Added more testing and fixed a bug in join queries

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

@@ -206,7 +206,7 @@ class SummaryDb(val db: Database) extends Closeable {
 
   /** Return a Query for [[Stats]] */
   def statsFilter(runId: Option[Int] = None, pipeline: Option[Either[Int, String]] = None, module: Option[Option[Either[Int, String]]] = None,
-                  sample: Option[Option[Either[Int, String]]] = None, lib: Option[Option[Either[Int, String]]] = None,
+                  sample: Option[Option[Either[Int, String]]] = None, library: Option[Option[Either[Int, String]]] = None,
                   mustHaveSample: Boolean = false, mustHaveLibrary: Boolean = false) = {
     var f: Query[Stats, Stats#TableElementType, Seq] = stats
     runId.foreach(r => f = f.filter(_.runId === r))
@@ -227,7 +227,7 @@ class SummaryDb(val db: Database) extends Closeable {
       case Some(None)              => f.filter(_.sampleId.isEmpty)
       case _                       => f
     }
-    f = module match {
+    f = library match {
       case Some(Some(Left(id)))    => f.filter(_.libraryId === id)
       case Some(Some(Right(name))) => f.join(libraries).on(_.libraryId === _.id).filter(_._2.name === name).map(_._1)
       case Some(None)              => f.filter(_.libraryId.isEmpty)
@@ -317,7 +317,7 @@ class SummaryDb(val db: Database) extends Closeable {
       case Some(None)              => f.filter(_.sampleId.isEmpty)
       case _                       => f
     }
-    f = module match {
+    f = library match {
       case Some(Some(Left(id)))    => f.filter(_.libraryId === id)
       case Some(Some(Right(name))) => f.join(libraries).on(_.libraryId === _.id).filter(_._2.name === name).map(_._1)
       case Some(None)              => f.filter(_.libraryId.isEmpty)

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

 package nl.lumc.sasc.biopet.utils.summary.db
 
 import java.io.File
+import java.sql.Date
 
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
@@ -36,10 +37,21 @@ class SummaryDbTest extends TestNGSuite with Matchers {
     val db = SummaryDb.openSqliteSummary(dbFile)
     db.createTables()
 
-    Await.result(db.createOrUpdateStat(0, 0, None, None, None, """{"content": "test" }"""), Duration.Inf)
-    Await.result(db.getStat(0, Left(0), None, None, None), Duration.Inf) shouldBe Some(Map("content" -> "test"))
-    Await.result(db.createOrUpdateStat(0, 0, None, None, None, """{"content": "test2" }"""), Duration.Inf)
-    Await.result(db.getStat(0, Left(0), None, None, None), Duration.Inf) shouldBe Some(Map("content" -> "test2"))
+    val runId = Await.result(db.createRun("test", "", "", "", new Date(System.currentTimeMillis())), Duration.Inf)
+    val pipelineId = Await.result(db.createPipeline("test_pipeline", runId), Duration.Inf)
+    val moduleId = Await.result(db.createModule("test_module", runId, pipelineId), Duration.Inf)
+    val sampleId = Await.result(db.createSample("test_sample", runId), Duration.Inf)
+    val libraryId = Await.result(db.createLibrary("test_library", runId, sampleId), Duration.Inf)
+
+    Await.result(db.createOrUpdateStat(runId, pipelineId, None, None, None, """{"content": "test" }"""), Duration.Inf)
+    Await.result(db.getStat(runId, Left(pipelineId), None, None, None), Duration.Inf) shouldBe Some(Map("content" -> "test"))
+    Await.result(db.createOrUpdateStat(runId, pipelineId, None, None, None, """{"content": "test2" }"""), Duration.Inf)
+    Await.result(db.getStat(runId, Left(pipelineId), None, None, None), Duration.Inf) shouldBe Some(Map("content" -> "test2"))
+
+    // Test join queries
+    Await.result(db.createOrUpdateStat(runId, pipelineId, Some(moduleId), Some(sampleId), Some(libraryId), """{"content": "test3" }"""), Duration.Inf)
+    Await.result(db.getStat(runId, Right("test_pipeline"), Some(Right("test_module")), Some(Right("test_sample")), Some(Right("test_library"))), Duration.Inf) shouldBe Some(Map("content" -> "test3"))
+
     db.close()
   }