Commit af6b885e authored by rhpvorderman's avatar rhpvorderman

Prepare for further defuturing of bammetrics

parent 58c2b606
...@@ -74,7 +74,104 @@ object BammetricsReport extends ReportBuilder { ...@@ -74,7 +74,104 @@ object BammetricsReport extends ReportBuilder {
sampleId: Option[Int], sampleId: Option[Int],
libId: Option[Int], libId: Option[Int],
metricsTag: String = "bammetrics"): Map[String, Any] = { 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 */ /** Generates a page with alignment stats */
...@@ -83,18 +180,18 @@ object BammetricsReport extends ReportBuilder { ...@@ -83,18 +180,18 @@ object BammetricsReport extends ReportBuilder {
libId: Option[Int], libId: Option[Int],
metricsTag: String = "bammetrics"): Future[ReportPage] = { metricsTag: String = "bammetrics"): Future[ReportPage] = {
val wgsExecuted = summary.getStatsSize(runId, val wgsExecuted: Boolean = summary.getStatsSize(runId,
metricsTag, metricsTag,
"wgs", "wgs",
sample = sampleId.map(SampleId), sample = sampleId.map(SampleId),
library = libId.map(LibraryId)) >= 1 library = libId.map(LibraryId)) >= 1
val rnaExecuted = summary.getStatsSize(runId, val rnaExecuted: Boolean = summary.getStatsSize(runId,
metricsTag, metricsTag,
"rna", "rna",
sample = sampleId.map(SampleId), sample = sampleId.map(SampleId),
library = libId.map(LibraryId)) >= 1 library = libId.map(LibraryId)) >= 1
val insertsizeMetrics = summary val insertsizeMetrics: Boolean = summary
.getStatKeys( .getStatKeys(
runId, runId,
metricsTag, metricsTag,
...@@ -105,7 +202,7 @@ object BammetricsReport extends ReportBuilder { ...@@ -105,7 +202,7 @@ object BammetricsReport extends ReportBuilder {
) )
.exists(_._2.isDefined) .exists(_._2.isDefined)
val targetSettings = summary.getSettingKeys( val targetSettings: Map[String, Option[Any]] = summary.getSettingKeys(
runId, runId,
metricsTag, metricsTag,
NoModule, NoModule,
...@@ -126,9 +223,9 @@ object BammetricsReport extends ReportBuilder { ...@@ -126,9 +223,9 @@ object BammetricsReport extends ReportBuilder {
for (t <- targets) { for (t <- targets) {
covstatsPlotValuesArray += Tuple2(t,BammetricsReportPage.covstatsPlotValues(summary, runId, sampleId, libId, Some(t))) 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, summary,
runId, runId,
samples, samples,
...@@ -136,7 +233,7 @@ object BammetricsReport extends ReportBuilder { ...@@ -136,7 +233,7 @@ object BammetricsReport extends ReportBuilder {
sampleId, sampleId,
libId libId
) )
val mappingQualityReportValues = BammetricsReportPage.mappingQualityValues( val mappingQualityReportValues: Map[String, Any] = BammetricsReportPage.mappingQualityValues(
summary, summary,
runId, runId,
samples, samples,
...@@ -145,7 +242,7 @@ object BammetricsReport extends ReportBuilder { ...@@ -145,7 +242,7 @@ object BammetricsReport extends ReportBuilder {
libId, libId,
showPlot = true showPlot = true
) )
val clippingReportValues = BammetricsReportPage.clippingValues( val clippingReportValues: Map[String, Any] = BammetricsReportPage.clippingValues(
summary, summary,
runId, runId,
samples, samples,
...@@ -154,7 +251,7 @@ object BammetricsReport extends ReportBuilder { ...@@ -154,7 +251,7 @@ object BammetricsReport extends ReportBuilder {
libId, libId,
showPlot= true showPlot= true
) )
val insertSizeReportValues = BammetricsReportPage.insertSizeValues( val insertSizeReportValues: Map[String, Any] = BammetricsReportPage.insertSizeValues(
summary, summary,
runId, runId,
samples, samples,
...@@ -163,10 +260,10 @@ object BammetricsReport extends ReportBuilder { ...@@ -163,10 +260,10 @@ object BammetricsReport extends ReportBuilder {
libId, libId,
showPlot= true showPlot= true
) )
val wgsHistogramReportValues = BammetricsReportPage.wgsHistogramValues( val wgsHistogramReportValues: Map[String, Any] = BammetricsReportPage.wgsHistogramValues(
summary,runId, samples, libraries, sampleId, libId, showPlot = true 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 summary,runId, samples, libraries, sampleId, libId, showPlot = true
) )
Future { Future {
......
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