Added basic unit tests

kopisu/pom.xml

@@ -43,5 +43,17 @@
             <artifactId>BiopetExtensions</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_2.10</artifactId>
+            <version>2.2.1</version>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
 </project>

kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/Kopisu.scala

@@ -16,9 +16,9 @@
 package nl.lumc.sasc.biopet.pipelines.kopisu
 
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference }
+import nl.lumc.sasc.biopet.core.{PipelineCommand, Reference}
 import nl.lumc.sasc.biopet.pipelines.kopisu.methods.FreecMethod
-import nl.lumc.sasc.biopet.utils.BamUtils
+import nl.lumc.sasc.biopet.utils.{BamUtils, Logging}
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
 
@@ -35,6 +35,7 @@ class Kopisu(val root: Configurable) extends QScript with SummaryQScript with Re
 
   def init(): Unit = {
     if (inputBamsArg.nonEmpty) inputBams = BamUtils.sampleBamMap(inputBamsArg)
+    if (inputBams.isEmpty) Logging.addError("No input bams found")
   }
 
   lazy val freecMethod = if (config("use_freec_method", default = true)) {
@@ -43,6 +44,8 @@ class Kopisu(val root: Configurable) extends QScript with SummaryQScript with Re
 
   // This script is in fact FreeC only.
   def biopetScript() {
+    if (freecMethod.isEmpty) Logging.addError("No method selected")
+
     freecMethod.foreach { method =>
       method.inputBams = inputBams
       method.outputDir = new File(outputDir, "freec_method")

kopisu/src/test/resources/ref.dict

+@HD	VN:1.4	SO:unsorted
+@SQ	SN:chr1	LN:9	UR:file:/home/pjvan_thof/pipelines/biopet/public/mapping/src/test/resources/ref.fa	M5:fe15dbbd0900310caf32827f6da57550

kopisu/src/test/resources/ref.fa

+>chr1
+AGTAGTAGT

kopisu/src/test/resources/ref.fa.fai

+chr1	9	6	9	10

kopisu/src/test/scala/nl/lumc/sasc/biopet/pipelines/kopisu/KopisuTest.scala

+/**
+  * Biopet is built on top of GATK Queue for building bioinformatic
+  * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+  * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+  * should also be able to execute Biopet tools and pipelines.
+  *
+  * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+  *
+  * Contact us at: sasc@lumc.nl
+  *
+  * A dual licensing mode is applied. The source code within this project that are
+  * not part of GATK Queue is freely available for non-commercial use under an AGPL
+  * license; For commercial users or users who do not want to follow the AGPL
+  * license, please contact us to obtain a separate license.
+  */
+package nl.lumc.sasc.biopet.pipelines.kopisu
+
+import java.io.{File, FileOutputStream}
+
+import com.google.common.io.Files
+import nl.lumc.sasc.biopet.extensions.freec.{FreeC, FreeCAssessSignificancePlot, FreeCCNVPlot}
+import nl.lumc.sasc.biopet.utils.ConfigUtils
+import nl.lumc.sasc.biopet.utils.config.Config
+import org.broadinstitute.gatk.queue.QSettings
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.{DataProvider, Test}
+
+import scala.collection.mutable.ListBuffer
+
+/**
+  * Test class for [[Kopisu]]
+  *
+  * Created by pjvan_thof on 3/2/15.
+  */
+class KopisuTest extends TestNGSuite with Matchers {
+  def initPipeline(map: Map[String, Any]): Kopisu = {
+    new Kopisu() {
+      override def configNamespace = "kopisu"
+      override def globalConfig = new Config(ConfigUtils.mergeMaps(map, KopisuTest.config))
+      qSettings = new QSettings
+      qSettings.runName = "test"
+    }
+  }
+
+  @DataProvider(name = "shivaSvCallingOptions")
+  def shivaSvCallingOptions = {
+    val bool = Array(true, false)
+    (for (
+      bams <- 0 to 3;
+      freec <- bool
+    ) yield Array(bams, freec)).toArray
+  }
+
+  @Test(dataProvider = "shivaSvCallingOptions")
+  def testShivaSvCalling(bams: Int,
+                         freec: Boolean) = {
+    val callers: ListBuffer[String] = ListBuffer()
+    val map = Map("sv_callers" -> callers.toList)
+    val pipeline = initPipeline(map ++ Map("use_freec_method" -> freec))
+
+    pipeline.inputBams = (for (n <- 1 to bams) yield n.toString -> KopisuTest.inputTouch("bam_" + n + ".bam")).toMap
+
+    val illegalArgumentException = pipeline.inputBams.isEmpty || (!freec)
+
+    if (illegalArgumentException) intercept[IllegalStateException] {
+      pipeline.init()
+      pipeline.script()
+    }
+
+    if (!illegalArgumentException) {
+      pipeline.init()
+      pipeline.script()
+
+      pipeline.freecMethod.isDefined shouldBe freec
+
+      pipeline.functions.count(_.isInstanceOf[FreeC]) shouldBe (if (freec) bams else 0)
+      pipeline.functions.count(_.isInstanceOf[FreeCAssessSignificancePlot]) shouldBe (if (freec) bams else 0)
+      pipeline.functions.count(_.isInstanceOf[FreeCCNVPlot]) shouldBe (if (freec) bams else 0)
+    }
+  }
+}
+
+object KopisuTest {
+  val outputDir = Files.createTempDir()
+  outputDir.deleteOnExit()
+  new File(outputDir, "input").mkdirs()
+  private def inputTouch(name: String): File = {
+    val file = new File(outputDir, "input" + File.separator + name).getAbsoluteFile
+    Files.touch(file)
+    file
+  }
+
+  private def copyFile(name: String): Unit = {
+    val is = getClass.getResourceAsStream("/" + name)
+    val os = new FileOutputStream(new File(outputDir, name))
+    org.apache.commons.io.IOUtils.copy(is, os)
+    os.close()
+  }
+
+  copyFile("ref.fa")
+  copyFile("ref.dict")
+  copyFile("ref.fa.fai")
+
+  val config = Map(
+    "name_prefix" -> "test",
+    "output_dir" -> outputDir,
+    "reference_fasta" -> (outputDir + File.separator + "ref.fa"),
+    "gatk_jar" -> "test",
+    "samtools" -> Map("exe" -> "test"),
+    "md5sum" -> Map("exe" -> "test"),
+    "bgzip" -> Map("exe" -> "test"),
+    "tabix" -> Map("exe" -> "test"),
+    "freec" -> Map("exe" -> "test", "chrFiles" -> "test", "chrLenFile" ->"test")
+  )
+}
\ No newline at end of file