Adding tests for Gears

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala

@@ -46,11 +46,15 @@ class Kraken(val root: Configurable) extends BiopetCommandLineFunction with Vers
   var paired: Boolean = config("paired", default = false)
 
   executable = config("exe", default = "kraken")
+
   def versionRegex = """^Kraken version ([\d\w\-\.]+)""".r
+
   override def versionExitcode = List(0, 1)
+
   def versionCommand = executable + " --version"
 
   override def defaultCoreMemory = 8.0
+
   override def defaultThreads = 4
 
   /** Sets readgroup when not set yet */

public/gears/pom.xml

@@ -52,6 +52,12 @@
             <version>2.2.1</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>

public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.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.gears
+
+import java.io.File
+
+import com.google.common.io.Files
+import nl.lumc.sasc.biopet.extensions.kraken.{Kraken, KrakenReport}
+import nl.lumc.sasc.biopet.extensions.picard.SamToFastq
+import nl.lumc.sasc.biopet.extensions.sambamba.SambambaView
+import nl.lumc.sasc.biopet.extensions.tools.{FastqSync, 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
+import org.testng.annotations._
+
+/**
+ * Test class for [[Gears]]
+ *
+ * Created by wyleung on 10/22/15.
+ */
+
+class GearsPipelineTest(val testset: String) extends TestNGSuite with Matchers {
+  def initPipeline(map: Map[String, Any]): Gears = {
+    new Gears {
+      override def configName = "gears"
+
+      override def globalConfig = new Config(map)
+
+      qSettings = new QSettings
+      qSettings.runName = "test"
+    }
+  }
+
+  @DataProvider(name = "gearsOptions")
+  def gearsOptions = {
+    val startFromBam = Array(true, false)
+    val paired = Array(true, false)
+    val hasOutputNames = Array(true, false)
+    val hasFileExtensions = Array(true, false)
+
+    for (
+      fromBam <- startFromBam;
+      pair <- paired;
+      hasOutputName <- hasOutputNames;
+      hasFileExtension <- hasFileExtensions
+    ) yield Array(testset, fromBam, pair, hasOutputName, hasFileExtension)
+  }
+
+  @Test(dataProvider = "gearsOptions")
+  def testGears(testset: String, fromBam: Boolean, paired: Boolean,
+                hasOutputName: Boolean, hasFileExtension: Boolean) = {
+    val map = ConfigUtils.mergeMaps(Map(
+      "output_dir" -> GearsTest.outputDir
+    ), Map(GearsTest.executables.toSeq: _*))
+
+    val gears: Gears = initPipeline(map)
+
+    if (fromBam) {
+      gears.bamFile = if (hasFileExtension) Some(GearsTest.bam) else Some(GearsTest.bam_noext)
+    } else {
+      gears.fastqR1 = if (hasFileExtension) Some(GearsTest.r1) else Some(GearsTest.r1_noext)
+      gears.fastqR2 = if (paired) if (hasFileExtension) Some(GearsTest.r2) else Some(GearsTest.r2_noext) else None
+    }
+    if (hasOutputName)
+      gears.outputName = "test"
+
+    gears.script()
+
+    if (hasOutputName) {
+      gears.outputName shouldBe "test"
+    } else {
+      // in the following cases the filename should have been determined by the filename
+      if (hasFileExtension) {
+        gears.outputName shouldBe (if (fromBam) "bamfile" else "R1")
+      } else {
+        // no real use-case for this one, have this is for sanity check
+        gears.outputName shouldBe (if (fromBam) "bamfile" else "R1")
+      }
+    }
+
+    // SamToFastq should have started if it was started from bam
+    gears.functions.count(_.isInstanceOf[SamToFastq]) shouldBe (if (fromBam) 1 else 0)
+    gears.functions.count(_.isInstanceOf[SambambaView]) shouldBe (if (fromBam) 1 else 0)
+    gears.functions.count(_.isInstanceOf[FastqSync]) shouldBe (if (fromBam) 1 else 0)
+
+    gears.functions.count(_.isInstanceOf[Kraken]) shouldBe 1
+    gears.functions.count(_.isInstanceOf[KrakenReport]) shouldBe 1
+    gears.functions.count(_.isInstanceOf[KrakenReportToJson]) shouldBe 1
+  }
+
+  // remove temporary run directory all tests in the class have been run
+  @AfterClass def removeTempOutputDir() = {
+    FileUtils.deleteDirectory(GearsTest.outputDir)
+  }
+}
+
+object GearsTest {
+  val outputDir = Files.createTempDir()
+  new File(outputDir, "input").mkdirs()
+
+  val r1 = new File(outputDir, "input" + File.separator + "R1.fq")
+  Files.touch(r1)
+  val r2 = new File(outputDir, "input" + File.separator + "R2.fq")
+  Files.touch(r2)
+  val bam = new File(outputDir, "input" + File.separator + "bamfile.bam")
+  Files.touch(bam)
+
+  val r1_noext = new File(outputDir, "input" + File.separator + "R1")
+  Files.touch(r1_noext)
+  val r2_noext = new File(outputDir, "input" + File.separator + "R2")
+  Files.touch(r2_noext)
+  val bam_noext = new File(outputDir, "input" + File.separator + "bamfile")
+  Files.touch(bam_noext)
+
+  val executables = Map(
+    "kraken" -> Map("exe" -> "test", "db" -> "test"),
+    "krakenreport" -> Map("exe" -> "test", "db" -> "test"),
+    "sambamba" -> Map("exe" -> "test"),
+    "md5sum" -> Map("exe" -> "test")
+  )
+}