Fixed flexiprep report

flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp

@@ -122,7 +122,7 @@
             #if (multisample)
                 <a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a>
             #else
-                ${sample}
+                ${sample.name}
             #end
             </td>
             #for (lib <- libraries.filter(_.sampleId == sample.id))

flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFront.ssp

-#import(nl.lumc.sasc.biopet.utils.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
+#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
+#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
 #import(nl.lumc.sasc.biopet.core.report.ReportPage)
-<%@ var summary: Summary %>
+#import(scala.concurrent.Await)
+#import(scala.concurrent.duration.Duration)
+<%@ var summary: SummaryDb %>
 <%@ var rootPath: String %>
-<%@ var sampleId: Option[String] %>
-<%@ var libId: Option[String] %>
-
+<%@ var runId: Int %>
+<%@ var sampleId: Option[Int] %>
+<%@ var libId: Option[Int] %>
+#{
+    val run = Await.result(summary.getRuns(runId = Some(runId)), Duration.Inf).head
+}#
 <table class="table">
 <tbody>
     <tr><th>Pipeline</th><td>Flexiprep</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>${summary.getValue("meta", "output_dir")}</td></tr>
-    <tr><th>Sample ID</th><td>${sampleId}</td></tr>
-    <tr><th>Library ID</th><td>${libId}</td></tr>
+    <tr><th>Version</th><td>${run.version}</td></tr>
+    <tr><th>Last commit hash</th><td>${run.commitHash}</td></tr>
+    <tr><th>Output directory</th><td>${run.outputDir}</td></tr>
+    <tr><th>Sample ID</th><td>${Await.result(summary.getSampleName(sampleId.get), Duration.Inf)}</td></tr>
+    <tr><th>Library ID</th><td>${Await.result(summary.getLibraryName(libId.get), Duration.Inf)}</td></tr>
 </tbody>
 </table>
 <br/>

flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp

@@ -127,7 +127,7 @@
             #if (multisample)
                 <a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a>
             #else
-                ${sample}
+                ${sample.name}
             #end
             </td>
             #for (lib <- libraries.filter(_.sampleId == sample.id))

flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala

@@ -45,8 +45,9 @@ object FlexiprepReport extends ReportBuilder {
     ReportPage(List("Versions" -> ReportPage(List(), List("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
     )), Map()),
       "Files" -> 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")
+        //TODO: Fix files
+//        "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")
       ), Map())
     ), List(
       "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFront.ssp")