diff --git a/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsFront.ssp b/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsFront.ssp
index 67d01100940d62c0bd443ca243ad676f840daf0b..df1f9a9be410de804d7dbd2887e224c6addfa91e 100644
--- a/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsFront.ssp
+++ b/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsFront.ssp
@@ -1,14 +1,20 @@
-#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
+}#
Pipeline | Gears |
- Version | ${summary.getValue("meta", "pipeline_version")} |
- Last commit hash | ${summary.getValue("meta", "last_commit_hash")} |
- Output directory | ${summary.getValue("meta", "output_dir")} |
+ Version | ${run.version} |
+ Last commit hash | ${run.commitHash} |
+ Output directory | ${run.outputDir} |
diff --git a/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsSingleFront.ssp b/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsSingleFront.ssp
index 27fa3bc8d8d1706cf5fb2952ad5980964ba2ec47..2c361d7d03cc75e63519dbc2e61feea59b35ef3c 100644
--- a/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsSingleFront.ssp
+++ b/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsSingleFront.ssp
@@ -1,16 +1,22 @@
-#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
+}#
- Pipeline | Gears |
- Version | ${summary.getValue("meta", "pipeline_version")} |
- Last commit hash | ${summary.getValue("meta", "last_commit_hash")} |
- Output directory | ${summary.getValue("meta", "output_dir")} |
+ Pipeline | GearsSingle |
+ Version | ${run.version} |
+ Last commit hash | ${run.commitHash} |
+ Output directory | ${run.outputDir} |
#if(sampleId.isDefined) Sample | ${sampleId} |
#end
#if(libId.isDefined) Library | ${libId} |
#end
diff --git a/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala b/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
index 49533c0b717f2f26492047fae5e4e050ed02b6ea..050c96fd7e00fad837bac36575ac9ebae0bd3129 100644
--- a/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
+++ b/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")
diff --git a/mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/mappingFront.ssp b/mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/mappingFront.ssp
index 036b2de01d29f86ab79e583bbb0cf9d3eb7a0912..0feb0457b39bf47bb7a882b272e9490073ab3156 100644
--- a/mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/mappingFront.ssp
+++ b/mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/mappingFront.ssp
@@ -20,7 +20,7 @@
}#
- Pipeline | ${run.name} |
+ Pipeline | Mapping |
Version | ${run.version} |
Last commit hash | ${run.commitHash} |
Output directory | ${run.outputDir} |