Added multisample gears report

public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsFront.ssp

@@ -2,8 +2,6 @@
 #import(nl.lumc.sasc.biopet.core.report.ReportPage)
 <%@ var summary: Summary %>
 <%@ var rootPath: String %>
-<%@ var sampleId: Option[String] = None %>
-<%@ var libId: Option[String] = None %>
 
 <table class="table">
 <tbody>
@@ -11,8 +9,6 @@
     <tr><th>Version</th><td>${summary.getValue("meta", "pipeline_version")}</td></tr>
     <tr><th>Last commit hash</th><td>${summary.getValue("meta", "last_commit_hash")}</td></tr>
     <tr><th>Output directory</th><td>${summary.getValue("meta", "output_dir")}</td></tr>
-    #if(sampleId.isDefined) <tr><th>Sample</th><td>${sampleId}</td></tr> #end
-    #if(libId.isDefined) <tr><th>Library</th><td>${libId}</td></tr> #end
 </tbody>
 </table>
 <br/>

public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsSingleFront.ssp

+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
+#import(nl.lumc.sasc.biopet.core.report.ReportPage)
+<%@ var summary: Summary %>
+<%@ var rootPath: String %>
+<%@ var sampleId: Option[String] = None %>
+<%@ var libId: Option[String] = None %>
+
+<table class="table">
+<tbody>
+    <tr><th>Pipeline</th><td>Gears</td></tr>
+    <tr><th>Version</th><td>${summary.getValue("meta", "pipeline_version")}</td></tr>
+    <tr><th>Last commit hash</th><td>${summary.getValue("meta", "last_commit_hash")}</td></tr>
+    <tr><th>Output directory</th><td>${summary.getValue("meta", "output_dir")}</td></tr>
+    #if(sampleId.isDefined) <tr><th>Sample</th><td>${sampleId}</td></tr> #end
+    #if(libId.isDefined) <tr><th>Library</th><td>${libId}</td></tr> #end
+</tbody>
+</table>
+<br/>
+<div class="row">
+<div class="col-md-1"></div>
+<div class="col-md-6">
+    <p>\
+        In this web document you can find your <em>Gears</em> pipeline report.
+        Different categories of data can be found in the left-side menu.
+        Statistics per sample and library can be accessed through the top-level menu.
+        Some statistics for target regions can be found in the regions tab.
+        Futhermore, you can view all versions of software tools used by selecting <em>Versions</em> from the top menu.
+    </p>
+
+    <p>
+        <small>Brought to you by <a href="https://sasc.lumc.nl" target="_blank"><abbr
+            title="Sequence Analysis Support Core">SASC</abbr></a> and <a
+        href="https://www.lumc.nl/org/klinische-genetica/" target="_blank"><abbr title="Clinical Genetics LUMC">KG</abbr></a>,
+        LUMC.
+        </small>
+    </p>
+</div>
+</div>
\ No newline at end of file

public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp

@@ -54,7 +54,7 @@
     <script type="application/ecmascript">
 
     #{
-        val rawreport = Map("kraken" -> summary.getValue(sampleId, libId, "gears", "stats", "krakenreport"))
+        val rawreport = Map("kraken" -> summary.getValue(sampleId, libId, "gearskraken", "stats", "krakenreport"))
         val jsonReport = ConfigUtils.mapToJson(rawreport)
     }#
 

public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala

+package nl.lumc.sasc.biopet.pipelines.gears
+
+import nl.lumc.sasc.biopet.core.report.{ ReportSection, ReportPage, MultisampleReportBuilder, ReportBuilderExtension }
+import nl.lumc.sasc.biopet.utils.config.Configurable
+
+/**
+ * Created by pjvan_thof on 12/10/15.
+ */
+class GearsReport(val root: Configurable) extends ReportBuilderExtension {
+  def builder = GearsReport
+}
+
+object GearsReport extends MultisampleReportBuilder {
+
+  def reportName = "Gears Report"
+
+  override def extFiles = super.extFiles ++ List("js/gears.js")
+    .map(x => ExtFile("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + x, x))
+
+  def indexPage = {
+    ReportPage(
+      List("Samples" -> generateSamplesPage(pageArgs)) ++
+        Map(
+          "Versions" -> ReportPage(List(), List(
+            "Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp")
+          ), Map())
+        ),
+      List(
+        "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsFront.ssp")) ++
+        List(
+          "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp",
+            Map("showPlot" -> true, "showTable" -> false)),
+          "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp",
+            Map("showPlot" -> true, "showTable" -> false))
+        ),
+      pageArgs
+    )
+  }
+
+  /** Single sample page */
+  def samplePage(sampleId: String, args: Map[String, Any]): ReportPage = {
+    ReportPage(List(
+      "Libraries" -> generateLibraryPage(args)
+    ), List("QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
+      "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
+    ), args)
+  }
+
+  /** Library page */
+  def libraryPage(sampleId: String, libId: String, args: Map[String, Any]): ReportPage = {
+    val krakenExecuted = summary.getValue(Some(sampleId), Some(libId), "gearskraken", "stats", "krakenreport").isDefined
+
+    ReportPage(
+      (if (krakenExecuted) List("Gears - Metagenomics" -> ReportPage(List(), List(
+        "Sunburst analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp"
+        )), Map()))
+      else Nil), List(
+        "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
+        "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
+      ), args)
+  }
+
+}
\ No newline at end of file

public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleReport.scala

@@ -38,7 +38,7 @@ object GearsSingleReport extends ReportBuilder {
           ))), Map())
       ),
       List(
-        "Gears intro" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsFront.ssp"),
+        "Gears intro" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsSingleFront.ssp"),
         "Sunburst analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp")
       ),
       pageArgs