Adding basic unit tests

public/shiva/.gitignore

+target

public/shiva/pom.xml

@@ -23,6 +23,18 @@
             <artifactId>Mapping</artifactId>
             <version>${project.version}</version>
         </dependency>
+        <dependency>
+            <groupId>org.testng</groupId>
+            <artifactId>testng</artifactId>
+            <version>6.8</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.scalatest</groupId>
+            <artifactId>scalatest_2.11</artifactId>
+            <version>2.2.1</version>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
 
 </project>
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public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala

@@ -40,6 +40,9 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
   def biopetScript: Unit = {
     val callers = usedCallers.sortBy(_.prio)
 
+    require(!inputBams.isEmpty, "No input bams found")
+    require(callers.exists(_.use), "must select atleast 1 variantcaller")
+
     val cv = new CombineVariants(qscript)
     cv.outputFile = finalFile
     cv.setKey = "VariantCaller"

public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala

+package nl.lumc.sasc.biopet.pipelines.shiva
+
+import java.io.File
+
+import com.google.common.io.Files
+import nl.lumc.sasc.biopet.core.config.Config
+import nl.lumc.sasc.biopet.extensions.bcftools.Bcftools
+import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
+import nl.lumc.sasc.biopet.tools.{VcfFilter, MpileupToVcf}
+import nl.lumc.sasc.biopet.utils.ConfigUtils
+import org.apache.commons.io.FileUtils
+import org.broadinstitute.gatk.queue.QSettings
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.{ AfterClass, Test, DataProvider }
+
+/**
+ * Created by pjvan_thof on 3/2/15.
+ */
+class ShivaVariantcallingTest extends TestNGSuite with Matchers {
+  def initPipeline(map: Map[String, Any]): ShivaVariantcalling = {
+    new ShivaVariantcalling {
+      override def configName = "shivavariantcalling"
+      override def globalConfig = new Config(ConfigUtils.mergeMaps(map, ShivaVariantcallingTest.config))
+      qSettings = new QSettings
+      qSettings.runName = "test"
+    }
+  }
+
+  @DataProvider(name = "shivaVariantcallingOptions")
+  def mappingOptions = {
+    val raw = Array(true, false)
+    val bcftools = Array(true, false)
+
+    (for (
+      bams <- 0 to 3;
+      raw <- raw;
+      bcftools <- bcftools
+    ) yield Array[Any](bams, raw, bcftools)
+    ).toArray
+  }
+
+  @Test(dataProvider = "shivaVariantcallingOptions")
+  def testShivaVariantcalling(bams: Int, raw: Boolean, bcftools: Boolean) = {
+    val map = Map("use_raw" -> raw, "use_bcftools" -> bcftools)
+    val pipeline = initPipeline(map)
+
+    pipeline.inputBams = (for (n <- 1 to bams) yield new File("bam_" + n + ".bam")).toList
+
+    val illegalArgumentException = pipeline.inputBams.isEmpty || !raw && !bcftools
+
+    if (illegalArgumentException) intercept[IllegalArgumentException] {
+      pipeline.script()
+    }
+
+    if (!illegalArgumentException) {
+      pipeline.script()
+
+      pipeline.functions.count(_.isInstanceOf[CombineVariants]) shouldBe 1 + (if (raw) 1 else 0)
+      //pipeline.functions.count(_.isInstanceOf[Bcftools]) shouldBe (if (bcftools) 1 else 0)
+      //FIXME: Can not check for bcftools because of piping
+      pipeline.functions.count(_.isInstanceOf[MpileupToVcf]) shouldBe (if (raw) bams else 0)
+      pipeline.functions.count(_.isInstanceOf[VcfFilter]) shouldBe (if (raw) bams else 0)
+    }
+  }
+
+  @AfterClass def removeTempOutputDir() = {
+    FileUtils.deleteDirectory(ShivaVariantcallingTest.outputDir)
+  }
+
+}
+
+object ShivaVariantcallingTest {
+  val outputDir = Files.createTempDir()
+
+  val config = Map(
+    "name_prefix" -> "test",
+    "output_dir" -> outputDir,
+    "reference" -> "test",
+    "gatk_jar" -> "test",
+    "samtools" -> Map("exe" -> "test"),
+    "bcftools" -> Map("exe" -> "test")
+  )
+}
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