Added unit tests

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/ReferenceTest.scala

@@ -22,13 +22,12 @@ import nl.lumc.sasc.biopet.utils.config.{ Config, Configurable }
 import org.scalatest.Matchers
 import org.scalatest.mock.MockitoSugar
 import org.scalatest.testng.TestNGSuite
-import org.mockito.Mockito._
 import org.testng.annotations.Test
 
 /**
  * Created by pjvan_thof on 12/30/15.
  */
-class ReferenceTest extends TestNGSuite with Matchers with MockitoSugar {
+class ReferenceTest extends TestNGSuite with Matchers {
 
   import ReferenceTest._
 

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/annotation/AnnotationTest.scala

+package nl.lumc.sasc.biopet.core.annotation
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.BiopetQScript
+import nl.lumc.sasc.biopet.core.annotations.{ AnnotationGff, AnnotationGtf, AnnotationRefFlat }
+import nl.lumc.sasc.biopet.utils.Logging
+import nl.lumc.sasc.biopet.utils.config.Config
+import org.broadinstitute.gatk.queue.QScript
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+/**
+ * Created by pjvanthof on 18/11/2016.
+ */
+class AnnotationTest extends TestNGSuite with Matchers {
+  @Test
+  def testAnnotationGtf: Unit = {
+    val s1 = new AnnotationTest.Script(AnnotationTest.config) with AnnotationGtf
+    s1.annotationGtf shouldBe new File("")
+    an[IllegalStateException] shouldBe thrownBy(Logging.checkErrors())
+
+    val s2 = new AnnotationTest.Script(AnnotationTest.config ++ Map("species" -> "s1", "reference_name" -> "g1")) with AnnotationGtf
+    s2.annotationGtf shouldBe new File("no_set.gtf")
+    noException should be thrownBy (Logging.checkErrors())
+
+    val s3 = new AnnotationTest.Script(AnnotationTest.config ++ Map("species" -> "s1", "reference_name" -> "g1", "gene_annotation_name" -> "set1")) with AnnotationGtf
+    s3.annotationGtf shouldBe new File("set1.gtf")
+    noException should be thrownBy (Logging.checkErrors())
+  }
+
+  @Test
+  def testAnnotationGff: Unit = {
+    val s1 = new AnnotationTest.Script(AnnotationTest.config) with AnnotationGff
+    s1.annotationGff shouldBe new File("")
+    an[IllegalStateException] shouldBe thrownBy(Logging.checkErrors())
+
+    val s2 = new AnnotationTest.Script(AnnotationTest.config ++ Map("species" -> "s1", "reference_name" -> "g1")) with AnnotationGff
+    s2.annotationGff shouldBe new File("no_set.gff")
+    noException should be thrownBy (Logging.checkErrors())
+
+    val s3 = new AnnotationTest.Script(AnnotationTest.config ++ Map("species" -> "s1", "reference_name" -> "g1", "gene_annotation_name" -> "set1")) with AnnotationGff
+    s3.annotationGff shouldBe new File("set1.gff")
+    noException should be thrownBy (Logging.checkErrors())
+  }
+
+  @Test
+  def testAnnotationRefFlat: Unit = {
+    val s1 = new AnnotationTest.Script(AnnotationTest.config) with AnnotationRefFlat
+    s1.annotationRefFlat.get shouldBe new File("")
+    an[IllegalStateException] shouldBe thrownBy(Logging.checkErrors())
+
+    val s2 = new AnnotationTest.Script(AnnotationTest.config ++ Map("species" -> "s1", "reference_name" -> "g1")) with AnnotationRefFlat
+    s2.annotationRefFlat.get shouldBe new File("no_set.refFlat")
+    noException should be thrownBy (Logging.checkErrors())
+
+    val s3 = new AnnotationTest.Script(AnnotationTest.config ++ Map("species" -> "s1", "reference_name" -> "g1", "gene_annotation_name" -> "set1")) with AnnotationRefFlat
+    s3.annotationRefFlat.get shouldBe new File("set1.refFlat")
+    noException should be thrownBy (Logging.checkErrors())
+  }
+}
+
+object AnnotationTest {
+  class Script(c: Map[String, Any]) extends QScript with BiopetQScript {
+    override def globalConfig: Config = new Config(c)
+    val root = null
+
+    /** Init for pipeline */
+    def init(): Unit = ???
+
+    /** Pipeline itself */
+    def biopetScript(): Unit = ???
+  }
+
+  val config: Map[String, Any] = Map("references" -> Map("s1" -> Map("g1" -> Map(
+    "annotation_gtf" -> "no_set.gtf",
+    "annotation_gff" -> "no_set.gff",
+    "annotation_refflat" -> "no_set.refFlat",
+    "gene_annotations" -> Map("set1" -> Map(
+      "annotation_gtf" -> "set1.gtf",
+      "annotation_gff" -> "set1.gff",
+      "annotation_refflat" -> "set1.refFlat"
+    ))
+  ))))
+}
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