Fixed filter bug

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

@@ -118,7 +118,9 @@ object Schema {
   }
   val files = TableQuery[Files]
 
-  case class Executable(runId: Int, toolName: String, version: Option[String], path: Option[String], javaVersion: Option[String], exeMd5: Option[String], javaMd5: Option[String], jarPath: Option[String])
+  case class Executable(runId: Int, toolName: String, version: Option[String] = None,
+                        path: Option[String] = None, javaVersion: Option[String] = None,
+                        exeMd5: Option[String] = None, javaMd5: Option[String] = None, jarPath: Option[String] = None)
   class Executables(tag: Tag) extends Table[Executable](tag, "Executables") {
     def runId = column[Int]("runId")
     def toolName = column[String]("toolName")

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

@@ -164,7 +164,8 @@ class SummaryDb(db: Database) extends Closeable {
 
   private def statsFilter(runId: Option[Int] = None, pipelineId: Option[Int] = None, moduleId: Option[Option[Int]] = None,
                           sampleId: Option[Option[Int]] = None, libId: Option[Option[Int]] = None) = {
-    var f = stats.filter(_.runId === runId)
+    var f: Query[Stats, Stats#TableElementType, Seq] = stats
+    runId.foreach(r => f = f.filter(_.runId === r))
     pipelineId.foreach(r => f = f.filter(_.pipelineId === r))
     moduleId.foreach(r => f = (if (r.isDefined) f.filter(_.moduleId === r.get) else f.filter(_.moduleId.isEmpty)))
     sampleId.foreach(r => f = (if (r.isDefined) f.filter(_.sampleId === r.get) else f.filter(_.sampleId.isEmpty)))
@@ -198,7 +199,9 @@ class SummaryDb(db: Database) extends Closeable {
 
   def settingsFilter(runId: Option[Int] = None, pipelineId: Option[Int] = None, moduleId: Option[Option[Int]] = None,
                      sampleId: Option[Option[Int]] = None, libId: Option[Option[Int]] = None) = {
-    var f = settings.filter(_.runId === runId).filter(_.pipelineId === pipelineId)
+    var f: Query[Settings, Settings#TableElementType, Seq] = settings
+    runId.foreach(r => f = f.filter(_.runId === r))
+    pipelineId.foreach(r => f = f.filter(_.pipelineId === r))
     moduleId.foreach(r => f = (if (r.isDefined) f.filter(_.moduleId === r.get) else f.filter(_.moduleId.isEmpty)))
     sampleId.foreach(r => f = (if (r.isDefined) f.filter(_.sampleId === r.get) else f.filter(_.sampleId.isEmpty)))
     libId.foreach(r => f = (if (r.isDefined) f.filter(_.libraryId === r.get) else f.filter(_.libraryId.isEmpty)))
@@ -235,7 +238,10 @@ class SummaryDb(db: Database) extends Closeable {
   def filesFilter(runId: Option[Int] = None, pipelineId: Option[Int] = None, moduleId: Option[Option[Int]],
                   sampleId: Option[Option[Int]] = None, libId: Option[Option[Int]] = None,
                   key: Option[String] = None) = {
-    var f = files.filter(_.runId === runId).filter(_.pipelineId === pipelineId).filter(_.key === key)
+    var f: Query[Files, Files#TableElementType, Seq] = files
+    runId.foreach(r => f = f.filter(_.runId === r))
+    pipelineId.foreach(r => f = f.filter(_.pipelineId === r))
+    key.foreach(r => f = f.filter(_.key === r))
     moduleId.foreach(r => f = (if (r.isDefined) f.filter(_.moduleId === r.get) else f.filter(_.moduleId.isEmpty)))
     sampleId.foreach(r => f = (if (r.isDefined) f.filter(_.sampleId === r.get) else f.filter(_.sampleId.isEmpty)))
     libId.foreach(r => f = (if (r.isDefined) f.filter(_.libraryId === r.get) else f.filter(_.libraryId.isEmpty)))
@@ -264,10 +270,13 @@ class SummaryDb(db: Database) extends Closeable {
   }
 
   def executablesFilter(runId: Option[Int], toolName: Option[String]) = {
-    executables.filter(_.runId === runId).filter(_.toolName === toolName)
+    var q: Query[Executables, Executables#TableElementType, Seq] = executables
+    runId.foreach(r => q = q.filter(_.runId === r))
+    toolName.foreach(r => q = q.filter(_.toolName === r))
+    q
   }
 
-  def getExecutables(runId: Option[Int], toolName: Option[String]) = {
+  def getExecutables(runId: Option[Int] = None, toolName: Option[String] = None) = {
     db.run(executablesFilter(runId, toolName).result)
   }
 

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

@@ -26,7 +26,7 @@ class SummaryDbTest extends TestNGSuite with Matchers {
     Await.result(db.getSetting(0,0, None, None, None), Duration.Inf) shouldBe Some(Map("content" -> "test"))
     Await.result(db.createOrUpdateSetting(0, 0, None, None, None, """{"content": "test2" }"""), Duration.Inf)
     Await.result(db.getSetting(0,0, None, None, None), Duration.Inf) shouldBe Some(Map("content" -> "test2"))
-
+    db.close()
   }
 
   @Test
@@ -40,6 +40,21 @@ class SummaryDbTest extends TestNGSuite with Matchers {
     Await.result(db.getStat(0, 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, 0, None, None, None), Duration.Inf) shouldBe Some(Map("content" -> "test2"))
+    db.close()
+  }
+
+  @Test
+  def testExecutable: Unit = {
+    val dbFile = File.createTempFile("summary.", ".db")
+    dbFile.deleteOnExit()
+    val db = SummaryDb.openSqliteSummary(dbFile)
+    db.createTables()
+
+    Await.result(db.createOrUpdateExecutable(0, "name"), Duration.Inf)
+    val bla1 = Await.result(db.getExecutables(Some(0)), Duration.Inf)
+    Await.result(db.createOrUpdateExecutable(0, "name", Some("test")), Duration.Inf)
+    Await.result(db.getExecutables(Some(0)), Duration.Inf).head shouldBe Schema.Executable(0, "name", Some("test"))
+    db.close()
   }
 
 }