Fixing unit tests

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala

@@ -297,7 +297,10 @@ trait ReportBuilder extends ToolCommand {
         summary.getPipelineName(pipelineId = pipelineId).map(_.get -> Future(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)))
+    val pipelineFiles = summary.getPipelineId(runId, pipelineName)
+      .flatMap(pipelinelineId => dbFiles
+        .map(x => x.get(pipelinelineId.get).getOrElse(Seq())
+          .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))) ::

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilderTest.scala

@@ -16,6 +16,7 @@ package nl.lumc.sasc.biopet.core.report
 
 import java.io.File
 import java.nio.file.Paths
+import java.sql.Date
 
 import com.google.common.io.Files
 import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
@@ -23,7 +24,7 @@ import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
 import org.testng.annotations.Test
 
-import scala.concurrent.{ Await, Future }
+import scala.concurrent.{Await, Future}
 import scala.concurrent.duration.Duration
 
 /**
@@ -54,6 +55,9 @@ class MultisampleReportBuilderTest extends TestNGSuite with Matchers {
     val db = SummaryDb.openSqliteSummary(dbFile)
     db.createTables()
 
+    Await.ready(db.createPipeline("test", 0), Duration.Inf)
+    Await.ready(db.createRun("test", "", "", "", new Date(System.currentTimeMillis())), Duration.Inf)
+
     val sample = Some("sampleName")
     val lib = Some("libName")
 

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/ReportBuilderTest.scala

@@ -16,14 +16,15 @@ package nl.lumc.sasc.biopet.core.report
 
 import java.io.File
 import java.nio.file.Paths
+import java.sql.Date
 
 import com.google.common.io.Files
 import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{ DataProvider, Test }
+import org.testng.annotations.{DataProvider, Test}
 
-import scala.concurrent.{ Await, Future }
+import scala.concurrent.{Await, Future}
 import scala.concurrent.duration.Duration
 
 /**
@@ -64,6 +65,8 @@ class ReportBuilderTest extends TestNGSuite with Matchers {
         Await.result(db.createLibrary(libName, 0, sampleId), Duration.Inf)
       }
     }
+    Await.ready(db.createPipeline("test", 0), Duration.Inf)
+    Await.ready(db.createRun("test", "", "", "", new Date(System.currentTimeMillis())), Duration.Inf)
 
     val tempDir = Files.createTempDir()
     tempDir.deleteOnExit()