Changed test for gears

gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala

@@ -48,8 +48,8 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
 
   /** Executed before running the script */
   def init(): Unit = {
-    require(fastqR1.isDefined || bamFile.isDefined, "Please specify fastq-file(s) or bam file")
-    require(fastqR1.isDefined != bamFile.isDefined, "Provide either a bam file or a R1/R2 file")
+    if (!fastqR1.isDefined && !bamFile.isDefined) Logging.addError("Please specify fastq-file(s) or bam file")
+    if (fastqR1.isDefined == bamFile.isDefined) Logging.addError("Provide either a bam file or a R1/R2 file")
     if (sampleId == null || sampleId == None) Logging.addError("Missing sample ID on GearsSingle module")
 
     if (outputName == null) {
@@ -64,7 +64,7 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
     if (fastqR1.isDefined) {
       fastqR1.foreach(inputFiles :+= InputFile(_))
       fastqR2.foreach(inputFiles :+= InputFile(_))
-    } else inputFiles :+= InputFile(bamFile.get)
+    } else bamFile.foreach(inputFiles :+= InputFile(_))
   }
 
   override def reportClass = {

gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala

@@ -23,7 +23,6 @@ import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
 import nl.lumc.sasc.biopet.extensions.tools.KrakenReportToJson
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import nl.lumc.sasc.biopet.utils.config.Config
-import org.apache.commons.io.FileUtils
 import org.broadinstitute.gatk.queue.QSettings
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
@@ -35,7 +34,7 @@ import org.testng.annotations._
  * Created by wyleung on 10/22/15.
  */
 
-class GearsSingleTest extends TestNGSuite with Matchers {
+abstract class TestGearsSingle extends TestNGSuite with Matchers {
   def initPipeline(map: Map[String, Any]): GearsSingle = {
     new GearsSingle {
       override def configNamespace = "gearssingle"
@@ -47,94 +46,159 @@ class GearsSingleTest extends TestNGSuite with Matchers {
     }
   }
 
-  @DataProvider(name = "gearsOptions")
-  def gearsOptions = {
-    val bool = Array(true, false)
-
-    for (
-      fromBam <- bool;
-      pair <- bool;
-      hasOutputName <- bool;
-      kraken <- bool;
-      qiimeClosed <- bool;
-      qiimeRtax <- bool;
-      seqCount <- bool
-    ) yield Array("", fromBam, pair, hasOutputName, kraken, qiimeClosed, qiimeRtax, seqCount)
-  }
+  def paired: Boolean = false
+  def hasOutputName: Boolean = false
+  def kraken: Option[Boolean] = None
+  def qiimeClosed: Boolean = false
+  def qiimeOpen: Boolean = false
+  def qiimeRtax: Boolean = false
+  def seqCount: Boolean = false
+  def downsample: Option[Int] = None
+
+  def inputMode: Option[String] = Some("fastq")
 
-  @Test(dataProvider = "gearsOptions")
-  def testGears(dummy: String,
-                fromBam: Boolean,
-                paired: Boolean,
-                hasOutputName: Boolean,
-                kraken: Boolean,
-                qiimeClosed: Boolean,
-                qiimeRtax: Boolean,
-                seqCount: Boolean) = {
+  @Test
+  def testGears(): Unit = {
     val map = ConfigUtils.mergeMaps(Map(
-      "gears_use_kraken" -> kraken,
       "gears_use_qiime_rtax" -> qiimeRtax,
       "gears_use_qiime_closed" -> qiimeClosed,
+      "gears_use_qiime_open" -> qiimeOpen,
       "gears_use_seq_count" -> seqCount,
-      "output_dir" -> GearsSingleTest.outputDir
-    ), Map(GearsSingleTest.executables.toSeq: _*))
+      "output_dir" -> TestGearsSingle.outputDir
+    ) ++
+      kraken.map("gears_use_kraken" -> _) ++
+      downsample.map("downsample" -> _),
+      Map(TestGearsSingle.executables.toSeq: _*))
 
     val gears: GearsSingle = initPipeline(map)
     gears.sampleId = Some("sampleName")
     gears.libId = Some("libName")
 
