CHORE: Add reproducibility test that includes covariates (#237)

src/test/scala/au/csiro/variantspark/misc/CovariateReproducibilityTest.scala

@@ -0,0 +1,48 @@
+package au.csiro.variantspark.misc
+
+import org.apache.spark.sql.functions._
+import au.csiro.variantspark.test.SparkTest
+import org.junit.Test
+import org.junit.Ignore
+import org.junit.Assert._
+import au.csiro.variantspark.api._
+import au.csiro.variantspark.algo.RandomForestParams
+import org.apache.spark.sql.{SparkSession, SQLContext}
+import org.apache.spark.SparkConf
+import java.util.{Arrays, ArrayList}
+import scala.jdk.CollectionConverters._
+
+/**
+  * This test needs to be run standalone as it need a different spark context than other tests.
+  */
+class CovariateReproducibilityTest extends SparkTest {
+
+  override implicit lazy val spark = SparkSession.builder
+    .config(new SparkConf(false))
+    .appName("test")
+    .master("local[*]")
+    .getOrCreate()
+
+  @Ignore
+  @Test
+  def testCovariateReproducibleResults() {
+    implicit val vsContext = VSContext(spark)
+    implicit val sqlContext = spark.sqlContext
+    val genotypes = vsContext.importVCF("data/chr22_1000.vcf", 3)
+    val optVariableTypes = new ArrayList[String](Arrays.asList("CONTINUOUS", "ORDINAL(2)",
+        "CONTINUOUS", "CONTINUOUS", "CONTINUOUS", "CONTINUOUS"))
+    val covariates =
+      vsContext.importStdCSV("data/chr22_1000_full_pheno.csv", optVariableTypes)
+    val label = vsContext.loadLabel("data/chr22-labels.csv", "22_16051249")
+    val features = vsContext.unionFeaturesAndCovariates(genotypes, covariates)
+    val inputData = features.features.zipWithIndex.cache()
+    val params = RandomForestParams(seed = 13L)
+    val rfModel1 = RFModelTrainer.trainModel(features, label, params, 40, 20)
+    val impAnalysis1 = new ImportanceAnalysis(sqlContext, features, rfModel1)
+    val topVariables1 = impAnalysis1.importantVariables(20, false)
+    val rfModel2 = RFModelTrainer.trainModel(features, label, params, 40, 20)
+    val impAnalysis2 = new ImportanceAnalysis(sqlContext, features, rfModel2)
+    val topVariables2 = impAnalysis2.importantVariables(20, false)
+    topVariables1.zip(topVariables2).foreach { p => assertEquals(p._1, p._2) }
+  }
+}