diff --git a/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala b/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala index 37f2f555597f3395490289aaeae1304492a7dadc..8d4cd5e1ec7263cab50c61743fc2508a876cbad6 100644 --- a/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala +++ b/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala @@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.core.report import java.io._ import nl.lumc.sasc.biopet.core.ToolCommandFunction -import nl.lumc.sasc.biopet.utils.summary.db.Schema.{ Library, Module, Pipeline, Sample } +import nl.lumc.sasc.biopet.utils.summary.db.Schema.{ Library, Module, Pipeline, Sample, Run } import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.{ LibraryId, SampleId } import nl.lumc.sasc.biopet.utils.{ IoUtils, Logging, ToolCommand } @@ -40,7 +40,7 @@ trait ReportBuilderExtension extends ToolCommandFunction { /** Report builder object */ def builder: ReportBuilder - def toolObject = builder + def toolObject: ReportBuilder = builder @Input(required = true) var summaryDbFile: File = _ @@ -114,20 +114,24 @@ trait ReportBuilder extends ToolCommand { private var setSummary: SummaryDb = _ /** Retrival of summary, read only */ - final def summary = setSummary + final def summary: SummaryDb = setSummary private var setRunId: Int = 0 - final def runId = setRunId + final def runId: Int = setRunId + + private var _setRun: Run = _ + + final def run: Run = _setRun private var _setPipelines = Seq[Pipeline]() - final def pipelines = _setPipelines + final def pipelines: Seq[Pipeline] = _setPipelines private var _setModules = Seq[Module]() - final def modules = _setModules + final def modules: Seq[Module] = _setModules private var _setSamples = Seq[Sample]() - final def samples = _setSamples + final def samples: Seq[Sample] = _setSamples private var _setLibraries = Seq[Library]() - final def libraries = _setLibraries + final def libraries: Seq[Library] = _setLibraries /** default args that are passed to all page withing the report */ def pageArgs: Map[String, Any] = Map() @@ -136,13 +140,13 @@ trait ReportBuilder extends ToolCommand { private var total = 0 private var _sampleId: Option[Int] = None - protected[report] def sampleId = _sampleId + protected[report] def sampleId: Option[Int] = _sampleId private var _libId: Option[Int] = None - protected[report] def libId = _libId + protected[report] def libId: Option[Int] = _libId case class ExtFile(resourcePath: String, targetPath: String) - def extFiles = List( + def extFiles: List[ExtFile] = List( "css/bootstrap_dashboard.css", "css/bootstrap.min.css", "css/bootstrap-theme.min.css", @@ -183,6 +187,7 @@ trait ReportBuilder extends ToolCommand { case _ => } + _setRun = Await.result(summary.getRuns(runId = Some(runId)), Duration.Inf).head _setPipelines = Await.result(summary.getPipelines(runId = Some(runId)), Duration.Inf) _setModules = Await.result(summary.getModules(runId = Some(runId)), Duration.Inf) _setSamples = Await.result(summary.getSamples(runId = Some(runId), sampleId = sampleId), Duration.Inf) @@ -264,6 +269,7 @@ trait ReportBuilder extends ToolCommand { val rootPath = "./" + Array.fill(path.size)("../").mkString args ++ page.args ++ Map("page" -> page, + "run" -> run, "path" -> path, "outputDir" -> pageOutputDir, "rootPath" -> rootPath, diff --git a/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFastQcPlot.ssp b/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFastQcPlot.ssp index 592e7b9b38a154a15477ee2e793d1a4f759d0a73..b5dab54136592fb616c8eac57c9437cb317e6604 100644 --- a/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFastQcPlot.ssp +++ b/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFastQcPlot.ssp @@ -1,3 +1,4 @@ +#import(nl.lumc.sasc.biopet.utils.summary.db.Schema.Run) #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._) @@ -10,6 +11,7 @@ #import(nl.lumc.sasc.biopet.core.report.ReportBuilder.ec) <%@ var summary: SummaryDb %> <%@ var runId: Int %> +<%@ var run: Run %> <%@ var sampleId: Option[Int] %> <%@ var libId: Option[Int] %> <%@ var plot: String %>