-    if (fromBam) {
-      gears.bamFile = Some(GearsSingleTest.bam)
-    } else {
-      gears.fastqR1 = Some(GearsSingleTest.r1)
-      gears.fastqR2 = if (paired) Some(GearsSingleTest.r2) else None
+    inputMode match {
+      case Some("fastq") =>
+        gears.fastqR1 = Some(TestGearsSingle.r1)
+        gears.fastqR2 = if (paired) Some(TestGearsSingle.r2) else None
+      case Some("bam") => gears.bamFile = Some(TestGearsSingle.bam)
+      case None        =>
+      case _           => new IllegalStateException(s"$inputMode not allowed as inputMode")
     }
+
     if (hasOutputName)
       gears.outputName = "test"
 
-    gears.script()
-
-    if (hasOutputName) {
-      gears.outputName shouldBe "test"
+    if (inputMode.isEmpty) {
+      intercept[IllegalArgumentException] {
+        gears.script()
+      }
     } else {
-      // in the following cases the filename should have been determined by the filename
-      gears.outputName shouldBe (if (fromBam) "bamfile" else "R1")
+
+      gears.script()
+
+      if (hasOutputName) {
+        gears.outputName shouldBe "test"
+      } else {
+        // in the following cases the filename should have been determined by the filename
+        gears.outputName shouldBe (if (inputMode == Some("bam")) "bamfile" else "R1")
+      }
+
+      gears.summarySettings("gears_use_kraken") shouldBe kraken.getOrElse(true)
+      gears.summarySettings("gear_use_qiime_rtax") shouldBe qiimeRtax
+      gears.summarySettings("gear_use_qiime_closed") shouldBe qiimeClosed
+      gears.summarySettings("gear_use_qiime_open") shouldBe qiimeOpen
+
+      gears.krakenScript.isDefined shouldBe kraken.getOrElse(true)
+      gears.qiimeClosed.isDefined shouldBe qiimeClosed
+      gears.qiimeOpen.isDefined shouldBe qiimeOpen
+      gears.qiimeRatx.isDefined shouldBe qiimeRtax
+      gears.seqCount.isDefined shouldBe seqCount
+
+      // SamToFastq should have started if it was started from bam
+      gears.functions.count(_.isInstanceOf[SamtoolsView]) shouldBe (if (inputMode == Some("bam")) 1 else 0)
+      gears.functions.count(_.isInstanceOf[SamToFastq]) shouldBe (if (inputMode == Some("bam")) 1 else 0)
+
+      gears.functions.count(_.isInstanceOf[Kraken]) shouldBe (if (kraken.getOrElse(true)) 1 else 0)
+      gears.functions.count(_.isInstanceOf[KrakenReport]) shouldBe (if (kraken.getOrElse(true)) 1 else 0)
+      gears.functions.count(_.isInstanceOf[KrakenReportToJson]) shouldBe (if (kraken.getOrElse(true)) 1 else 0)
     }
+  }
+}
 
-    gears.krakenScript.isDefined shouldBe kraken
-    gears.qiimeClosed.isDefined shouldBe qiimeClosed
-    gears.qiimeRatx.isDefined shouldBe qiimeRtax
-    gears.seqCount.isDefined shouldBe seqCount
+class GearsSingleNoInputTest extends TestGearsSingle {
+  override def inputMode = None
+}
 
-    // SamToFastq should have started if it was started from bam
-    gears.functions.count(_.isInstanceOf[SamtoolsView]) shouldBe (if (fromBam) 1 else 0)
-    gears.functions.count(_.isInstanceOf[SamToFastq]) shouldBe (if (fromBam) 1 else 0)
+class GearsSingleDefaultTest extends TestGearsSingle
+class GearsSingleKrakenTest extends TestGearsSingle {
+  override def kraken = Some(true)
+}
+class GearsSingleQiimeClosedTest extends TestGearsSingle {
+  override def qiimeClosed = true
+}
+class GearsSingleQiimeOpenTest extends TestGearsSingle {
+  override def qiimeOpen = true
+}
+class GearsSingleQiimeRtaxTest extends TestGearsSingle {
+  override def qiimeRtax = true
+}
+class GearsSingleseqCountTest extends TestGearsSingle {
+  override def seqCount = true
+}
 
