Merge pull request #4 from biopet/fix-BIOPET-379

Fix BIOPET-379

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

@@ -177,4 +177,52 @@ object BiopetQScript {
     require(outputDir.getAbsoluteFile.canWrite, s"No premision to write outputdir: $outputDir")
   }
 
+  def safeInputs(function: QFunction): Option[Seq[File]] = {
+    try {
+      Some(function.inputs)
+    } catch {
+      case e: NullPointerException => None
+    }
+  }
+
+  def safeOutputs(function: QFunction): Option[Seq[File]] = {
+    try {
+      Some(function.outputs)
+    } catch {
+      case e: NullPointerException => None
+    }
+  }
+
+  def safeDoneFiles(function: QFunction): Option[Seq[File]] = {
+    try {
+      Some(function.doneOutputs)
+    } catch {
+      case e: NullPointerException => None
+    }
+  }
+
+  def safeFailFiles(function: QFunction): Option[Seq[File]] = {
+    try {
+      Some(function.failOutputs)
+    } catch {
+      case e: NullPointerException => None
+    }
+  }
+
+  def safeIsDone(function: QFunction): Option[Boolean] = {
+    try {
+      Some(function.isDone)
+    } catch {
+      case e: NullPointerException => None
+    }
+  }
+
+  def safeIsFail(function: QFunction): Option[Boolean] = {
+    try {
+      Some(function.isFail)
+    } catch {
+      case e: NullPointerException => None
+    }
+  }
+
 }

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

@@ -141,11 +141,17 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
 
     /** returns a set with library names or throws error when not found */
     protected def libIds: Set[String] = {
-      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")
+      val ids: Set[String] = try {
+        ConfigUtils.getMapFromPath(globalConfig.map, List("samples", sampleId, "libraries")).getOrElse(Map()).keySet
+      } catch {
+        case e: IllegalStateException if e.getMessage == "Value is not a map: library" =>
+          Logging.addError("libraries for samples are not formatted correctly")
+          Set()
       }
-      ids
+      if (ids.isEmpty) {
+        Logging.addError(s"No libraries found in config for sample $sampleId")
+        Set("placeholder")
+      } else ids
     }
 
     /** Name overules the one from qscript */

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

@@ -90,18 +90,13 @@ object WriteDependencies extends Logging with Configurable {
 
     val files: mutable.Map[File, QueueFile] = mutable.Map()
 
-    def outputFiles(function: QFunction) = {
-      if (function.jobErrorFile == null) function.outputs :+ function.jobOutputFile
-      else function.outputs :+ function.jobOutputFile :+ function.jobErrorFile
-    }
-
     for (function <- functions) {
-      for (input <- function.inputs) {
+      for (input <- BiopetQScript.safeInputs(function).getOrElse(Seq())) {
         val file = files.getOrElse(input, QueueFile(input))
         file.addInputJob(function)
         files += input -> file
       }
-      for (output <- outputFiles(function)) {
+      for (output <- BiopetQScript.safeOutputs(function).getOrElse(Seq())) {
         val file = files.getOrElse(output, QueueFile(output))
         file.addOutputJob(function)
         files += output -> file
@@ -118,16 +113,16 @@ object WriteDependencies extends Logging with Configurable {
           case s: WriteSummary if s.qscript.root == null => true
           case _                                         => false
         }), "intermediate" -> f.isIntermediate,
-          "depends_on_intermediate" -> f.inputs.exists(files(_).isIntermediate),
-          "depends_on_jobs" -> f.inputs.toList.flatMap(files(_).outputJobNames).distinct,
-          "output_used_by_jobs" -> outputFiles(f).toList.flatMap(files(_).inputJobNames).distinct,
-          "outputs" -> outputFiles(f).toList,
-          "inputs" -> f.inputs.toList,
-          "done_files" -> f.doneOutputs.toList,
-          "fail_files" -> f.failOutputs.toList,
+          "depends_on_intermediate" -> BiopetQScript.safeOutputs(f).getOrElse(Seq()).exists(files(_).isIntermediate),
+          "depends_on_jobs" -> BiopetQScript.safeOutputs(f).getOrElse(Seq()).toList.flatMap(files(_).outputJobNames).distinct,
+          "output_used_by_jobs" -> BiopetQScript.safeOutputs(f).getOrElse(Seq()).toList.flatMap(files(_).inputJobNames).distinct,
+          "outputs" -> BiopetQScript.safeOutputs(f).getOrElse(Seq()).toList,
+          "inputs" -> BiopetQScript.safeOutputs(f).getOrElse(Seq()).toList,
+          "done_files" -> BiopetQScript.safeDoneFiles(f).getOrElse(Seq()).toList,
+          "fail_files" -> BiopetQScript.safeFailFiles(f).getOrElse(Seq()).toList,
           "stdout_file" -> f.jobOutputFile,
-          "done_at_start" -> f.isDone,
-          "fail_at_start" -> f.isFail)
+          "done_at_start" -> BiopetQScript.safeIsDone(f),
+          "fail_at_start" -> BiopetQScript.safeIsFail(f))
     }.toIterator.toMap
 
     val outputFile = new File(outputDir, s"deps.json")

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

@@ -15,11 +15,12 @@
 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.{ ConfigUtils, Logging }
+import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
 import nl.lumc.sasc.biopet.utils.config.Config
-import org.broadinstitute.gatk.queue.QScript
+import org.broadinstitute.gatk.queue.{QScript, QSettings}
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
 import org.testng.annotations.Test
@@ -121,7 +122,7 @@ class MultiSampleQScriptTest extends TestNGSuite with Matchers {
 
   @Test
   def testNoLibSample(): Unit = {
-    an[IllegalStateException] shouldBe thrownBy(MultiSampleQScriptTest(noLibSample :: Nil))
+    an[IllegalStateException] shouldBe thrownBy(MultiSampleQScriptTest(Map("output_dir" -> ".") :: noLibSample :: Nil).script())
   }
 }
 
@@ -203,6 +204,9 @@ object MultiSampleQScriptTest {
   def apply(configs: List[Map[String, Any]], only: List[String] = Nil) = {
     new QScript with MultiSampleQScript { qscript =>
 
+      qSettings = new QSettings()
+      qSettings.runName = "test"
+
       override val onlySamples = only
 
       var buffer = new ListBuffer[String]()
@@ -272,7 +276,7 @@ object MultiSampleQScriptTest {
       def summaryFiles: Map[String, File] = Map()
 
       /** Name of summary output file */
-      def summaryFile: File = null
+      def summaryFile: File = new File("./summary.json")
 
       /** Init for pipeline */
       def init(): Unit = {