Commit 32e20bf4 authored by Peter van 't Hof's avatar Peter van 't Hof

Fixing gears templates

parent 106b05f0
#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) #import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %> #import(scala.concurrent.Await)
<%@ var rootPath: String %> #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"> <table class="table">
<tbody> <tbody>
<tr><th>Pipeline</th><td>Gears</td></tr> <tr><th>Pipeline</th><td>Gears</td></tr>
<tr><th>Version</th><td>${summary.getValue("meta", "pipeline_version")}</td></tr> <tr><th>Version</th><td>${run.version}</td></tr>
<tr><th>Last commit hash</th><td>${summary.getValue("meta", "last_commit_hash")}</td></tr> <tr><th>Last commit hash</th><td>${run.commitHash}</td></tr>
<tr><th>Output directory</th><td>${summary.getValue("meta", "output_dir")}</td></tr> <tr><th>Output directory</th><td>${run.outputDir}</td></tr>
</tbody> </tbody>
</table> </table>
<br/> <br/>
......
#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) #import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %> #import(scala.concurrent.Await)
<%@ var rootPath: String %> #import(scala.concurrent.duration.Duration)
<%@ var summary: SummaryDb %>
<%@ var runId: Int %>
<%@ var sampleId: Option[String] = None %> <%@ var sampleId: Option[String] = None %>
<%@ var libId: Option[String] = None %> <%@ var libId: Option[String] = None %>
#{
val run = Await.result(summary.getRuns(runId = Some(runId)), Duration.Inf).head
}#
<table class="table"> <table class="table">
<tbody> <tbody>
<tr><th>Pipeline</th><td>Gears</td></tr> <tr><th>Pipeline</th><td>GearsSingle</td></tr>
<tr><th>Version</th><td>${summary.getValue("meta", "pipeline_version")}</td></tr> <tr><th>Version</th><td>${run.version}</td></tr>
<tr><th>Last commit hash</th><td>${summary.getValue("meta", "last_commit_hash")}</td></tr> <tr><th>Last commit hash</th><td>${run.commitHash}</td></tr>
<tr><th>Output directory</th><td>${summary.getValue("meta", "output_dir")}</td></tr> <tr><th>Output directory</th><td>${run.outputDir}</td></tr>
#if(sampleId.isDefined) <tr><th>Sample</th><td>${sampleId}</td></tr> #end #if(sampleId.isDefined) <tr><th>Sample</th><td>${sampleId}</td></tr> #end
#if(libId.isDefined) <tr><th>Library</th><td>${libId}</td></tr> #end #if(libId.isDefined) <tr><th>Library</th><td>${libId}</td></tr> #end
</tbody> </tbody>
......
...@@ -14,11 +14,13 @@ ...@@ -14,11 +14,13 @@
*/ */
package nl.lumc.sasc.biopet.pipelines.gears 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.pipelines.flexiprep.FlexiprepReport
import nl.lumc.sasc.biopet.utils.config.Configurable 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.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.Await
import scala.concurrent.duration.Duration import scala.concurrent.duration.Duration
...@@ -57,10 +59,10 @@ object GearsReport extends MultisampleReportBuilder { ...@@ -57,10 +59,10 @@ object GearsReport extends MultisampleReportBuilder {
)), Map())) )), Map()))
else Nil) ::: (if (qiimeClosesOtuTable.isDefined) List("Qiime closed reference analysis" -> ReportPage(List(), List( else Nil) ::: (if (qiimeClosesOtuTable.isDefined) List("Qiime closed reference analysis" -> ReportPage(List(), List(
"Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp" "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( else Nil) ::: (if (qiimeOpenOtuTable.isDefined) List("Qiime open reference analysis" -> ReportPage(List(), List(
"Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp" "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)) ++ else Nil) ::: List("Samples" -> generateSamplesPage(pageArgs)) ++
Map( Map(
"Versions" -> ReportPage(List(), List( "Versions" -> ReportPage(List(), List(
...@@ -97,10 +99,10 @@ object GearsReport extends MultisampleReportBuilder { ...@@ -97,10 +99,10 @@ object GearsReport extends MultisampleReportBuilder {
)), Map())) )), Map()))
else Nil) ::: (if (qiimeClosesOtuTable.isDefined) List("Qiime closed reference analysis" -> ReportPage(List(), List( else Nil) ::: (if (qiimeClosesOtuTable.isDefined) List("Qiime closed reference analysis" -> ReportPage(List(), List(
"Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp" "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( else Nil) ::: (if (qiimeOpenOtuTable.isDefined) List("Qiime open reference analysis" -> ReportPage(List(), List(
"Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp" "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( else Nil) ::: List(
"Libraries" -> generateLibraryPage(args) "Libraries" -> generateLibraryPage(args)
), List("QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"), ), List("QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
...@@ -133,10 +135,10 @@ object GearsReport extends MultisampleReportBuilder { ...@@ -133,10 +135,10 @@ object GearsReport extends MultisampleReportBuilder {
)), Map())) )), Map()))
else Nil) ::: (if (qiimeClosesOtuTable.isDefined) List("Qiime closed reference analysis" -> ReportPage(List(), List( else Nil) ::: (if (qiimeClosesOtuTable.isDefined) List("Qiime closed reference analysis" -> ReportPage(List(), List(
"Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp" "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( else Nil) ::: (if (qiimeOpenOtuTable.isDefined) List("Qiime open reference analysis" -> ReportPage(List(), List(
"Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp" "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( else Nil), List(
"QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"), "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
"QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp") "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
......
...@@ -20,7 +20,7 @@ ...@@ -20,7 +20,7 @@
}# }#
<table class="table"> <table class="table">
<tbody> <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>Version</th><td>${run.version}</td></tr>
<tr><th>Last commit hash</th><td>${run.commitHash}</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>Output directory</th><td>${run.outputDir}</td></tr>
......
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