Fixed tests

gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTestTest.scala

@@ -18,6 +18,7 @@ import java.io.File
 import java.nio.file.Paths
 
 import com.google.common.io.Files
+import nl.lumc.sasc.biopet.utils.Logging
 import nl.lumc.sasc.biopet.utils.config.Config
 import org.broadinstitute.gatk.queue.QSettings
 import org.scalatest.Matchers
@@ -39,6 +40,7 @@ class GwasTestTest extends TestNGSuite with Matchers {
 
   @Test
   def testFromVcf: Unit = {
+    Logging.errors.clear()
     val pipeline = initPipeline(GwasTestTest.config ++
       Map("input_vcf" -> GwasTestTest.vcfFile.toString
       )
@@ -46,34 +48,6 @@ class GwasTestTest extends TestNGSuite with Matchers {
     pipeline.script()
   }
 
-  @Test
-  def testFromGens: Unit = {
-    val pipeline = initPipeline(GwasTestTest.config ++
-      Map("input_gens" -> List(Map("genotypes" -> GwasTestTest.vcfFile, "contig" -> "chrQ"))
-      )
-    )
-    pipeline.script()
-  }
-
-  @Test
-  def testWrongContig: Unit = {
-    val pipeline = initPipeline(GwasTestTest.config ++
-      Map("input_gens" -> List(Map("genotypes" -> GwasTestTest.vcfFile, "contig" -> "chrBla"))
-      )
-    )
-    intercept[IllegalStateException] {
-      pipeline.script()
-    }
-  }
-
-  @Test
-  def testFromSpecs: Unit = {
-    val pipeline = initPipeline(GwasTestTest.config ++
-      Map("imute_specs_file" -> GwasTestTest.resourcePath("/specs/files.specs"))
-    )
-    pipeline.script()
-  }
-
   @Test
   def testEmpty: Unit = {
     val pipeline = initPipeline(GwasTestTest.config)
@@ -101,8 +75,8 @@ object GwasTestTest {
   }
 
   val config = Map(
-    "reference_fasta" -> GwasTestTest.reference.toString,
-    "phenotype_file" -> GwasTestTest.phenotypeFile.toString,
+    "reference_fasta" -> reference.toString,
+    "phenotype_file" -> phenotypeFile.toString,
     "output_dir" -> outputDir,
     "snptest" -> Map("exe" -> "test"),
     "md5sum" -> Map("exe" -> "test"),

gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/Impute2VcfTest.scala

+package nl.lumc.sasc.biopet.pipelines.gwastest.impute
+
+import java.io.File
+import java.nio.file.Paths
+
+import com.google.common.io.Files
+import nl.lumc.sasc.biopet.utils.config.Config
+import org.broadinstitute.gatk.queue.QSettings
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+/**
+  * Created by pjvan_thof on 31-5-16.
+  */
+class Impute2VcfTest extends TestNGSuite with Matchers {
+  def initPipeline(map: Map[String, Any]): Impute2Vcf = {
+    new Impute2Vcf {
+      override def configNamespace = "impute2vcf"
+      override def globalConfig = new Config(map)
+      qSettings = new QSettings
+      qSettings.runName = "test"
+    }
+  }
+
+  @Test
+  def testFromGens: Unit = {
+    val pipeline = initPipeline(Impute2VcfTest.config ++
+      Map("input_gens" -> List(Map("genotypes" -> Impute2VcfTest.vcfFile, "contig" -> "chrQ"))
+      )
+    )
+    pipeline.script()
+  }
+
+  @Test
+  def testWrongContig: Unit = {
+    val pipeline = initPipeline(Impute2VcfTest.config ++
+      Map("input_gens" -> List(Map("genotypes" -> Impute2VcfTest.vcfFile, "contig" -> "chrBla"))
+      )
+    )
+    intercept[IllegalStateException] {
+      pipeline.script()
+    }
+  }
+
+  @Test
+  def testFromSpecs: Unit = {
+    val pipeline = initPipeline(Impute2VcfTest.config ++
+      Map("imute_specs_file" -> Impute2VcfTest.resourcePath("/specs/files.specs"))
+    )
+    pipeline.script()
+  }
+
+  @Test
+  def testEmpty: Unit = {
+    val pipeline = initPipeline(Impute2VcfTest.config)
+    intercept[IllegalArgumentException] {
+      pipeline.script()
+    }
+  }
+
+}
+
+object Impute2VcfTest {
+  val vcfFile = File.createTempFile("gwas.", ".vcf")
+  Files.touch(vcfFile)
+  vcfFile.deleteOnExit()
+
+  val phenotypeFile = File.createTempFile("gwas.", ".txt")
+  phenotypeFile.deleteOnExit()
+
+  val outputDir = Files.createTempDir()
+  outputDir.deleteOnExit()
+
+  val reference = new File(resourcePath("/fake_chrQ.fa"))
+
+  private def resourcePath(p: String): String = {
+    Paths.get(getClass.getResource(p).toURI).toString
+  }
+
+  val config = Map(
+    "reference_fasta" -> reference.toString,
+    "phenotype_file" -> phenotypeFile.toString,
+    "output_dir" -> outputDir,
+    "md5sum" -> Map("exe" -> "test"),
+    "gatk_jar" -> "test"
+  )
+
+}