Commit 1d2d9186 authored by Peter van 't Hof's avatar Peter van 't Hof

Fixing templates

parent 32e20bf4
......@@ -8,6 +8,7 @@
<%@ var runId: Int %>
#{
val run = Await.result(summary.getRuns(runId = Some(runId)), Duration.Inf).head
val samples = Await.result(summary.getSamples(Some(runId)), Duration.Inf)
}#
<table class="table">
<tbody>
......@@ -15,6 +16,7 @@
<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>${run.outputDir}</td></tr>
<tr><th>Number of samples</th><td>${samples.size}</td></tr>
</tbody>
</table>
<br/>
......
......@@ -16,11 +16,11 @@ package nl.lumc.sasc.biopet.pipelines.gears
import java.io.File
import nl.lumc.sasc.biopet.core.report.{MultisampleReportBuilder, ReportBuilderExtension, ReportPage, ReportSection}
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
......
#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
val samples = Await.result(summary.getSamples(Some(runId)), Duration.Inf)
val settings = summary.getSettingKeys(runId, run.name,
keyValues = Map(
"contigs" -> List("reference", "contigs"),
"species" -> List("reference", "species"),
"name" -> List("reference", "name"),
"annotation" -> List("annotation"),
"multisample_variantcalling" -> List("multisample_variantcalling"),
"sv_calling" -> List("sv_calling"),
"variantcallers" -> List("variantcallers")
))
}#
<table class="table">
<tbody>
<tr><th>Pipeline</th><td>Shiva</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>${summary.getValue("meta", "output_dir")}</td></tr>
<tr><th>Pipeline</th><td>Gears</td></tr>
<tr><th>Version</th><td>${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>Variantcallers</th>
<td>${summary.getValue("shivavariantcalling", "settings", "variantcallers").getOrElse(List("None")).asInstanceOf[List[String]].mkString(", ")}</td>
<td>${settings.get("variantcallers")}</td>
</tr>
<tr><th>Reference</th><td>${summary.getValue("shiva", "settings", "reference", "species")} - ${summary.getValue("shiva", "settings", "reference", "name")}</td></tr>
<tr><th>Number of samples</th><td>${summary.samples.size}</td></tr>
<tr><th>Annotation</th><td>${summary.getValue("shiva", "settings", "annotation")}</td></tr>
<tr><th>Multisample variantcalling</th><td>${summary.getValue("shiva", "settings", "multisample_variantcalling")}</td></tr>
<tr><th>Sv calling</th><td>${summary.getValue("shiva", "settings", "sv_calling")}</td></tr>
<tr><th>Reference</th><td>${settings.get("species")} - ${settings.get("name")}</td></tr>
<tr><th>Number of samples</th><td>${samples.size}</td></tr>
<tr><th>Annotation</th><td>${settings.get("annotation")}</td></tr>
<tr><th>Multisample variantcalling</th><td>${settings.get("multisample_variantcalling")}</td></tr>
<tr><th>Sv calling</th><td>${settings.get("sv_calling")}</td></tr>
</tbody>
</table>
<br/>
......
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