From a149f43992d0496b04ebe317a31bdae8f9299aa1 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 29 Jun 2015 18:10:43 +0200
Subject: [PATCH] Added reference page
---
.../sasc/biopet/core/report/reference.ssp | 31 +++++++++++++++++++
.../biopet/pipelines/shiva/ShivaReport.scala | 5 ++-
2 files changed, 35 insertions(+), 1 deletion(-)
create mode 100644 public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/reference.ssp
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/reference.ssp b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/reference.ssp
new file mode 100644
index 000000000..530d21735
--- /dev/null
+++ b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/reference.ssp
@@ -0,0 +1,31 @@
+#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.core.report.ReportPage)
+<%@ var summary: Summary %>
+<%@ var rootPath: String %>
+<%@ var pipeline: String %>
+
+#{
+ val contigs = summary.getValue(pipeline, "settings", "reference", "contigs").get.asInstanceOf[Map[String, Map[String, Any]]]
+}#
+
+<table class="table">
+ <tbody>
+ <tr><th>Species</th><td>${summary.getValue(pipeline, "settings", "reference", "species")}</td></tr>
+ <tr><th>Name</th><td>${summary.getValue(pipeline, "settings", "reference", "name")}</td></tr>
+ <tr><th>File</th><td>${summary.getValue(pipeline, "files", "pipeline", "referenceFasta", "path")}</td></tr>
+ <tr><th>MD5</th><td>${summary.getValue(pipeline, "files", "pipeline", "referenceFasta", "md5")}</td></tr>
+ </tbody>
+</table>
+
+<br/>
+
+<table class="table sortable-theme-bootstrap" data-sortable>
+ <thead>
+ <tr><th>Contig Name</th><th data-sorted="true" data-sorted-direction="descending">Length</th><th>MD5</th></tr>
+ </thead>
+ <tbody>
+ #for (c <- contigs.toList.sortBy(_._2("length").asInstanceOf[Long]).reverse)
+ <tr><th>${c._1}</th><td>${c._2.get("length")}</td><td>${c._2.get("md5")}</td></tr>
+ #end
+ </tbody>
+</table>
\ No newline at end of file
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 05aef3cd5..4463b192a 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
@@ -25,7 +25,10 @@ object ShivaReport extends MultisampleReportBuilder {
ReportPage(
List("Samples" -> generateSamplesPage(pageArgs)) ++
(if (regions.isDefined) Map(regions.get) else Map()) ++
- Map("Files" -> filesPage,
+ Map("Reference" -> ReportPage(List(), List(
+ "Reference" -> ReportSection("/nl/lumc/sasc/biopet/core/report/reference.ssp", Map("pipeline" -> "shiva"))
+ ), Map()),
+ "Files" -> filesPage,
"Versions" -> ReportPage(List(), List((
"Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
))), Map())
--
GitLab