Commit 200da965 authored by Peter van 't Hof's avatar Peter van 't Hof

Fixed flexiprep report

parent 99c245a2
......@@ -122,7 +122,7 @@
#if (multisample)
<a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a>
#else
${sample}
${sample.name}
#end
</td>
#for (lib <- libraries.filter(_.sampleId == sample.id))
......
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %>
#import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration)
<%@ var summary: SummaryDb %>
<%@ var rootPath: String %>
<%@ var sampleId: Option[String] %>
<%@ var libId: Option[String] %>
<%@ var runId: Int %>
<%@ var sampleId: Option[Int] %>
<%@ var libId: Option[Int] %>
#{
val run = Await.result(summary.getRuns(runId = Some(runId)), Duration.Inf).head
}#
<table class="table">
<tbody>
<tr><th>Pipeline</th><td>Flexiprep</td></tr>
<tr><th>Version</th><td>${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>${Await.result(summary.getLibraryName(libId.get), Duration.Inf)}</td></tr>
</tbody>
</table>
<br/>
......
......@@ -127,7 +127,7 @@
#if (multisample)
<a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a>
#else
${sample}
${sample.name}
#end
</td>
#for (lib <- libraries.filter(_.sampleId == sample.id))
......
......@@ -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")
......
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