Merge remote-tracking branch 'remotes/origin/develop' into fix-BIOPET-306

# Conflicts:
#	shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala

Jenkinsfile

 node('local') {
-    timeout(45) {
-        try {
+    try {
 
-            stage('Init') {
-                tool 'JDK 8u102'
-                tool 'Apache Maven 3.3.9'
-            }
+        stage('Init') {
+            tool 'JDK 8u102'
+            tool 'Apache Maven 3.3.9'
+        }
 
+        timeout(45) {
             stage('Checkout') {
                 checkout scm
                 sh 'git submodule update --init --recursive'
             }
+        }
 
+        timeout(45) {
             stage('Build and Test') {
                 withMaven(maven: 'Apache Maven 3.3.9', jdk: 'JDK 8u102') {
                     sh 'mvn -B -T 2 -Dmaven.test.failure.ignore clean package'
                 }
             }
+        }
 
-            stage('Report Tests') {
-                junit '*/target/surefire-reports/*.xml'
-            }
-
-            stage('Check git on changes') {
-                sh 'if [ $(git diff | wc -l) -eq 0 ]; then true; else echo "[ERROR] Git is not clean anymore after build"; git diff; echo "[ERROR] This might be caused by reformated code, if so run maven locally"; false; fi'
-            }
+        stage('Report Tests') {
+            junit '*/target/surefire-reports/*.xml'
+        }
 
-            stage('Check Documentation') {
-                sh 'mkdocs build --clean --strict'
-            }
+        stage('Check git on changes') {
+            sh 'if [ $(git diff | wc -l) -eq 0 ]; then true; else echo "[ERROR] Git is not clean anymore after build"; git diff; echo "[ERROR] This might be caused by reformated code, if so run maven locally"; false; fi'
+        }
 
-            if (currentBuild.result == null || "SUCCESS".equals(currentBuild.result)) {
-                currentBuild.result = "SUCCESS"
-                slackSend(color: '#00FF00', message: "${currentBuild.result}: Job '${env.JOB_NAME} #${env.BUILD_NUMBER}' (<${env.BUILD_URL}|Open>)", channel: '#biopet-bot', teamDomain: 'lumc', tokenCredentialId: 'lumc')
-            } else {
-                slackSend(color: '#FFFF00', message: "${currentBuild.result}: Job '${env.JOB_NAME} #${env.BUILD_NUMBER}' (<${env.BUILD_URL}|Open>)", channel: '#biopet-bot', teamDomain: 'lumc', tokenCredentialId: 'lumc')
-            }
+        stage('Check Documentation') {
+            sh 'mkdocs build --clean --strict'
+        }
 
-        } catch (e) {
-            if (currentBuild.result == null || "FAILED".equals(currentBuild.result)) {
-                currentBuild.result = "FAILED"
-            }
-            slackSend(color: '#FF0000', message: "${currentBuild.result}: Job '${env.JOB_NAME} #${env.BUILD_NUMBER}' (<${env.BUILD_URL}|Open>)", channel: '#biopet-bot', teamDomain: 'lumc', tokenCredentialId: 'lumc')
+        if (currentBuild.result == null || "SUCCESS".equals(currentBuild.result)) {
+            currentBuild.result = "SUCCESS"
+            slackSend(color: '#00FF00', message: "${currentBuild.result}: Job '${env.JOB_NAME} #${env.BUILD_NUMBER}' (<${env.BUILD_URL}|Open>)", channel: '#biopet-bot', teamDomain: 'lumc', tokenCredentialId: 'lumc')
+        } else {
+            slackSend(color: '#FFFF00', message: "${currentBuild.result}: Job '${env.JOB_NAME} #${env.BUILD_NUMBER}' (<${env.BUILD_URL}|Open>)", channel: '#biopet-bot', teamDomain: 'lumc', tokenCredentialId: 'lumc')
+        }
 
-            throw e
+    } catch (e) {
+        if (currentBuild.result == null || "FAILED".equals(currentBuild.result)) {
+            currentBuild.result = "FAILED"
         }
+        slackSend(color: '#FF0000', message: "${currentBuild.result}: Job '${env.JOB_NAME} #${env.BUILD_NUMBER}' (<${env.BUILD_URL}|Open>)", channel: '#biopet-bot', teamDomain: 'lumc', tokenCredentialId: 'lumc')
+
+        throw e
     }
 }

