diff --git a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
index 2473089933b10da19ccde3100913e6213ef63546..834c68d0cb94cd58e2f5df69d64cf39e5616e7d4 100644
--- a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
+++ b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
@@ -14,7 +14,7 @@ object BammetricsReport extends ReportBuilder {
val reportName = "Bam Metrics"
- def indexPage = ReportPage(Map(), List(), Map())
+ def indexPage = ReportPage(List(), List(), Map())
def bamMetricsPage(summary: Summary, sampleId: Option[String], libId: Option[String]) = {
val targets = (
@@ -27,8 +27,8 @@ object BammetricsReport extends ReportBuilder {
}
ReportPage(
- (if (targets.isEmpty) Map() else Map("Targets" -> ReportPage(
- Map(),
+ (if (targets.isEmpty) List() else List("Targets" -> ReportPage(
+ List(),
targets.map(t => (t -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp", Map("target" -> t)))),
Map()))),
List(
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/main.ssp b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/main.ssp
index 7af4fb1daf3f0fa383b4f006f459d1ee19a6bc46..2bf9f3f8a6d8f15eb477a912741f1f4556c58bac 100644
--- a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/main.ssp
+++ b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/main.ssp
@@ -36,7 +36,11 @@
}
def getSubPage(path:List[String]): ReportPage = {
- path.foldLeft(indexPage)(_.subPages(_))
+ path.foldLeft(indexPage)((c, p) => {
+ val foundPages = c.subPages.filter(_._1 == p)
+ require(foundPages.size == 1, "Name of page not found or duplicate is found, page:: " + p + " in path: " + path)
+ foundPages.head._2
+ })
}
}#
<!DOCTYPE html>
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilder.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilder.scala
index 7b0d693cf38544479a989a81ca88ed0cac400616..3b43b435bf5a60862506fec8c41b99d499eb530b 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilder.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilder.scala
@@ -23,7 +23,7 @@ trait MultisampleReportBuilder extends ReportBuilder {
def generateSamplesPage(args: Map[String, Any]): ReportPage = {
val samplePages = summary.samples
.map(sampleId => (sampleId -> samplePage(sampleId, args ++ Map("sampleId" -> Some(sampleId)))))
- .toMap
+ .toList
ReportPage(samplePages, samplesSections, args)
}
@@ -35,7 +35,7 @@ trait MultisampleReportBuilder extends ReportBuilder {
val libPages = summary.libraries(sampleId)
.map(libId => (libId -> libraryPage(sampleId, libId, args ++ Map("libId" -> Some(libId)))))
- .toMap
+ .toList
ReportPage(libPages, libririesSections, args)
}
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportPage.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportPage.scala
index b2c0ff1f9667f6b106d077ed404e903798b7a59e..533c18384cda6ea60dbce4c587f8224611568ccf 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportPage.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportPage.scala
@@ -3,6 +3,6 @@ package nl.lumc.sasc.biopet.core.report
/**
* Created by pjvan_thof on 3/27/15.
*/
-case class ReportPage(subPages: Map[String, ReportPage],
+case class ReportPage(subPages: List[(String, ReportPage)],
sections: List[(String, ReportSection)],
args: Map[String, Any])
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
index 2857a7be4ac9abbff3708e20bb22761c71b490ad..5981f2a33f3bd166f72a27337677cbeabc79a622 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
@@ -12,7 +12,7 @@ import nl.lumc.sasc.biopet.extensions.rscript.StackedBarPlot
object FlexiprepReport extends ReportBuilder {
val reportName = "Flexiprep"
- def indexPage = ReportPage(Map(
+ def indexPage = ReportPage(List(
"QC" -> flexiprepPage
), List(
"Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFront.ssp")
@@ -21,7 +21,7 @@ object FlexiprepReport extends ReportBuilder {
)
def flexiprepPage = ReportPage(
- Map(),
+ List(),
List(
"Read Summary" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
"Base Summary" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp"),
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 fe830808034f0a1e34e6bfaacc7a53bb9dd8416f..f61859c1975f5e477f1d539779a7025f2c0844f0 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
@@ -25,10 +25,10 @@ object ShivaReport extends MultisampleReportBuilder {
def indexPage = {
val regions = regionsPage
ReportPage(
- Map("Samples" -> generateSamplesPage(pageArgs)) ++
+ List("Samples" -> generateSamplesPage(pageArgs)) ++
(if (regions.isDefined) Map(regions.get) else Map()) ++
Map("Files" -> filesPage,
- "Versions" -> ReportPage(Map(), List((
+ "Versions" -> ReportPage(List(), List((
"Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
))), Map())
),
@@ -58,7 +58,7 @@ object ShivaReport extends MultisampleReportBuilder {
def createPage(name: String, amplicon: Boolean = false): ReportPage = {
ReportPage(
- Map(),
+ List(),
List("Coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp")),
Map("target" -> name)
)
@@ -76,16 +76,17 @@ object ShivaReport extends MultisampleReportBuilder {
}
if (regionPages.nonEmpty) Some("Regions" -> ReportPage(
- Map(),
+ List(),
regionPages.map(p => (p._1 -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp",
Map("target" -> p._1.stripSuffix(" (Amplicon)"))
))).toList.sortBy(_._1),
Map())
- ) else None
+ )
+ else None
}
- def filesPage = ReportPage(Map(), List(
+ def filesPage = ReportPage(List(), List(
"Input fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepInputfiles.ssp"),
"After QC fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepOutputfiles.ssp"),
"Bam files per lib" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp", Map("sampleLevel" -> false)),
@@ -95,7 +96,7 @@ object ShivaReport extends MultisampleReportBuilder {
), Map())
def samplePage(sampleId: String, args: Map[String, Any]) = {
- ReportPage(Map(
+ ReportPage(List(
"Libraries" -> generateLibraryPage(args),
"Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), None),
"Files" -> filesPage
@@ -110,7 +111,7 @@ object ShivaReport extends MultisampleReportBuilder {
}
def libraryPage(sampleId: String, libId: String, args: Map[String, Any]) = {
- ReportPage(Map(
+ ReportPage(List(
"Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), Some(libId)),
"QC" -> FlexiprepReport.flexiprepPage
), List(