From 89bc7d9abd154b193772c32c35a997bd7bb8ac0a Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 2 Nov 2015 09:30:26 +0100
Subject: [PATCH] Added sunburst plot to mapping and shiva
---
.../sasc/biopet/pipelines/gears/gearsSunburst.ssp | 4 ++--
.../sasc/biopet/pipelines/gears/GearsReport.scala | 2 --
.../biopet/pipelines/mapping/MappingReport.scala | 13 +++++++++++--
.../sasc/biopet/pipelines/shiva/ShivaReport.scala | 10 +++++++++-
4 files changed, 22 insertions(+), 7 deletions(-)
diff --git a/public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp b/public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp
index 0915decbe..0ea325108 100644
--- a/public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp
+++ b/public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp
@@ -57,10 +57,10 @@
#{
val rawreport = Map("kraken" -> summary.getValue(sampleId, libId, "gears", "stats", "krakenreport"))
- val bla = ConfigUtils.mapToJson(rawreport)
+ val jsonReport = ConfigUtils.mapToJson(rawreport)
}#
- var krakenresult = JSON.parse('<%= unescape(bla) %>');
+ var krakenresult = JSON.parse('<%= unescape(jsonReport) %>');
loadGears(krakenresult.kraken.classified);
</script>
diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
index cf9a9c366..f8b367dbb 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
+++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
@@ -9,8 +9,6 @@ class GearsReport(val root: Configurable) extends ReportBuilderExtension {
object GearsReport extends ReportBuilder {
- // FIXME: Not yet finished
- // TODO: Sample specific: Add summary (sunflare plot)
// TODO: Add dustbin analysis (aggregated)
// TODO: Add alignment stats per sample for the dustbin analysis
diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
index b2f1b7a84..6c8b2b500 100644
--- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
+++ b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
@@ -16,7 +16,7 @@
package nl.lumc.sasc.biopet.pipelines.mapping
import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.report.{ ReportBuilderExtension, ReportSection, ReportPage, ReportBuilder }
+import nl.lumc.sasc.biopet.core.report._
import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
@@ -33,6 +33,11 @@ object MappingReport extends ReportBuilder {
/** Name of report */
val reportName = "Mapping Report"
+ override def extFiles = super.extFiles ++ List("js/gears.js")
+ .map(x => ExtFile("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + x, x))
+
+ def krakenExecuted = summary.getValue(sampleId, libId, "gears", "stats", "krakenreport").isDefined
+
/** Root page for single BamMetrcis report */
def indexPage = {
val skipFlexiprep = summary.getValue(sampleId, libId, "mapping", "settings", "skip_flexiprep").getOrElse(false) == true
@@ -48,7 +53,11 @@ object MappingReport extends ReportBuilder {
"After QC fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepOutputfiles.ssp"))) :::
List("Bam files per lib" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp", Map("sampleLevel" -> false))
), Map())
- ), List(
+ ) :::
+ (if (krakenExecuted) List("Gears - Metagenomics" -> ReportPage(List(), List(
+ "Sunburst analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp"
+ )), Map()))
+ else Nil), List(
"Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/mappingFront.ssp")
) ::: bamMetricsPage.map(_.sections).getOrElse(Nil),
Map()
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
index 7e32d72fe..8749071df 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
@@ -36,6 +36,9 @@ class ShivaReport(val root: Configurable) extends ReportBuilderExtension {
/** Object for report generation for Shiva pipeline */
object ShivaReport extends MultisampleReportBuilder {
+ override def extFiles = super.extFiles ++ List("js/gears.js")
+ .map(x => ExtFile("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + x, x))
+
/** Root page for the shiva report */
def indexPage = {
val regions = regionsPage
@@ -136,10 +139,15 @@ object ShivaReport extends MultisampleReportBuilder {
/** Library page */
def libraryPage(sampleId: String, libId: String, args: Map[String, Any]): ReportPage = {
+ def krakenExecuted = summary.getValue(Some(sampleId), Some(libId), "gears", "stats", "krakenreport").isDefined
+
ReportPage(List(
"Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), Some(libId)),
"QC" -> FlexiprepReport.flexiprepPage
- ), List(
+ ) ::: (if (krakenExecuted) List("Gears - Metagenomics" -> ReportPage(List(), List(
+ "Sunburst analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp"
+ )), Map()))
+ else Nil), List(
"Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
"QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
"QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
--
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