Fixed Kopisu unit tests

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/PythonCommandLineFunction.scala

@@ -14,9 +14,10 @@
  */
 package nl.lumc.sasc.biopet.core.extensions
 
-import java.io.{ File, FileOutputStream }
+import java.io.{File, FileOutputStream}
 
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.utils.Logging
 import org.broadinstitute.gatk.utils.commandline.Input
 
 trait PythonCommandLineFunction extends BiopetCommandLineFunction {
@@ -50,9 +51,11 @@ trait PythonCommandLineFunction extends BiopetCommandLineFunction {
     pythonScript = new File(".queue/tmp/" + subpackage + pythonScriptName)
     if (!pythonScript.getParentFile.exists) pythonScript.getParentFile.mkdirs
     val is = getClass.getResourceAsStream(subpackage + pythonScriptName)
-    val os = new FileOutputStream(pythonScript)
-    org.apache.commons.io.IOUtils.copy(is, os)
-    os.close()
+    if (is != null) {
+      val os = new FileOutputStream(pythonScript)
+      org.apache.commons.io.IOUtils.copy(is, os)
+      os.close()
+    } else Logging.addError(s"Python script not found: $pythonScriptName")
   }
 
   /** return basic command to prefix the complete command with */

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

@@ -34,10 +34,11 @@ import scala.collection.mutable.ListBuffer
  * Created by pjvan_thof on 3/2/15.
  */
 class KopisuTest extends TestNGSuite with Matchers {
-  def initPipeline(map: Map[String, Any], outputDir: File): Kopisu = {
+  def initPipeline(map: Map[String, Any], dir: File): Kopisu = {
     new Kopisu() {
       override def configNamespace = "kopisu"
-      override def globalConfig = new Config(ConfigUtils.mergeMaps(map, KopisuTest.config(outputDir)))
+      override def globalConfig = new Config(ConfigUtils.mergeMaps(map, KopisuTest.config(dir)))
+      outputDir = dir
       qSettings = new QSettings
       qSettings.runName = "test"
     }
@@ -121,6 +122,9 @@ object KopisuTest {
   val controlDir = Files.createTempDir()
   Files.touch(new File(controlDir, "test.txt"))
 
+  val coniferScript = File.createTempFile("conifer.", ".py")
+  coniferScript.deleteOnExit()
+
   def config(outputDir: File) = Map(
     "skip_write_dependencies" -> true,
     "name_prefix" -> "test",
@@ -133,7 +137,7 @@ object KopisuTest {
     "tabix" -> Map("exe" -> "test"),
     "freec" -> Map("exe" -> "test", "chrFiles" -> "test", "chrLenFile" -> "test"),
     "controls_dir" -> controlDir.getAbsolutePath,
-    "conifer" -> Map("script" -> "/usr/bin/test"),
+    "conifer" -> Map("script" -> coniferScript.getAbsolutePath),
     "probe_file" -> "test",
     "rscript" -> Map("exe" -> "test")
   )