-    gears.functions.count(_.isInstanceOf[Kraken]) shouldBe (if (kraken) 1 else 0)
-    gears.functions.count(_.isInstanceOf[KrakenReport]) shouldBe (if (kraken) 1 else 0)
-    gears.functions.count(_.isInstanceOf[KrakenReportToJson]) shouldBe (if (kraken) 1 else 0)
-  }
+class GearsSingleKrakenPairedTest extends TestGearsSingle {
+  override def paired = true
+  override def kraken = Some(true)
+}
+class GearsSingleQiimeClosedPairedTest extends TestGearsSingle {
+  override def paired = true
+  override def qiimeClosed = true
+}
+class GearsSingleQiimeOpenPairedTest extends TestGearsSingle {
+  override def paired = true
+  override def qiimeOpen = true
+}
+class GearsSingleQiimeRtaxPairedTest extends TestGearsSingle {
+  override def paired = true
+  override def qiimeRtax = true
+}
+class GearsSingleseqCountPairedTest extends TestGearsSingle {
+  override def paired = true
+  override def seqCount = true
+}
 
-  @Test
-  def testNoSample: Unit = {
-    val map = ConfigUtils.mergeMaps(Map(
-      "output_dir" -> GearsSingleTest.outputDir
-    ), Map(GearsSingleTest.executables.toSeq: _*))
-    val gears: GearsSingle = initPipeline(map)
+class GearsSingleAllTest extends TestGearsSingle {
+  override def kraken = Some(true)
+  override def qiimeClosed = true
+  override def qiimeOpen = true
+  override def qiimeRtax = true
+  override def seqCount = true
+}
+class GearsSingleAllPairedTest extends TestGearsSingle {
+  override def kraken = Some(true)
+  override def qiimeClosed = true
+  override def qiimeOpen = true
+  override def qiimeRtax = true
+  override def seqCount = true
+  override def paired = true
+}
 
-    intercept[IllegalArgumentException] {
-      gears.script()
-    }
-  }
+class GearsSingleBamTest extends TestGearsSingle {
+  override def inputMode = Some("bam")
+}
 
-  // remove temporary run directory all tests in the class have been run
-  @AfterClass def removeTempOutputDir() = {
-    FileUtils.deleteDirectory(GearsSingleTest.outputDir)
-  }
+class GearsSingleQiimeClosedDownsampleTest extends TestGearsSingle {
+  override def paired = true
+  override def qiimeClosed = true
+  override def downsample = Some(10000)
+}
+class GearsSingleQiimeOpenDownsampleTest extends TestGearsSingle {
+  override def paired = true
+  override def qiimeOpen = true
+  override def downsample = Some(10000)
 }
 
-object GearsSingleTest {
+object TestGearsSingle {
   val outputDir = Files.createTempDir()
+  outputDir.deleteOnExit()
   new File(outputDir, "input").mkdirs()
 
   val r1 = new File(outputDir, "input" + File.separator + "R1.fq")
@@ -155,6 +219,7 @@ object GearsSingleTest {
     "md5sum" -> Map("exe" -> "test"),
     "assigntaxonomy" -> Map("exe" -> "test"),
     "pickclosedreferenceotus" -> Map("exe" -> "test"),
+    "pickopenreferenceotus" -> Map("exe" -> "test"),
     "pickotus" -> Map("exe" -> "test"),
     "pickrepset" -> Map("exe" -> "test"),
     "splitlibrariesfastq" -> Map("exe" -> "test"),

pom.xml

@@ -81,6 +81,7 @@
                 <artifactId>maven-surefire-plugin</artifactId>
                 <version>2.18.1</version>
                 <configuration>
+                    <reuseForks>false</reuseForks>
                     <forkCount>1C</forkCount>
                     <argLine>-Xmx300m</argLine>
                     <workingDirectory>${project.build.directory}</workingDirectory>