Merge branch 'fix-BIOPET-383' into 'develop'

Fix biopet 383



See merge request !473

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala

@@ -52,7 +52,7 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
 
       /** Adds the library jobs */
       final def addAndTrackJobs(): Unit = {
-        if (nameRegex.findFirstIn(libId) == None)
+        if (nameRegex.findFirstIn(libId).isEmpty)
           Logging.addError(s"Library '$libId' $nameError")
         currentSample = Some(sampleId)
         currentLib = Some(libId)
@@ -139,9 +139,13 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
      */
     def makeLibrary(id: String): Library
 
-    /** returns a set with library names */
+    /** returns a set with library names or throws error when not found */
     protected def libIds: Set[String] = {
-      ConfigUtils.getMapFromPath(globalConfig.map, List("samples", sampleId, "libraries")).getOrElse(Map()).keySet
+      val ids = ConfigUtils.getMapFromPath(globalConfig.map, List("samples", sampleId, "libraries")).getOrElse(Map()).keySet
+      if (ids.isEmpty) {
+        throw new IllegalStateException(s"No libraries found in config for sample $sampleId")
+      }
+      ids
     }
 
     /** Name overules the one from qscript */
@@ -151,7 +155,7 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
 
     /** Adds sample jobs */
     final def addAndTrackJobs(): Unit = {
-      if (nameRegex.findFirstIn(sampleId) == None)
+      if (nameRegex.findFirstIn(sampleId).isEmpty)
         Logging.addError(s"Sample '$sampleId' $nameError")
       currentSample = Some(sampleId)
       addJobs()

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

@@ -15,10 +15,9 @@
 package nl.lumc.sasc.biopet.core
 
 import java.io.File
-
 import nl.lumc.sasc.biopet.core.MultiSampleQScript.Gender
 import nl.lumc.sasc.biopet.core.extensions.Md5sum
-import nl.lumc.sasc.biopet.utils.{ Logging, ConfigUtils }
+import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
 import nl.lumc.sasc.biopet.utils.config.Config
 import org.broadinstitute.gatk.queue.QScript
 import org.scalatest.Matchers
@@ -119,6 +118,11 @@ class MultiSampleQScriptTest extends TestNGSuite with Matchers {
       "Dash (-) and underscore (_) are permitted."
 
   }
+
+  @Test
+  def testNoLibSample(): Unit = {
+    an[IllegalStateException] shouldBe thrownBy(MultiSampleQScriptTest(noLibSample :: Nil))
+  }
 }
 
 object MultiSampleQScriptTest {
@@ -153,10 +157,48 @@ object MultiSampleQScriptTest {
     "lib1" -> Map("test" -> "4-1")
   ))))
 
-  val child = Map("samples" -> Map("child" -> Map("tags" -> Map(
-    "gender" -> "male", "father" -> "father", "mother" -> "mother"))))
-  val father = Map("samples" -> Map("father" -> Map("tags" -> Map("gender" -> "male"))))
-  val mother = Map("samples" -> Map("mother" -> Map("tags" -> Map("gender" -> "female"))))
+  val child = Map(
+    "samples" -> Map(
+      "child" -> Map(
+        "tags" -> Map(
+          "gender" -> "male",
+          "father" -> "father",
+          "mother" -> "mother"
+        ),
+        "libraries" -> Map(
+          "lib1" -> Map("test" -> "child-1")
+        )
+      )
+    )
+  )
+  val father = Map(
+    "samples" -> Map(
+      "father" -> Map(
+        "tags" -> Map("gender" -> "male"),
+        "libraries" -> Map(
+          "lib1" -> Map("test" -> "father-1")
+        )
+      )
+    )
+  )
+  val mother = Map(
+    "samples" -> Map(
+      "mother" -> Map(
+        "tags" -> Map("gender" -> "female"),
+        "libraries" -> Map(
+          "lib1" -> Map("test" -> "mother-1")
+        )
+      )
+    )
+  )
+
+  val noLibSample = Map(
+    "samples" -> Map(
+      "sample1" -> Map(
+        "tags" -> Map("gender" -> "female")
+      )
+    )
+  )
 
   def apply(configs: List[Map[String, Any]], only: List[String] = Nil) = {
     new QScript with MultiSampleQScript { qscript =>

mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala

@@ -14,7 +14,7 @@
  */
 package nl.lumc.sasc.biopet.pipelines.mapping
 
-import java.io.{File, FileOutputStream}
+import java.io.{ File, FileOutputStream }
 
 import com.google.common.io.Files
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction