Added files to report

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.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)
+<%@ var summary: SummaryDb %>
+<%@ var sampleId: Option[Int] = None %>
+<%@ var libId: Option[Int] = None %>
+<%@ var runId: Int %>
+<%@ var pipelineNames: List[Option[String]] %>
+<table class="table">
+<thead><tr>
+    <th>Pipeline</th>
+</tr></thead>
+<tbody>
+    #for (pipelineName <- pipelineNames)
+        <tr><td><a href="./${pipelineName}/index.html" >${pipelineName}</a></td></tr>
+    #end
+</tbody>
+</table>

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.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)
+<%@ var summary: SummaryDb %>
+<%@ var sampleId: Option[Int] = None %>
+<%@ var libId: Option[Int] = None %>
+<%@ var runId: Int %>
+<%@ var files: Seq[File]%>
+<table class="table">
+<thead><tr>
+    <th data-sorted="true" data-sorted-direction="ascending">Key</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>
+#end
+</tbody>
+</table>

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

@@ -177,6 +177,11 @@ class SummaryDb(val db: Database) extends Closeable {
     getPipelines(runId = Some(runId), name = Some(pipelineName)).map(_.headOption.map(_.id))
   }
 
+  /** Return name of a pipeline */
+  def getPipelineName(pipelineId: Int): Future[Option[String]] = {
+    getPipelines(pipelineId = Some(pipelineId)).map(_.headOption.map(_.name))
+  }
+
   /** Creates a new module, even if it already exist. This may give a database exeption */
   def forceCreateModule(name: String, runId: Int, pipelineId: Int): Future[Int] = {
     val id = Await.result(db.run(modules.size.result), Duration.Inf)
@@ -211,6 +216,11 @@ class SummaryDb(val db: Database) extends Closeable {
     getModules(runId = Some(runId), name = Some(moduleName), pipelineId = Some(pipelineId)).map(_.headOption.map(_.id))
   }
 
+  /** Returns name of a module */
+  def getModuleName(pipelineId: Int, moduleId: Int): Future[Option[String]] = {
+    getModules(pipelineId = Some(pipelineId), moduleId = Some(moduleId)).map(_.headOption.map(_.name))
+  }
+
   /** Create a new stat in the database, This method is need checking before */
   def createStat(runId: Int, pipelineId: Int, moduleId: Option[Int] = None,
                  sampleId: Option[Int] = None, libId: Option[Int] = None, content: String): Future[Int] = {

biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/summary/db/SummaryDbTest.scala

@@ -101,7 +101,9 @@ class SummaryDbTest extends TestNGSuite with Matchers {
 
     val runId = Await.result(db.createRun("name", "dir", "version", "hash", date), Duration.Inf)
     Await.result(db.getPipelines(), Duration.Inf) shouldBe empty
+    Await.result(db.getPipelineName(0), Duration.Inf) shouldBe None
     val pipelineId = Await.result(db.createPipeline("test", runId), Duration.Inf)
+    Await.result(db.getPipelineName(pipelineId), Duration.Inf) shouldBe Some("test")
     Await.result(db.getPipelines(), Duration.Inf) shouldBe Seq(Schema.Pipeline(pipelineId, "test", runId))
     Await.result(db.getPipelineId(runId, "test"), Duration.Inf) shouldBe Some(pipelineId)
     Await.result(db.createPipeline("test", runId), Duration.Inf) shouldBe pipelineId
@@ -122,8 +124,10 @@ class SummaryDbTest extends TestNGSuite with Matchers {
     val runId = Await.result(db.createRun("name", "dir", "version", "hash", date), Duration.Inf)
     val pipelineId = Await.result(db.createPipeline("test", runId), Duration.Inf)
     Await.result(db.getModules(), Duration.Inf) shouldBe empty
+    Await.result(db.getModuleName(pipelineId, 0), Duration.Inf) shouldBe None
     val moduleId = Await.result(db.createModule("test", runId, pipelineId), Duration.Inf)
     Await.result(db.getmoduleId(runId, "test", pipelineId), Duration.Inf) shouldBe Some(moduleId)
+    Await.result(db.getModuleName(pipelineId, moduleId), Duration.Inf) shouldBe Some("test")
     Await.result(db.getModules(), Duration.Inf) shouldBe Seq(Schema.Module(pipelineId, "test", runId, pipelineId))
     Await.result(db.createModule("test", runId, pipelineId), Duration.Inf) shouldBe pipelineId
     Await.result(db.getModules(), Duration.Inf) shouldBe Seq(Schema.Module(pipelineId, "test", runId, pipelineId))

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

@@ -14,14 +14,14 @@
  */
 package nl.lumc.sasc.biopet.pipelines.mapping
 
-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.bammetrics.BammetricsReport
 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._
 
-import scala.concurrent.{Await, Future}
+import scala.concurrent.{ Await, Future }
 import scala.concurrent.duration.Duration
 import scala.concurrent.ExecutionContext.Implicits.global
 
@@ -119,15 +119,22 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
     val dbFiles = summary.getFiles(runId, sample = Some(sampleId.map(SampleId).getOrElse(NoSample)),
       library = Some(libraryId.map(LibraryId).getOrElse(NoLibrary)))
       .map(_.groupBy(_.pipelineId))
-      .map(_.map { case (pipelineId, files) =>
-        val moduleSections = files.groupBy(_.moduleId).map { case (moduleId, files) =>
-          summary.getModules(moduleId = moduleId, pipelineId = pipelineId)
-            .map(_.headOption.map(_.name).getOrElse("Pipeline") -> ReportSection("/nl/lumc/sasc/biopet/core/report/files.ssp"))
-        }
-        summary.getPipelines(pipelineId = pipelineId).map(_.head.name -> ReportPage(Nil, Await.result(Future.sequence(moduleSections), Duration.Inf).toList, Map()))
+    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()))
       })
 
-    dbFiles.flatMap(Future.sequence(_)).map(x => ReportPage(x.toList, Nil, 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()))
   }
 
   /** Single sample page */
@@ -184,7 +191,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
         else Nil) ::: (if (krakenExecuted) List("Dustbin analysis" -> ReportPage(List(), List(
           "Krona Plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
           )), Map()))
-        else Nil),
+        else Nil) ::: List("Files" -> Await.result(filesPage(sampleId = sampleId, libraryId = libId), Duration.Inf)),
       "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp") ::
         (if (flexiprepExecuted) List("QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
           "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp"))