Merge branch 'develop' into fix-BIOPET-583

bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp

+#import(nl.lumc.sasc.biopet.utils.summary.db.Schema._)
 #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._)
@@ -16,8 +17,13 @@
 <%@ var showTable: Boolean = true %>
 <%@ var showIntro: Boolean = true%>
 <%@ var runId: Int %>
+<%@ var allSamples: Seq[Sample] %>
+<%@ var allLibraries: Seq[Library] %>
 #{
-    val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
+    val samples = sampleId match {
+    case Some(id) => allSamples.filter(_.id == id).toList
+    case _ => allSamples.toList
+    }
 }#
 #if (showIntro)
     <br/>
@@ -74,12 +80,12 @@
                 val libs: List[Option[Int]] = (libId, sampleLevel) match {
                 case (_, true) => List(None)
                 case (Some(_), _) => List(libId)
-                case _ => Await.result(summary.getLibraries(sampleId = Some(sample.id), runId = Some(runId)), Duration.Inf).map(x => Some(x.id)).toList
+                case _ => allLibraries.filter(_.sampleId == sample.id).map(x => Some(x.id)).toList
                 }
             }#
             <tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a></td>
             #for (libId <- libs)
-                #{ val libName = libId.map(l => Await.result(summary.getLibraryName(l), Duration.Inf)) }#
+                #{ val libName = libId.map(l => allLibraries.find(_.id == l).get.name) }#
                 #if (libs.head != libId) <tr> #end
                     #if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
                     #{

bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp

@@ -2,9 +2,8 @@
 #import(nl.lumc.sasc.biopet.core.report.ReportPage)
 <%@ var summary: Summary %>
 <%@ var rootPath: String %>
-<%@ var sampleId: Option[String] %>
-<%@ var libId: Option[String] = None %>
-
+<%@ var sampleId: Option[Int] %>
+<%@ var libId: Option[Int] = None %>
 <table class="table">
 <tbody>
     <tr><th>Pipeline</th><td>BamMetrics</td></tr>

bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamStats.ssp

-#import(nl.lumc.sasc.biopet.utils.summary.Summary)
-#import(nl.lumc.sasc.biopet.core.report.ReportPage)
-<%@ var summary: Summary %>
-<%@ var sampleId: Option[String] %>
-<%@ var libId: Option[String] = None %>
-<%@ var rootPath: String %>
-<%@ var metricsTag: String = "bammetrics" %>
-<%@ var fields: List[String] = List("All", "Mapped", "Duplicates", "MAPQ>30", "MateUnmapped", "Mate on other chr")%>
-
-<table>
-<tbody>
-#for (field <- fields)
-    <tr><th>${field}</th><td>
-    #if (libId.isDefined)
-        ${summary.getLibraryValue(sampleId.get, libId.get, metricsTag, "stats", "bamstats", "flagstats", field)}
-    #else
-        ${summary.getSampleValue(sampleId.get, metricsTag, "stats", "bamstats", "flagstats", field)}
-    #end
-    </td></tr>
-#end
-</tbody>
-</table>

bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bammetricsInputFile.ssp

-#import(nl.lumc.sasc.biopet.utils.summary.Summary)
-#import(nl.lumc.sasc.biopet.core.report.ReportPage)
-#import(java.io.File)
-<%@ var summary: Summary %>
-<%@ var sampleId: Option[String] %>
-<%@ var libId: Option[String] = None %>
-<%@ var metricsTag: String = "bammetrics" %>
-
-<table class="table sortable-theme-bootstrap">
-<thead><tr>
-    <th>Path</th>
-    <th>MD5</th>
-</tr></thead>
-<tbody>
-<tr>
-<td>${summary.getValue(sampleId, libId, metricsTag, "files", "pipeline", "bamfile", "path")}</td>
-<td>${summary.getValue(sampleId, libId, metricsTag, "files", "pipeline", "bamfile", "md5")}</td>
-</tr>
-</tbody>
-</table>
\ No newline at end of file

bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/clipping.ssp

+#import(nl.lumc.sasc.biopet.utils.summary.db.Schema._)
 #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(scala.concurrent.Await)
-#import(scala.concurrent.duration.Duration)
 #import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
 #import(java.io.File)
 <%@ var summary: SummaryDb %>
@@ -17,10 +16,14 @@
 <%@ var showIntro: Boolean = true%>
 <%@ var runId: Int %>
 <%@ var fields: List[String] = List("min", "max", "mean", "median", "modal")%>
+<%@ var allSamples: Seq[Sample] %>
+<%@ var allLibraries: Seq[Library] %>
 #{
-    val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
+    val samples = sampleId match {
+    case Some(id) => allSamples.filter(_.id == id).toList
+    case _ => allSamples.toList
+    }
 }#
-
 #if (showIntro)
     <br/>
     <div class="row">
@@ -74,12 +77,12 @@
                 val libs: List[Option[Int]] = (libId, sampleLevel) match {
                 case (_, true) => List(None)
                 case (Some(_), _) => List(libId)
-                case _ => Await.result(summary.getLibraries(sampleId = Some(sample.id), runId = Some(runId)), Duration.Inf).map(x => Some(x.id)).toList
+                case _ => allLibraries.filter(_.sampleId == sample.id).map(x => Some(x.id)).toList
                 }
             }#
             <tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a></td>
             #for (libId <- libs)
-                #{ val libName = libId.map(l => Await.result(summary.getLibraryName(l), Duration.Inf)) }#
+                #{ val libName = libId.map(l => allLibraries.find(_.id == l).get.name) }#
                 #if (libs.head != libId) <tr> #end
                     #if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
                     #{

bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp

 #import(nl.lumc.sasc.biopet.utils.IoUtils)
 #import(org.apache.commons.io.FileUtils)
+#import(nl.lumc.sasc.biopet.utils.summary.db.Schema._)
 #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._)
@@ -18,11 +19,14 @@
 <%@ var target: Option[String] %>
 <%@ var runId: Int %>
 <%@ var fields: List[String] = List("mean", "median", "max", "horizontal", "frac_min_10x", "frac_min_20x", "frac_min_30x", "frac_min_40x", "frac_min_50x") %>
+<%@ var allSamples: Seq[Sample] %>
+<%@ var allLibraries: Seq[Library] %>
 #{
-    val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
+    val samples = sampleId match {
+    case Some(id) => allSamples.filter(_.id == id).toList
+    case _ => allSamples.toList
+    }
 }#
-
-
 <table class="table">
 <thead><tr>
     <th>sample</th>
@@ -36,7 +40,7 @@
             val libs: List[Option[Int]] = (libId, sampleLevel) match {
                 case (_, true) => List(None)
                 case (Some(_), _) => List(libId)
-                case _ => Await.result(summary.getLibraries(sampleId = Some(sample.id), runId = Some(runId)), Duration.Inf).map(x => Some(x.id)).toList
+                case _ => allLibraries.filter(_.sampleId == sample.id).map(x => Some(x.id)).toList
             }
         }#
         <tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a></td>

bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/gcBias.ssp

-#{ //TODO: Need content }#
-
-Todo
\ No newline at end of file

bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp

 #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.utils.summary.db.Schema._)
 #import(nl.lumc.sasc.biopet.core.report.ReportPage)
-#import(scala.concurrent.Await)
-#import(scala.concurrent.duration.Duration)
 #import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
 #import(java.io.File)
 <%@ var summary: SummaryDb %>
@@ -18,10 +17,14 @@
 <%@ var showTable: Boolean = true %>
 <%@ var showIntro: Boolean = true%>
 <%@ var runId: Int %>
+<%@ var allSamples: Seq[Sample] %>
+<%@ var allLibraries: Seq[Library] %>
 #{
-    val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
+    val samples = sampleId match {
+    case Some(id) => allSamples.filter(_.id == id).toList
+    case _ => allSamples.toList
+    }
 }#
-
 #if (showIntro)
     <br/>
     <div class="row">
@@ -76,12 +79,12 @@
                 val libs: List[Option[Int]] = (libId, sampleLevel) match {
                 case (_, true) => List(None)
                 case (Some(_), _) => List(libId)
-                case _ => Await.result(summary.getLibraries(sampleId = Some(sample.id), runId = Some(runId)), Duration.Inf).map(x => Some(x.id)).toList
+                case _ => allLibraries.filter(_.sampleId == sample.id).map(x => Some(x.id)).toList
                 }
             }#
             <tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a></td>
             #for (libId <- libs)
-                #{ val libName = libId.map(l => Await.result(summary.getLibraryName(l), Duration.Inf)) }#
+                #{ val libName = libId.map(l => allLibraries.find(_.id == l).get.name) }#
                 #if (libs.head != libId) <tr> #end
                         #if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
                         #{

bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp

 #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
+#import(nl.lumc.sasc.biopet.utils.summary.db.Schema._)
 #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(scala.concurrent.Await)
-#import(scala.concurrent.duration.Duration)
 #import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
 #import(java.io.File)
 <%@ var summary: SummaryDb %>
@@ -17,11 +16,14 @@
 <%@ var showIntro: Boolean = true%>
 <%@ var runId: Int %>
 <%@ var fields: List[String] = List("min", "max", "mean", "median", "modal")%>
-
+<%@ var allSamples: Seq[Sample] %>
+<%@ var allLibraries: Seq[Library] %>
 #{
-    val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
+    val samples = sampleId match {
+    case Some(id) => allSamples.filter(_.id == id).toList
+    case _ => allSamples.toList
+    }
 }#
-
 #if (showIntro)
     <br/>
     <div class="row">
@@ -75,12 +77,12 @@
                 val libs: List[Option[Int]] = (libId, sampleLevel) match {
                 case (_, true) => List(None)
                 case (Some(_), _) => List(libId)
-                case _ => Await.result(summary.getLibraries(sampleId = Some(sample.id), runId = Some(runId)), Duration.Inf).map(x => Some(x.id)).toList
+                case _ => allLibraries.filter(_.sampleId == sample.id).map(x => Some(x.id)).toList
                 }
             }#
             <tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a></td>
             #for (libId <- libs)
-                #{ val libName = libId.map(l => Await.result(summary.getLibraryName(l), Duration.Inf)) }#
+                #{ val libName = libId.map(l => allLibraries.find(_.id == l).get.name) }#
                 #if (libs.head != libId) <tr> #end
                     #if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
                     #{

bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/rna.ssp

-#{ //TODO: Need content }#
-
-Todo
\ No newline at end of file

bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp

+#import(nl.lumc.sasc.biopet.utils.summary.db.Schema._)
 #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(scala.concurrent.Await)
-#import(scala.concurrent.duration.Duration)
 #import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
 #import(java.io.File)
 <%@ var summary: SummaryDb %>
@@ -18,10 +17,14 @@
 <%@ var showTable: Boolean = true %>
 <%@ var showIntro: Boolean = true%>
 <%@ var runId: Int %>
+<%@ var allSamples: Seq[Sample] %>
+<%@ var allLibraries: Seq[Library] %>
 #{
-    val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
+    val samples = sampleId match {
+    case Some(id) => allSamples.filter(_.id == id).toList
+    case _ => allSamples.toList
+    }
 }#
-
 #if (showIntro)
     <br/>
     <div class="row">
@@ -66,12 +69,12 @@
                 val libs: List[Option[Int]] = (libId, sampleLevel) match {
                 case (_, true) => List(None)
                 case (Some(_), _) => List(libId)
-                case _ => Await.result(summary.getLibraries(sampleId = Some(sample.id), runId = Some(runId)), Duration.Inf).map(x => Some(x.id)).toList
+                case _ => allLibraries.filter(_.sampleId == sample.id).map(x => Some(x.id)).toList
                 }
             }#
             <tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
             #for (libId <- libs)
-                #{ val libName = libId.map(l => Await.result(summary.getLibraryName(l), Duration.Inf)) }#
+                #{ val libName = libId.map(l => allLibraries.find(_.id == l).get.name) }#
                 #if (libs.head != libId) <tr> #end
                     #if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
                     #{

bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/target.ssp

-#{ //TODO: Need content }#
-
-Todo
\ No newline at end of file

bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp

+#import(nl.lumc.sasc.biopet.utils.summary.db.Schema._)
 #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(scala.concurrent.Await)
-#import(scala.concurrent.duration.Duration)
 #import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
 #import(java.io.File)
 <%@ var summary: SummaryDb %>
@@ -17,10 +16,14 @@
 <%@ var showIntro: Boolean = true%>
 <%@ var runId: Int %>
 <%@ var fields: List[String] = List("mean_coverage", "pct_5x", "pct_10x", "pct_15x", "pct_20x", "pct_25x", "pct_30x", "pct_40x", "pct_50x", "pct_60x", "pct_70x", "pct_80x", "pct_90x", "pct_100x")%>
+<%@ var allSamples: Seq[Sample] %>
+<%@ var allLibraries: Seq[Library] %>
 #{
-    val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
+    val samples = sampleId match {
+    case Some(id) => allSamples.filter(_.id == id).toList
+    case _ => allSamples.toList
+    }
 }#
-
 #if (showIntro)
     <br/>
     <div class="row">
@@ -65,12 +68,12 @@
                 val libs: List[Option[Int]] = (libId, sampleLevel) match {
                 case (_, true) => List(None)
                 case (Some(_), _) => List(libId)
-                case _ => Await.result(summary.getLibraries(sampleId = Some(sample.id), runId = Some(runId)), Duration.Inf).map(x => Some(x.id)).toList
+                case _ => allLibraries.filter(_.sampleId == sample.id).map(x => Some(x.id)).toList
                 }
             }#
             <tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a></td>
             #for (libId <- libs)
-                #{ val libName = libId.map(l => Await.result(summary.getLibraryName(l), Duration.Inf)) }#
+                #{ val libName = libId.map(l => allLibraries.find(_.id == l).get.name) }#
                 #if (libs.head != libId) <tr> #end
                     #if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
                     #{

bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala

@@ -48,9 +48,7 @@ object BammetricsReport extends ReportBuilder {
     ReportPage(bamMetricsPage.subPages ::: 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/bammetrics/bammetricsInputFile.ssp")
-      ), Map())
+      "Files" -> ReportPage(List(), List(), Map())
     ), List(
       "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp")
     ) ::: bamMetricsPage.sections,

biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/librariesList.ssp

-#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
-#import(nl.lumc.sasc.biopet.core.report.ReportPage)
-#import(scala.concurrent.Await)
-#import(scala.concurrent.duration.Duration)
-<%@ var summary: SummaryDb %>
+#import(nl.lumc.sasc.biopet.utils.summary.db.Schema._)
 <%@ var rootPath: String %>
 <%@ var sampleId: Option[Int] = None %>
-<%@ var runId: Int %>
+<%@ var allLibraries: Seq[Library] %>
+<%@ var allSamples: Seq[Sample] %>
 <table class="table">
 <thead><tr><th>Libraries</th></tr></thead>
 <tbody>
-#for (lib <- Await.result(summary.getLibraries(runId = Some(runId)), Duration.Inf))
-    <tr><td><a href="${rootPath}Samples/${Await.result(summary.getSampleName(lib.sampleId), Duration.Inf)}/Libraries/${lib.name}/index.html">${lib}</a></td></tr>
+#{ val libs = sampleId match {
+    case Some(id) => allLibraries.filter(_.sampleId == id)
+    case _ => allLibraries
+} }#
+#for (lib <- libs)
+    #{ val sampleName: String = allSamples.find(_.id == lib.sampleId).get.name }#
+    <tr><td><a href="${rootPath}Samples/${sampleName}/Libraries/${lib.name}/index.html">${lib}</a></td></tr>
 #end
 </tbody>
 </table>
\ No newline at end of file

biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/samplesList.ssp

-#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
-#import(nl.lumc.sasc.biopet.core.report.ReportPage)
-#import(scala.concurrent.Await)
-#import(scala.concurrent.duration.Duration)
-<%@ var summary: SummaryDb %>
+#import(nl.lumc.sasc.biopet.utils.summary.db.Schema._)
 <%@ var rootPath: String %>
-<%@ var runId: Int %>
+<%@ var allSamples: Seq[Sample] %>
 <table class="table sortable-theme-bootstrap" data-sortable>
     <thead><tr><th data-sorted="true" data-sorted-direction="ascending">Sample</th></tr></thead>
     <tbody>
-        #for (sample <- Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf))
+        #for (sample <- allSamples)
             <tr><td><a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a></td></tr>
         #end
     </tbody>

flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepInputfiles.ssp

-#import(nl.lumc.sasc.biopet.utils.summary.Summary)
-#import(nl.lumc.sasc.biopet.core.report.ReportPage)
-#import(nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport)
-#import(java.io.File)
-<%@ var summary: Summary %>
-<%@ var sampleId: Option[String] = None %>
-<%@ var libId: Option[String] = None %>
-<%@ var rootPath: String %>
-<%@ var outputDir: File %>
-<%@ var showPlot: Boolean = false %>
-<%@ var showTable: Boolean = true %>
-#{
-    val samples = sampleId match {
-        case Some(sample) => List(sample.toString)
-        case _ => summary.samples.toList
-    }
-    val pipelineOutputDir = summary.getValue("meta", "output_dir").getOrElse("").toString
-    def removeDir(value: Option[Any]): Option[Any] = {
-        value.collect { case a =>
-            if (a.toString.startsWith(pipelineOutputDir) && pipelineOutputDir.nonEmpty) "./" + a.toString.stripPrefix(pipelineOutputDir + File.separator)
-            else a
-        }
-    }
-}#
-
-<table class="table">
-
-<thead><tr>
-    <th>Sample</th>
-    <th colspan="2">Library</th>
-    <th>Path</th>
-    <th>MD5</th>
-</tr></thead>
-<tbody>
-    #for (sample <- samples.toList.sorted)
-        #{
-            val libs = libId match {
-            case Some(libId) => List(libId.toString).sorted
-            case _ => summary.libraries(sample).toList.sorted
-            }
-
-            val sampleRowspan = {
-            libs.size +
-            libs.count(summary.getLibraryValue(sample, _, "flexiprep", "settings", "paired").getOrElse(false) == true)
-            }
-        }#
-        <tr><td rowspan="${sampleRowspan}"><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
-        #for (libId <- libs)
-            #if (libs.head != libId) <tr> #end
-                #{ val paired = summary.getLibraryValue(sample, libId, "flexiprep", "settings", "paired").getOrElse(false) }#
-                <td #if (paired == true) rowspan="2" #end><a href="${rootPath}Samples/${sample}/Libraries/${libId}/index.html">${libId}</a></td>
-                #{ val reads = if (paired == true) List("R1", "R2") else List("R1") }#
-                #for (read <- reads)
-                    #if (read == "R2") </tr><tr> #end
-                    <td>${read}</td>
-                    <td>${removeDir(summary.getLibraryValue(sample, libId, "flexiprep", "files", "pipeline", "input_" + read, "path"))}</td>
-                    <td>${summary.getLibraryValue(sample, libId, "flexiprep", "files", "pipeline", "input_" + read, "md5")}</td>
-                #end
-            </tr>
-        #end
-    #end
-</tbody>
-</table>
\ No newline at end of file

flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepOutputfiles.ssp

-#import(nl.lumc.sasc.biopet.utils.summary.Summary)
-#import(nl.lumc.sasc.biopet.core.report.ReportPage)
-#import(nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport)
-#import(java.io.File)
-<%@ var summary: Summary %>
-<%@ var sampleId: Option[String] = None %>
-<%@ var libId: Option[String] = None %>
-<%@ var rootPath: String %>
-<%@ var outputDir: File %>
-<%@ var showPlot: Boolean = false %>
-<%@ var showTable: Boolean = true %>
-#{
-    val samples = sampleId match {
-        case Some(sample) => List(sample.toString)
-        case _ => summary.samples.toList
-    }
-    val pipelineOutputDir = summary.getValue("meta", "output_dir").getOrElse("").toString
-    def removeDir(value: Option[Any]): Option[Any] = {
-        value.collect { case a =>
-            if (a.toString.startsWith(pipelineOutputDir) && pipelineOutputDir.nonEmpty) "./" + a.toString.stripPrefix(pipelineOutputDir + File.separator)
-            else a
-        }
-    }
-}#
-
-<table class="table">
-
-<thead><tr>
-    <th>Sample</th>
-    <th colspan="2">Library</th>
-    <th>Path</th>
-    <th>MD5</th>
-</tr></thead>
-<tbody>
-    #for (sample <- samples.toList.sorted)
-        #{
-            val libs = libId match {
-            case Some(libId) => List(libId.toString).sorted
-            case _ => summary.libraries(sample).toList.sorted
-            }
-
-            val sampleRowspan = {
-            libs.size +
-            libs.count(summary.getLibraryValue(sample, _, "flexiprep", "settings", "paired").getOrElse(false) == true)
-            }
-        }#
-        <tr><td rowspan="${sampleRowspan}"><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
-        #for (libId <- libs)
-            #if (libs.head != libId) <tr> #end
-                #{ val paired = summary.getLibraryValue(sample, libId, "flexiprep", "settings", "paired").getOrElse(false) }#
-                <td #if (paired == true) rowspan="2" #end><a href="${rootPath}Samples/${sample}/Libraries/${libId}/index.html">${libId}</a></td>
-                #{ val reads = if (paired == true) List("R1", "R2") else List("R1") }#
-                #for (read <- reads)
-                    #if (read == "R2") </tr><tr> #end
-                    <td>${read}</td>
-                    <td>${removeDir(summary.getLibraryValue(sample, libId, "flexiprep", "files", "pipeline", "output_" + read, "path"))}</td>
-                    <td>${summary.getLibraryValue(sample, libId, "flexiprep", "files", "pipeline", "output_" + read, "md5")}</td>
-                #end
-            </tr>
-        #end
-    #end
-</tbody>
-</table>
\ No newline at end of file

shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/outputVcfFiles.ssp

-#import(nl.lumc.sasc.biopet.utils.summary.Summary)
-#import(nl.lumc.sasc.biopet.core.report.ReportPage)
-#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
-#import(java.io.File)
-<%@ var summary: Summary %>
-<%@ var sampleId: Option[String] = None %>
-<%@ var libId: Option[String] = None %>
-<%@ var sampleLevel: Boolean = true %>
-<%@ var rootPath: String %>
-<%@ var outputDir: File %>
-#{
-    val variantCallers = summary.getValue(sampleId, libId, "shivavariantcalling", "settings", "variantcallers").get.asInstanceOf[List[String]]
-    val pipelineOutputDir = summary.getValue("meta", "output_dir").getOrElse("").toString
-    def removeDir(value: Option[Any]): Option[Any] = {
-        value.collect { case a =>
-            if (a.toString.startsWith(pipelineOutputDir) && pipelineOutputDir.nonEmpty) "./" + a.toString.stripPrefix(pipelineOutputDir + File.separator)
-            else a
-        }
-    }
-}#
-
-<div class="panel-body">
-<!-- Table -->
-<table class="table">
-    <thead><tr>
-        <th>Variantcaller</th>
-        <th>Path</th>
-        <th>MD5</th>
-    </tr></thead>
-    <tbody>
-        #if (variantCallers.size > 1)
-            <tr>
-                <td>Final (merged)</td>
-                <td>${removeDir(summary.getValue(sampleId, libId, "shivavariantcalling", "files", "pipeline", "final", "path"))}</td>
-                <td>${summary.getValue(sampleId, libId, "shivavariantcalling", "files", "pipeline", "final", "md5")}</td>
-            </tr>
-        #end
-        #for (variantCaller <- variantCallers)
-            <tr>
-                <td>${variantCaller}</td>
-                <td>${removeDir(summary.getValue(sampleId, libId, "shivavariantcalling", "files", "pipeline", variantCaller, "path"))}</td>
-                <td>${summary.getValue(sampleId, libId, "shivavariantcalling", "files", "pipeline", variantCaller, "md5")}</td>
-            </tr>
-        #end
-    </tbody>
-</table>
-
-</div>

toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/ManweActivateAfterAnnotImport.scala → toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/ManweActivateAfterImport.scala

@@ -25,15 +25,12 @@ import scala.io.Source
  * Created by ahbbollen on 9-10-15.
  * Wrapper for manwe activate after importing and annotating
  */