Fixing BIOPET-577

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

 #import(nl.lumc.sasc.biopet.utils.summary.db.Schema.File)
+#import(nl.lumc.sasc.biopet.utils.summary.db.Schema.Pipeline)
 #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._)
@@ -9,7 +10,9 @@
 <%@ var sampleId: Option[Int] = None %>
 <%@ var libId: Option[Int] = None %>
 <%@ var runId: Int %>
-<%@ var pipelineNames: List[Option[String]] %>
+<%@ var pipelineIds: List[Int] %>
+<%@ var allPipelines: Seq[Pipeline] %>
+#{ val pipelineNames = pipelineIds.map(x => allPipelines.find(_.id == x).map(_.name)) }#
 <table class="table">
 <thead><tr>
     <th>Pipeline</th>

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

 #import(nl.lumc.sasc.biopet.utils.summary.db.Schema.File)
+#import(nl.lumc.sasc.biopet.utils.summary.db.Schema.Pipeline)
+#import(nl.lumc.sasc.biopet.utils.summary.db.Schema.Module)
+#import(nl.lumc.sasc.biopet.utils.summary.db.Schema.Sample)
+#import(nl.lumc.sasc.biopet.utils.summary.db.Schema.Library)
 #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._)
@@ -10,14 +14,29 @@
 <%@ var libId: Option[Int] = None %>
 <%@ var runId: Int %>
 <%@ var files: Seq[File]%>
-<table class="table">
+<%@ var allPipelines: Seq[Pipeline]%>
+<%@ var allModules: Seq[Module]%>
+<%@ var allSamples: Seq[Sample]%>
+<%@ var allLibraries: Seq[Library]%>
+<table class="table sortable-theme-bootstrap" data-sortable>
 <thead><tr>
+    <th>Pipeline</th>
+    <th>Module</th>
+    <th>Sample</th>
+    <th>Library</th>
     <th data-sorted="true" data-sorted-direction="ascending">Key</th>
-    <th>path</th><th>md5</th>
+    <th>path</th>
+    <th>md5</th>
 </tr></thead>
 <tbody>
 #for (file <- files)
-    <tr><td>${file.key}</td><td>${file.path}</td><td>${file.md5}</td></tr>
+    <tr><td>${allPipelines.find(_.id == file.pipelineId).map(_.name)}</td>
+    <td>${file.moduleId.map(id => allModules.find(x => x.pipelineId == file.pipelineId && file.moduleId == id).map(_.name)).flatten.getOrElse(("-"))}</td>
+    <td>${file.sampleId.map(id => allSamples.find(_.id == id).map(_.name)).flatten.getOrElse(("-"))}</td>
+    <td>${file.libraryId.map(id => allLibraries.find(_.id == id).map(_.name)).flatten.getOrElse(("-"))}</td>
+    <td>${file.key}</td>
+    <td>${file.path}</td>
+    <td>${file.md5}</td></tr>
 #end
 </tbody>
 </table>

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, Sample }
+import nl.lumc.sasc.biopet.utils.summary.db.Schema.{ Library, Module, Pipeline, Sample }
 import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
 import nl.lumc.sasc.biopet.utils.{ IoUtils, Logging, ToolCommand }
 import org.broadinstitute.gatk.utils.commandline.Input
@@ -118,6 +118,10 @@ trait ReportBuilder extends ToolCommand {
 
   final def runId = setRunId
 
+  private var _setPipelines = Seq[Pipeline]()
+  final def pipelines = _setPipelines
+  private var _setModules = Seq[Module]()
+  final def modules = _setModules
   private var _setSamples = Seq[Sample]()
   final def samples = _setSamples
   private var _setLibraries = Seq[Library]()
@@ -177,6 +181,8 @@ trait ReportBuilder extends ToolCommand {
       case _ =>
     }
 
+    _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)
     _setLibraries = Await.result(summary.getLibraries(runId = Some(runId), sampleId = sampleId, libId = libId), Duration.Inf)
 
@@ -236,7 +242,11 @@ trait ReportBuilder extends ToolCommand {
       Map("page" -> page,
         "path" -> path,
         "outputDir" -> pageOutputDir,
-        "rootPath" -> rootPath
+        "rootPath" -> rootPath,
+        "allPipelines" -> pipelines,
+        "allModules" -> modules,
+        "allSamples" -> samples,
+        "allLibraries" -> libraries
       )
 
