Prepare for further defuturing of bammetrics

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

@@ -74,7 +74,104 @@ object BammetricsReport extends ReportBuilder {
                            sampleId: Option[Int],
                            libId: Option[Int],
                            metricsTag: String = "bammetrics"): Map[String, Any] = {
-    Map("" -> "")
+    val wgsExecuted = summary.getStatsSize(runId,
+      metricsTag,
+      "wgs",
+      sample = sampleId.map(SampleId),
+      library = libId.map(LibraryId)) >= 1
+    val rnaExecuted = summary.getStatsSize(runId,
+      metricsTag,
+      "rna",
+      sample = sampleId.map(SampleId),
+      library = libId.map(LibraryId)) >= 1
+
+    val insertsizeMetrics = summary
+      .getStatKeys(
+        runId,
+        metricsTag,
+        "CollectInsertSizeMetrics",
+        sampleId.map(SampleId).getOrElse(NoSample),
+        libId.map(LibraryId).getOrElse(NoLibrary),
+        Map("metrics" -> List("metrics"))
+      )
+      .exists(_._2.isDefined)
+
+    val targetSettings = summary.getSettingKeys(
+      runId,
+      metricsTag,
+      NoModule,
+      sample = sampleId.map(SampleId).getOrElse(NoSample),
+      library = libId.map(LibraryId).getOrElse(NoLibrary),
+      Map("amplicon_name" -> List("amplicon_name"), "roi_name" -> List("roi_name"))
+    )
+    val targets = (
+      targetSettings("amplicon_name"),
+      targetSettings("roi_name")
+    ) match {
+      case (Some(amplicon: String), Some(roi: List[_])) => amplicon :: roi.map(_.toString)
+      case (_, Some(roi: List[_])) => roi.map(_.toString)
+      case _ => Nil
+    }
+
+    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
+
+    val alignmentSummaryReportValues = BammetricsReportPage.alignmentSummaryValues(
+      summary,
+      runId,
+      samples,
+      libraries,
+      sampleId,
+      libId
+    )
+    val mappingQualityReportValues = BammetricsReportPage.mappingQualityValues(
+      summary,
+      runId,
+      samples,
+      libraries,
+      sampleId,
+      libId,
+      showPlot = true
+    )
+    val clippingReportValues = BammetricsReportPage.clippingValues(
+      summary,
+      runId,
+      samples,
+      libraries,
+      sampleId,
+      libId,
+      showPlot= true
+    )
+    val insertSizeReportValues = BammetricsReportPage.insertSizeValues(
+      summary,
+      runId,
+      samples,
+      libraries,
+      sampleId,
+      libId,
+      showPlot= true
+    )
+    val wgsHistogramReportValues = BammetricsReportPage.wgsHistogramValues(
+      summary,runId, samples, libraries, sampleId, libId, showPlot = true
+    )
+    val rnaHistogramReportValues = BammetricsReportPage.rnaHistogramValues(
+      summary,runId, samples, libraries, sampleId, libId, showPlot = true
+    )
+    Map("wgsExecuted" -> wgsExecuted,
+      "rnaExecuted" -> rnaExecuted,
+      "insertsizeMetrics" -> insertsizeMetrics,
+      "targetSettings" -> targetSettings,
+      "covstatsPlotValuesList" -> covstatsPlotValuesList,
+      "alignmentSummaryReportValues" -> alignmentSummaryReportValues,
+      "clippingReportValues" -> clippingReportValues,
+      "insertSizeReportValues" -> insertSizeReportValues,
+      "wgsHistogramReportValues" -> wgsHistogramReportValues,
+      "rnaHistogramReportValues" -> rnaHistogramReportValues
+    )
+
   }
 
   /** Generates a page with alignment stats */
@@ -83,18 +180,18 @@ object BammetricsReport extends ReportBuilder {
                      libId: Option[Int],
                      metricsTag: String = "bammetrics"): Future[ReportPage] = {
 
-    val wgsExecuted = summary.getStatsSize(runId,
+    val wgsExecuted: Boolean = summary.getStatsSize(runId,
                                            metricsTag,
                                            "wgs",
                                            sample = sampleId.map(SampleId),
                                            library = libId.map(LibraryId)) >= 1
-    val rnaExecuted = summary.getStatsSize(runId,
+    val rnaExecuted: Boolean = summary.getStatsSize(runId,
                                            metricsTag,
                                            "rna",
                                            sample = sampleId.map(SampleId),
                                            library = libId.map(LibraryId)) >= 1
 
-    val insertsizeMetrics = summary
+    val insertsizeMetrics: Boolean = summary
       .getStatKeys(
         runId,
         metricsTag,
@@ -105,7 +202,7 @@ object BammetricsReport extends ReportBuilder {
       )
       .exists(_._2.isDefined)
 
-    val targetSettings = summary.getSettingKeys(
+    val targetSettings: Map[String, Option[Any]] = summary.getSettingKeys(
       runId,
       metricsTag,
       NoModule,
@@ -126,9 +223,9 @@ object BammetricsReport extends ReportBuilder {
       for (t <- targets) {
         covstatsPlotValuesArray += Tuple2(t,BammetricsReportPage.covstatsPlotValues(summary, runId, sampleId, libId, Some(t)))
       }
-    val covstatsPlotValuesList = covstatsPlotValuesArray.toList
+    val covstatsPlotValuesList: List[(String, Map[String, Any])] = covstatsPlotValuesArray.toList
 
-    val alignmentSummaryReportValues = BammetricsReportPage.alignmentSummaryValues(
+    val alignmentSummaryReportValues: Map[String, Any] = BammetricsReportPage.alignmentSummaryValues(
       summary,
       runId,
       samples,
@@ -136,7 +233,7 @@ object BammetricsReport extends ReportBuilder {
       sampleId,
       libId
     )
-    val mappingQualityReportValues = BammetricsReportPage.mappingQualityValues(
+    val mappingQualityReportValues: Map[String, Any] = BammetricsReportPage.mappingQualityValues(
       summary,
       runId,
       samples,
@@ -145,7 +242,7 @@ object BammetricsReport extends ReportBuilder {
       libId,
       showPlot = true
     )
-    val clippingReportValues = BammetricsReportPage.clippingValues(
+    val clippingReportValues: Map[String, Any] = BammetricsReportPage.clippingValues(
       summary,
       runId,
       samples,
@@ -154,7 +251,7 @@ object BammetricsReport extends ReportBuilder {
       libId,
       showPlot= true
     )
-    val insertSizeReportValues = BammetricsReportPage.insertSizeValues(
+    val insertSizeReportValues: Map[String, Any] = BammetricsReportPage.insertSizeValues(
       summary,
       runId,
       samples,
@@ -163,10 +260,10 @@ object BammetricsReport extends ReportBuilder {
       libId,
       showPlot= true
     )
-    val wgsHistogramReportValues = BammetricsReportPage.wgsHistogramValues(
+    val wgsHistogramReportValues: Map[String, Any] = BammetricsReportPage.wgsHistogramValues(
       summary,runId, samples, libraries, sampleId, libId, showPlot = true
     )
-    val rnaHistogramReportValues = BammetricsReportPage.rnaHistogramValues(
+    val rnaHistogramReportValues: Map[String, Any] = BammetricsReportPage.rnaHistogramValues(
       summary,runId, samples, libraries, sampleId, libId, showPlot = true
     )
     Future {