Fixing gears templates

gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsFront.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 %>
-<%@ var rootPath: String %>
-
+#import(scala.concurrent.Await)
+#import(scala.concurrent.duration.Duration)
+<%@ var summary: SummaryDb %>
+<%@ var runId: Int %>
+#{
+    val run = Await.result(summary.getRuns(runId = Some(runId)), Duration.Inf).head
+}#
 <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>${summary.getValue("meta", "output_dir")}</td></tr>
+    <tr><th>Version</th><td>${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>
 </tbody>
 </table>
 <br/>

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.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 %>
-<%@ var rootPath: String %>
+#import(scala.concurrent.Await)
+#import(scala.concurrent.duration.Duration)
+<%@ var summary: SummaryDb %>
+<%@ var runId: Int %>
 <%@ var sampleId: Option[String] = None %>
 <%@ var libId: Option[String] = None %>
-
+#{
+    val run = Await.result(summary.getRuns(runId = Some(runId)), Duration.Inf).head
+}#
 <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>${summary.getValue("meta", "output_dir")}</td></tr>
+    <tr><th>Pipeline</th><td>GearsSingle</td></tr>
+    <tr><th>Version</th><td>${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>
     #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>

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

@@ -14,11 +14,13 @@
  */
 package nl.lumc.sasc.biopet.pipelines.gears
 
-import nl.lumc.sasc.biopet.core.report.{ MultisampleReportBuilder, ReportBuilderExtension, ReportPage, ReportSection }
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.report.{MultisampleReportBuilder, ReportBuilderExtension, ReportPage, ReportSection}
 import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._
-import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.{ NoLibrary, NoModule, SampleId }
+import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.{NoLibrary, NoModule, SampleId}
 
 import scala.concurrent.Await
 import scala.concurrent.duration.Duration
@@ -57,10 +59,10 @@ object GearsReport extends MultisampleReportBuilder {
         )), Map()))
       else Nil) ::: (if (qiimeClosesOtuTable.isDefined) List("Qiime closed reference analysis" -> ReportPage(List(), List(
         "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
-        )), Map("biomFile" -> qiimeClosesOtuTable.get)))
+        )), Map("biomFile" -> new File(qiimeClosesOtuTable.get.path))))
       else Nil) ::: (if (qiimeOpenOtuTable.isDefined) List("Qiime open reference analysis" -> ReportPage(List(), List(
         "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
-        )), Map("biomFile" -> qiimeOpenOtuTable.get)))
+        )), Map("biomFile" -> new File(qiimeOpenOtuTable.get.path))))
       else Nil) ::: List("Samples" -> generateSamplesPage(pageArgs)) ++
         Map(
           "Versions" -> ReportPage(List(), List(
@@ -97,10 +99,10 @@ object GearsReport extends MultisampleReportBuilder {
       )), Map()))
     else Nil) ::: (if (qiimeClosesOtuTable.isDefined) List("Qiime closed reference analysis" -> ReportPage(List(), List(
       "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
-      )), Map("biomFile" -> qiimeClosesOtuTable.get)))
+      )), Map("biomFile" -> new File(qiimeClosesOtuTable.get.path))))
     else Nil) ::: (if (qiimeOpenOtuTable.isDefined) List("Qiime open reference analysis" -> ReportPage(List(), List(
       "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
-      )), Map("biomFile" -> qiimeOpenOtuTable.get)))
+      )), Map("biomFile" -> new File(qiimeOpenOtuTable.get.path))))
     else Nil) ::: List(
       "Libraries" -> generateLibraryPage(args)
     ), List("QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
@@ -133,10 +135,10 @@ object GearsReport extends MultisampleReportBuilder {
         )), Map()))
       else Nil) ::: (if (qiimeClosesOtuTable.isDefined) List("Qiime closed reference analysis" -> ReportPage(List(), List(
         "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
-        )), Map("biomFile" -> qiimeClosesOtuTable.get)))
+        )), Map("biomFile" -> new File(qiimeClosesOtuTable.get.path))))
       else Nil) ::: (if (qiimeOpenOtuTable.isDefined) List("Qiime open reference analysis" -> ReportPage(List(), List(
         "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
-        )), Map("biomFile" -> qiimeOpenOtuTable.get)))
+        )), Map("biomFile" -> new File(qiimeOpenOtuTable.get.path))))
       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")

mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/mappingFront.ssp

@@ -20,7 +20,7 @@
 }#
 <table class="table">
 <tbody>
-    <tr><th>Pipeline</th><td>${run.name}</td></tr>
+    <tr><th>Pipeline</th><td>Mapping</td></tr>
     <tr><th>Version</th><td>${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>