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