Trim down general test to test for expMeasure and strandProtocol combinations

public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala

@@ -15,9 +15,6 @@ import org.testng.annotations.{ AfterClass, DataProvider, Test }
 
 import nl.lumc.sasc.biopet.core.config.Config
 import nl.lumc.sasc.biopet.extensions._
-import nl.lumc.sasc.biopet.pipelines.gentrap.extensions._
-import nl.lumc.sasc.biopet.pipelines.gentrap.scripts._
-import nl.lumc.sasc.biopet.tools.{ MergeTables, WipeReads }
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 
 class GentrapTest extends TestNGSuite with Matchers {
@@ -25,66 +22,75 @@ class GentrapTest extends TestNGSuite with Matchers {
   def initPipeline(map: Map[String, Any]): Gentrap = {
     new Gentrap() {
       override def configName = "gentrap"
+
       override def globalConfig = new Config(map)
+
       qSettings = new QSettings
       qSettings.runName = "test"
     }
   }
 
+  /** Convenience method for making library config */
+  private def makeLibConfig(idx: Int, paired: Boolean = true) = {
+    val files = Map("R1" -> "test_R1.fq")
+    if (paired) (s"lib_$idx", files ++ Map("R2" -> "test_R2.fq"))
+    else (s"lib_$idx", files)
+  }
+
+  /** Convenience method for making sample config */
+  private def makeSampleConfig(sampleIdx: Int, numLibs: Int, paired: String) =
+    Map("samples" ->
+      Map(s"sample_$sampleIdx" ->
+        Map("libraries" ->
+          (0 to numLibs)
+            // if paired == "mixed", alternate paired/not paired between each number
+            .map(n => makeLibConfig(n, if (paired == "mixed") n % 2 == 0 else paired == "paired"))
+            .toMap
+        )
+      )
+    )
+
+  private val pairedOneSampleOneLib = makeSampleConfig(1, 1, "paired")
+  private val pairedOneSampleTwoLib = makeSampleConfig(1, 2, "paired")
+  private val pairedOneSampleThreeLib = makeSampleConfig(1, 3, "paired")
+
   private lazy val validExpressionMeasures = Set(
     "fragments_per_gene", "fragments_per_exon", "bases_per_gene", "bases_per_exon",
     "cufflinks_strict", "cufflinks_guided", "cufflinks_blind")
 
-  @DataProvider(name = "gentrapOptions")
+  @DataProvider(name = "expMeasures_strandProtocol")
   def flexiprepOptions = {
 
-    val pairTypes = Array(true, false)
-    val aligners = Array("gsnap")
     val strandProtocols = Array("non_specific", "dutp")
-    val callVariants = Array(true, false)
     // get all possible combinations of expression measures
     val expressionMeasures = validExpressionMeasures
       .subsets
       .map(_.toList)
       .toArray
 
-    for (
-      pair <- pairTypes;
-      aligner <- aligners;
-      expressionMeasure <- expressionMeasures;
-      strandProtocol <- strandProtocols;
-      callVariant <- callVariants
-    ) yield Array("", pair, aligner, expressionMeasure, strandProtocol, callVariant)
+    for {
+      expressionMeasure <- expressionMeasures
+      strandProtocol <- strandProtocols
+    } yield Array(expressionMeasure, strandProtocol)
   }
 
-  @Test(dataProvider = "gentrapOptions")
-  def testGentrap(name: String, paired: Boolean, aligner: String, expMeasures: List[String],
-                  strandProtocol: String, callVariant: Boolean) = {
-
-    val map = ConfigUtils.mergeMaps(
-      Map(
-        "output_dir" -> GentrapTest.outputDir,
-        "gsnap" -> Map("db" -> "test", "dir" -> "test"),
-        "aligner" -> "gsnap",
-        "expression_measures" -> expMeasures,
-        "strand_protocol" -> strandProtocol,
-        "call_variants" -> callVariant,
-        "samples" -> Map(
-          "sample_1" -> Map(
-            "libraries" -> Map(
-              "lib_1" -> Map(
-                "R1" -> "test_R1.fq"
-              )
-            )
-          )
-        )
-      ),
-      Map(GentrapTest.executables.toSeq: _*))
-    val gentrap: Gentrap = initPipeline(map)
+  @Test(dataProvider = "expMeasures_strandProtocol")
+  def testGentrap(expMeasures: List[String], strandProtocol: String) = {
+
+    val settings = Map(
+      "output_dir" -> GentrapTest.outputDir,
+      "gsnap" -> Map("db" -> "test", "dir" -> "test"),
+      "aligner" -> "gsnap",
+      "expression_measures" -> expMeasures,
+      "strand_protocol" -> strandProtocol
+    )
+    val config = ConfigUtils.mergeMaps(settings ++ pairedOneSampleOneLib, Map(GentrapTest.executables.toSeq: _*))
+    val gentrap: Gentrap = initPipeline(config)
 
     gentrap.script()
+    val functions = gentrap.functions.groupBy(_.getClass)
 
-    gentrap.functions.count(_.isInstanceOf[Gsnap]) shouldBe 1
+    functions(classOf[Gsnap]).size should be >= 1
   }
 
   // remove temporary run directory all tests in the class have been run