Simplify the report for plots for Gentrap / TinyCap heatmaps. Only 1 template...

Simplify the report for plots for Gentrap / TinyCap heatmaps. Only 1 template file, defining the picture path in the Report instead of the template.

public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/measure_fragmentspergene.ssp → public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/measure_plotreport.ssp

@@ -3,7 +3,8 @@
 #import(java.io.File)
 <%@ var summary: Summary %>
 <%@ var outputDir: File %>
-<%@ var pipelineName: String = "gentrap" %>
+<%@ var pipelineName: String %>
+<%@ var plotPath: Option[Any] %>
 #{
 
 def getPlot(path:Option[Any], targetPath:String) = {
@@ -27,7 +28,7 @@ def getPlot(path:Option[Any], targetPath:String) = {
 <tbody>
     <tr>
         <td>
-            <img src="${getPlot(summary.getValue("fragmentspergene", "files", "pipeline", "fragments_per_gene_heatmap", "path"), "measurements" )}" class="img-responsive" />
+            <img src="${getPlot(plotPath, "measurements" )}" class="img-responsive center-block" />
         </td>
     </tr>
 </tbody>

public/tinycap/src/main/resources/nl/lumc/sasc/biopet/pipelines/tinycap/measure_fragmentspersmallrna.ssp

-#import(nl.lumc.sasc.biopet.utils.summary.Summary)
-#import(org.apache.commons.io.FileUtils)
-#import(java.io.File)
-<%@ var summary: Summary %>
-<%@ var outputDir: File %>
-<%@ var pipelineName: String = "tinycap" %>
-#{
-
-def getPlot(path:Option[Any], targetPath:String) = {
-    path.collect {
-        case value =>
-            new File(targetPath).mkdirs()
-            val file = new File(value.toString)
-            val newFile = new File(outputDir, targetPath + File.separator + file.getName)
-
-            if (file.exists()) FileUtils.copyFile(file, newFile)
-            targetPath + File.separator + file.getName
-    }
-}
-
-}#
-<div class="panel-body">
-<!-- Table -->
-<table class="table">
-<thead>
-</thead>
-<tbody>
-    <tr>
-        <td>
-            <img src="${getPlot(summary.getValue("fragmentspersmallrna", "files", "pipeline", "fragments_per_gene_heatmap", "path"), "measurements" )}" class="img-responsive" />
-        </td>
-    </tr>
-</tbody>
-</table>
-
-</div>

public/tinycap/src/main/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapReport.scala

@@ -20,10 +20,15 @@ object TinyCapReport extends MultisampleMappingReportTrait {
   override def frontSection: ReportSection = ReportSection("/nl/lumc/sasc/biopet/pipelines/tinycap/tinycapFront.ssp")
 
   override def additionalSections = List(
-    "Fragments per gene" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gentrap/measure_fragmentspergene.ssp",
-      Map("pipelineName" -> pipelineName)),
-    "Fragments per microRNA" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/tinycap/measure_fragmentspersmallrna.ssp",
-      Map("pipelineName" -> pipelineName))
+    "Fragments per gene" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gentrap/measure_plotreport.ssp",
+      Map("pipelineName" -> pipelineName,
+        "plotName" -> "fragmentspergene",
+        "plotPath" -> summary.getValue("fragmentspergene", "files", "pipeline", "fragments_per_gene_heatmap", "path")
+      ) ),
+    "Fragments per microRNA" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gentrap/measure_plotreport.ssp",
+      Map("pipelineName" -> pipelineName,
+        "plotName" -> "fragmentspersmallrna",
+        "plotPath" -> summary.getValue("fragmentspersmallrna", "files", "pipeline", "fragments_per_gene_heatmap", "path")))
   )
 
   override def pipelineName = "tinycap"