From 32e20bf4a1423864fdec5e490105a6b114b72b62 Mon Sep 17 00:00:00 2001 From: Peter van 't Hof Date: Fri, 10 Mar 2017 13:33:35 +0100 Subject: [PATCH] Fixing gears templates --- .../biopet/pipelines/gears/gearsFront.ssp | 20 +++++++++++------ .../pipelines/gears/gearsSingleFront.ssp | 22 ++++++++++++------- .../biopet/pipelines/gears/GearsReport.scala | 18 ++++++++------- .../biopet/pipelines/mapping/mappingFront.ssp | 2 +- 4 files changed, 38 insertions(+), 24 deletions(-) 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 67d011009..df1f9a9be 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 +}# - - - + + +
PipelineGears
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 27fa3bc8d..2c361d7d0 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 +}# - - - - + + + + #if(sampleId.isDefined) #end #if(libId.isDefined) #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 49533c0b7..050c96fd7 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 036b2de01..0feb0457b 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 @@ }#
PipelineGears
Version${summary.getValue("meta", "pipeline_version")}
Last commit hash${summary.getValue("meta", "last_commit_hash")}
Output directory${summary.getValue("meta", "output_dir")}
PipelineGearsSingle
Version${run.version}
Last commit hash${run.commitHash}
Output directory${run.outputDir}
Sample${sampleId}
Library${libId}
- + -- GitLab
Pipeline${run.name}
PipelineMapping
Version${run.version}
Last commit hash${run.commitHash}
Output directory${run.outputDir}