     // Generating subpages

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/db/Schema.scala

@@ -105,7 +105,7 @@ object Schema {
   }
   val settings = TableQuery[Settings]
 
-  case class File(runId: Int, pipelineId: Int, moduleId: Option[Int], sampleId: Option[Int], library: Option[Int], key: String, path: String, md5: String, link: Boolean, size: Long)
+  case class File(runId: Int, pipelineId: Int, moduleId: Option[Int], sampleId: Option[Int], libraryId: Option[Int], key: String, path: String, md5: String, link: Boolean, size: Long)
   class Files(tag: Tag) extends Table[File](tag, "Files") {
     def runId = column[Int]("runId")
     def pipelineId = column[Int]("pipelineId")

mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala

@@ -116,25 +116,28 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
 
   /** Files page, can be used general or at sample level */
   def filesPage(sampleId: Option[Int] = None, libraryId: Option[Int] = None): Future[ReportPage] = {
-    val dbFiles = summary.getFiles(runId, sample = Some(sampleId.map(SampleId).getOrElse(NoSample)),
-      library = Some(libraryId.map(LibraryId).getOrElse(NoLibrary)))
+    val dbFiles = summary.getFiles(runId, sample = sampleId.map(SampleId),
+      library = libraryId.map(LibraryId))
       .map(_.groupBy(_.pipelineId))
     val modulePages = dbFiles.map(_.map {
-        case (pipelineId, files) =>
-          val moduleSections = files.groupBy(_.moduleId).map {
-            case (moduleId, files) =>
-              val moduleName: Future[String] = moduleId match {
-                case Some(id) => summary.getModuleName(pipelineId, id).map(_.getOrElse("Pipeline"))
-                case _        => Future("Pipeline")
-              }
-              moduleName.map(_ -> ReportSection("/nl/lumc/sasc/biopet/core/report/files.ssp", Map("files" -> files)))
-          }
-          summary.getPipelineName(pipelineId = pipelineId).map(_.get -> ReportPage(Nil, Await.result(Future.sequence(moduleSections), Duration.Inf).toList, Map()))
-      })
-
-    val pipelineNames = dbFiles.flatMap(x => Future.sequence(x.map(y => summary.getPipelineName(y._1))))
-
-    modulePages.flatMap(Future.sequence(_)).map(x => ReportPage(x.toList, "Pipelines" -> ReportSection("/nl/lumc/sasc/biopet/core/report/fileModules.ssp", Map("pipelineNames" -> Await.result(pipelineNames, Duration.Inf).toList)) ::Nil, Map()))
+      case (pipelineId, files) =>
+        val moduleSections = files.groupBy(_.moduleId).map {
+          case (moduleId, files) =>
+            val moduleName: Future[String] = moduleId match {
+              case Some(id) => summary.getModuleName(pipelineId, id).map(_.getOrElse("Pipeline"))
+              case _        => Future("Pipeline")
+            }
+            moduleName.map(_ -> ReportSection("/nl/lumc/sasc/biopet/core/report/files.ssp", Map("files" -> files)))
+        }
+        val moduleSectionsSorted = moduleSections.find(_._1 == "Pipeline") ++ moduleSections.filter(_._1 != "Pipeline")
+        summary.getPipelineName(pipelineId = pipelineId).map(_.get -> ReportPage(Nil, Await.result(Future.sequence(moduleSectionsSorted), Duration.Inf).toList, Map()))
+    })
+
+    val pipelineFiles = summary.getPipelineId(runId, pipelineName).flatMap(pipelinelineId => dbFiles.map(x => x(pipelinelineId.get).filter(_.moduleId.isEmpty)))
+
+    modulePages.flatMap(Future.sequence(_)).map(x => ReportPage(x.toList,
+      s"$pipelineName files" -> ReportSection("/nl/lumc/sasc/biopet/core/report/files.ssp", Map("files" -> Await.result(pipelineFiles, Duration.Inf))) ::
+        "Sub pipelines/modules" -> ReportSection("/nl/lumc/sasc/biopet/core/report/fileModules.ssp", Map("pipelineIds" -> Await.result(dbFiles.map(_.keys.toList), Duration.Inf))) :: Nil, Map()))
   }
 
   /** Single sample page */