From b118cadf8969d91dc662e382c07a1a5ea72eb0a9 Mon Sep 17 00:00:00 2001 From: Peter van 't Hof Date: Mon, 20 Mar 2017 09:16:21 +0100 Subject: [PATCH] Fixed rna template --- .../pipelines/bammetrics/rnaHistogram.ssp | 49 +++++++++---------- 1 file changed, 23 insertions(+), 26 deletions(-) diff --git a/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp b/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp index 94b33a155..b766dc9bf 100644 --- a/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp +++ b/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp @@ -1,11 +1,14 @@ -#import(nl.lumc.sasc.biopet.utils.summary.Summary) +#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb) +#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._) +#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._) #import(nl.lumc.sasc.biopet.core.report.ReportPage) +#import(scala.concurrent.Await) +#import(scala.concurrent.duration.Duration) #import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport) #import(java.io.File) -#import(org.apache.commons.io.FileUtils) -<%@ var summary: Summary %> -<%@ var sampleId: Option[String] = None %> -<%@ var libId: Option[String] = None %> +<%@ var summary: SummaryDb %> +<%@ var sampleId: Option[Int] = None %> +<%@ var libId: Option[Int] = None %> <%@ var rootPath: String %> <%@ var metricsTag: String = "bammetrics" %> <%@ var sampleLevel: Boolean = false %> @@ -14,13 +17,9 @@ <%@ var showPlot: Boolean = false %> <%@ var showTable: Boolean = true %> <%@ var showIntro: Boolean = true%> +<%@ var runId: Int %> #{ - val samples = sampleId match { - case Some(sample) => { - List(sample.toString) - } - case _ => summary.samples.toList - } + val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf) }# #if (showIntro) @@ -36,7 +35,7 @@ #end #if (showPlot) - #{ BammetricsReport.rnaHistogramPlot(outputDir, "rna", summary, !sampleLevel, sampleId = sampleId, libId = libId) }# + #{ BammetricsReport.rnaHistogramPlot(outputDir, "rna", summary, !sampleLevel, sampleId = sampleId, libraryId = libId) }#
@@ -47,7 +46,7 @@ #else #end - +
#end @@ -62,27 +61,25 @@ #end - #for (sample <- samples.toList.sorted) + #for (sample <- samples.sortBy(_.name)) #{ - val libs = (libId, sampleLevel) match { - case (_, true) => List("") - case (Some(libId), _) => List(libId.toString) - case _ => summary.libraries(sample).toList + val libs: List[Option[Int]] = (libId, sampleLevel) match { + case (_, true) => List(None) + case (Some(_), _) => List(libId) + case _ => Await.result(summary.getLibraries(sampleId = Some(sample.id), runId = Some(runId)), Duration.Inf).map(x => Some(x.id)).toList } }# ${sample} #for (libId <- libs) + #{ val libName = libId.map(l => Await.result(summary.getLibraryName(l), Duration.Inf)) }# #if (libs.head != libId) #end - #if (!sampleLevel) ${libId} #end + #if (!sampleLevel) ${libName} #end #{ - val prefixPath = List("samples", sample) ::: (if (libId.isEmpty) Nil else List("libraries", libId)) ::: List("bammetrics", "stats") - - val fieldValues = for (field <- fields) yield { - summary.getValue((prefixPath ::: List("rna", "metrics", field.toUpperCase)):_*).getOrElse(prefixPath ::: metricsTag :: Nil) - } + 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) }# - #for (value <- fieldValues) - ${value} + #for (field <- fields) + ${results(field)} #end #end -- 2.22.2