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

-#import(nl.lumc.sasc.biopet.utils.summary.Summary)
-#import(nl.lumc.sasc.biopet.core.report.ReportPage)
-<%@ var summary: Summary %>
-<%@ var rootPath: String %>
-<%@ var sampleId: Option[String] %>
-<%@ var libId: Option[String] = None %>
-
+#import(nl.lumc.sasc.biopet.utils.summary.db.Schema.Run)
+#import(nl.lumc.sasc.biopet.utils.summary.db.Schema.Sample)
+#import(nl.lumc.sasc.biopet.utils.summary.db.Schema.Library)
+<%@ var runId: Int %>
+<%@ var sampleId: Option[Int] = None %>
+<%@ var libId: Option[Int] = None %>
+<%@ var run: Run %>
+<%@ var allSamples: Seq[Sample] %>
+<%@ var allLibraries: Seq[Library] %>
 <table class="table">
 <tbody>
-    <tr><th>Pipeline</th><td>BamMetrics</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>
-    #if (libId.isDefined) <tr><th>Library ID</th><td>${libId}</td></tr> #end
+    <tr><th>Pipeline</th><td>GearsSingle</td></tr>
+    <tr><th>Version</th><td>${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</th><td>${allSamples.filter(_.id == sampleId.get).headOption.map(_.name)}</td></tr>
+    <tr><th>Library</th><td>${allLibraries.filter(_.id == libId.get).headOption.map(_.name)}</td></tr>
 </tbody>
 </table>
 <br/>

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

@@ -24,8 +24,7 @@ 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.SummaryDb._
 
-import scala.concurrent.ExecutionContext.Implicits.global
-import scala.concurrent.Await
+import scala.concurrent.{ Await, Future }
 import scala.concurrent.duration.Duration
 
 class BammetricsReport(val parent: Configurable) extends ReportBuilderExtension {
@@ -42,30 +41,27 @@ object BammetricsReport extends ReportBuilder {
   /** Name of report */
   val reportName = "Bam Metrics"
 
+  def pipelineName = "bammetrics"
+
   /** Root page for single BamMetrcis report */
-  def indexPage = {
-    val bamMetricsPage = this.bamMetricsPage(summary, sampleId, libId)
-    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())
-    ), List(
-      "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp")
-    ) ::: bamMetricsPage.sections,
-      Map()
-    )
-  }
+  def indexPage: Future[ReportPage] =
+    bamMetricsPage(summary, sampleId, libId).map { bamMetricsPage =>
+      ReportPage(bamMetricsPage.subPages ::: List(
+        "Versions" -> Future(ReportPage(List(), List("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
+        )), Map())),
+        "Files" -> filesPage(sampleId, libId)
+      ), List(
+        "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp")
+      ) ::: bamMetricsPage.sections,
+        Map()
+      )
+    }
 
   /** Generates a page with alignment stats */
   def bamMetricsPage(summary: SummaryDb,
                      sampleId: Option[Int],
                      libId: Option[Int],
-                     metricsTag: String = "bammetrics") = {
-
-    //val pipelineId: Int = summary.getPipelineId(runId, metricsTag).map(_.get)
-
+                     metricsTag: String = "bammetrics"): Future[ReportPage] = Future {
     val wgsExecuted = summary.getStatsSize(runId, metricsTag, "wgs", sample = sampleId.map(SampleId), library = libId.map(LibraryId)) >= 1
     val rnaExecuted = summary.getStatsSize(runId, metricsTag, "rna", sample = sampleId.map(SampleId), library = libId.map(LibraryId)) >= 1
 
@@ -87,10 +83,10 @@ object BammetricsReport extends ReportBuilder {
 
     ReportPage(
       if (targets.isEmpty) List()
-      else List("Targets" -> ReportPage(
+      else List("Targets" -> Future.successful(ReportPage(
         List(),
         targets.map(t => t -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp", Map("target" -> Some(t)))),
-        Map())),
+        Map()))),
       List(
         "Summary" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
         "Mapping Quality" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp", Map("showPlot" -> true)),
@@ -163,7 +159,7 @@ object BammetricsReport extends ReportBuilder {
     plot.output = pngFile
     plot.ylabel = Some("Reads")
     plot.width = Some(200 + (results.size * 10))
-    plot.title = Some("Aligned reads")
+    plot.title = Some("Aligned_reads")
     plot.runLocal()
   }
 

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/main.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)
+#import(scala.concurrent.Future)
 <%@ var summary: SummaryDb %>
-<%@ var indexPage: ReportPage %>
+<%@ var indexPage: Future[ReportPage] %>
 <%@ var reportName: String %>
 <%@ var page: ReportPage %>
 <%@ var path: List[String] %>
 <%@ var args: Map[String, Any] %>
 <%@ var rootPath: String %>
 #{
+    val iPage = Await.result(indexPage, Duration.Inf)
+
     def createMenu(page: ReportPage, path: List[String] = Nil, first: Boolean = true): String = {
         val buffer: StringBuffer = new StringBuffer()
 
@@ -15,11 +20,13 @@
             buffer.append("<ul class=\"dropdown-menu list-group\">")
         }
 
-        for (subPage <- page.subPages.sortBy(_._1)) {
+        for (subPageFuture <- page.subPages.sortBy(_._1)) {
 
+            val subPageName = subPageFuture._1
+            val subPage = Await.result(subPageFuture._2, Duration.Inf)
             val href: String = {
-                if (path.isEmpty) rootPath + subPage._1 + "/index.html"
-                else rootPath + path.mkString("","/","/") + subPage._1 + "/index.html"
+                if (path.isEmpty) rootPath + subPageName + "/index.html"