId.get)
-    this.flexiprepPage(flexiprepPageSummaries).map {
-      page =>
-        ReportPage(
-          Nil,
-          List(
-            "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFront.ssp")
-          ) ::: page.sections,
-          Map())
-    }}
+    this.flexiprepPage(flexiprepPageSummaries).map { page =>
+      ReportPage(
+        Nil,
+        List(
+          "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFront.ssp")
+        ) ::: page.sections,
+        Map())
+    }
+  }
+
   /** Generate a QC report page for 1 single library, sampleId and libId must be defined in the arguments */
   def flexiprepPageSummaries(summary: SummaryDb,
-                          sampleId: Int,
-                          libId: Int): Map[String, Map[String, Any]] = {
+                             sampleId: Int,
+                             libId: Int): Map[String, Map[String, Any]] = {
     val flexiprepReadSummary: Map[String, Any] = FlexiprepReadSummary.values(summary,
-      runId,
-      samples,
-      libraries,
-      sampleId,
-      libId,
-      multisample = false)
-    val flexiprepBaseSummary: Map[String,Any] = FlexiprepBaseSummary.values(summary,
-      runId,
-      samples,
-      libraries,
-      sampleId,
-      libId,
-      multisample = false)
+                                                                             runId,
+                                                                             samples,
+                                                                             libraries,
+                                                                             sampleId,
+                                                                             libId,
+                                                                             multisample = false)
+    val flexiprepBaseSummary: Map[String, Any] = FlexiprepBaseSummary.values(summary,
+                                                                             runId,
+                                                                             samples,
+                                                                             libraries,
+                                                                             sampleId,
+                                                                             libId,
+                                                                             multisample = false)
     Map("flexiprepReadSummary" -> flexiprepReadSummary,
-      "flexiprepBaseSummary" -> flexiprepBaseSummary
-    )
+        "flexiprepBaseSummary" -> flexiprepBaseSummary)
   }
 
   def flexiprepPage(summaries: Map[String, Map[String, Any]]): Future[ReportPage] = {

gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala

@@ -345,10 +345,10 @@ object GearsReport extends MultisampleReportBuilder {
 
     val flexiprepReportPage =
       if (flexiprepExecuted) {
-        val flexiprepPageSummaries = FlexiprepReport.flexiprepPageSummaries(summary,sampleId,libId)
+        val flexiprepPageSummaries =
+          FlexiprepReport.flexiprepPageSummaries(summary, sampleId, libId)
         Some("QC" -> FlexiprepReport.flexiprepPage(flexiprepPageSummaries))
-      }
-      else None
+      } else None
 
     val centrifugePageAllMappingsKronaPlot = GearsKronaPlot.values(summary,
                                                                    runId,