Intial unit test for Carp

public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala

+package nl.lumc.sasc.biopet.pipelines.carp
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.config.{ConfigValueIndex, Config}
+import nl.lumc.sasc.biopet.utils.ConfigUtils
+import org.broadinstitute.gatk.queue.QSettings
+import org.testng.annotations.{DataProvider, Test}
+import org.testng.annotations.{Test, DataProvider}
+import org.scalatest.Assertions._
+
+/**
+ * Created by pjvan_thof on 2/13/15.
+ */
+class CarpTest {
+  def initPipeline(map: Map[String, Any]): Carp = {
+    new Carp() {
+      override def configName = "carp"
+      override def globalConfig = new Config(map)
+      qSettings = new QSettings
+      qSettings.runName = "test"
+    }
+  }
+
+  @DataProvider(name = "carpOptions", parallel = true)
+  def carpOptions = {
+    val bool = Array(true, false)
+
+    for (s1 <- bool; s2 <- bool; s3 <- bool; t <- bool; c <- bool) yield
+      Array("", s1, s2, s3, t, c)
+  }
+
+  @Test(dataProvider = "carpOptions")
+  def testCarp(f:String, sample1:Boolean, sample2:Boolean, sample3:Boolean, threatment:Boolean, control:Boolean): Unit = {
+    val map = {
+      var m = ConfigUtils.mergeMaps(Map("output_dir" -> CarpTest.outputDir
+      ), CarpTest.excutables)
+
+      if (sample1) m = ConfigUtils.mergeMaps(CarpTest.sample1, m.toMap)
+      if (sample2) m = ConfigUtils.mergeMaps(CarpTest.sample2, m.toMap)
+      if (sample3) m = ConfigUtils.mergeMaps(CarpTest.sample3, m.toMap)
+      if (threatment) m = ConfigUtils.mergeMaps(CarpTest.threatment1, m.toMap)
+      if (control) m = ConfigUtils.mergeMaps(CarpTest.control1, m.toMap)
+      m
+    }
+
+    if (!sample1 && !sample2 && !sample3 && !threatment && !control) { // When no samples
+      intercept[IllegalArgumentException] {
+        initPipeline(map).script()
+      }
+    } else if (threatment && !control) { // If control of a samples does not exist in samples
+      intercept[IllegalStateException] {
+        initPipeline(map).script()
+      }
+    } else { // When samples are correct
+      val carp = initPipeline(map)
+      carp.script()
+
+
+    }
+  }
+}
+
+object CarpTest {
+  val outputDir = System.getProperty("java.io.tmpdir") + File.separator + "flexiprep"
+
+  val excutables = Map(
+    "reference" -> "test",
+    "seqstat" -> Map("exe" -> "test"),
+    "fastqc" -> Map("exe" -> "test"),
+    "seqtk" -> Map("exe" -> "test"),
+    "sickle" -> Map("exe" -> "test"),
+    "bwa" -> Map("exe" -> "test"),
+    "samtools" -> Map("exe" -> "test"),
+    "macs2" -> Map("exe" -> "test")
+  )
+
+  val sample1 = Map(
+    "samples" -> Map( "sample1" -> Map( "libraries" -> Map(
+      "lib1" -> Map(
+        "R1" -> "1_1_R1.fq",
+        "R2" -> "1_1_R2.fq"
+      )
+    )
+    )))
+
+  val sample2 = Map(
+    "samples" -> Map( "sample2" -> Map( "libraries" -> Map(
+      "lib1" -> Map(
+        "R1" -> "2_1_R1.fq",
+        "R2" -> "2_1_R2.fq"
+      )
+    )
+  )))
+
+  val sample3 = Map(
+    "samples" -> Map( "sample3" -> Map( "libraries" -> Map(
+      "lib1" -> Map(
+        "R1" -> "3_1_R1.fq",
+        "R2" -> "3_1_R2.fq"
+      ),
+      "lib2" -> Map(
+        "R1" -> "3_2_R1.fq",
+        "R2" -> "3_2_R2.fq"
+      )
+    )
+    )))
+
+  val threatment1 = Map(
+    "samples" -> Map( "threatment" -> Map( "control" -> "control1","libraries" -> Map(
+      "lib1" -> Map(
+        "R1" -> "threatment_1_R1.fq",
+        "R2" -> "threatment_1_R2.fq"
+      )
+    )
+    )))
+
+  val control1 = Map(
+    "samples" -> Map( "control1" -> Map( "libraries" -> Map(
+      "lib1" -> Map(
+        "R1" -> "control_1_R1.fq",
+        "R2" -> "control_1_R2.fq"
+      )
+    )
+    )))
+
+}
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