GwasTestTest.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 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.gwastest

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.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{ AfterClass, Test }

/**
 * Created by pjvan_thof on 4/11/16.
 */
class GwasTestTest extends TestNGSuite with Matchers {
  def initPipeline(map: Map[String, Any]): GwasTest = {
    new GwasTest {
      override def configNamespace = "gwastest"
      override def globalConfig = new Config(map)
      qSettings = new QSettings
      qSettings.runName = "test"
    }
  }

  private var dirs: List[File] = Nil

  @Test
  def testFromVcf: Unit = {
    val outputDir = Files.createTempDir()
    dirs :+= outputDir
    Logging.errors.clear()
    val pipeline = initPipeline(GwasTestTest.config(outputDir) ++
      Map("input_vcf" -> GwasTestTest.vcfFile.toString
      )
    )
    pipeline.script()
  }

  @Test
  def testEmpty: Unit = {
    val outputDir = Files.createTempDir()
    dirs :+= outputDir
    val pipeline = initPipeline(GwasTestTest.config(outputDir))
    intercept[IllegalArgumentException] {
      pipeline.script()
    }
  }

  // remove temporary run directory all tests in the class have been run
  @AfterClass def removeTempOutputDir() = {
    dirs.foreach(FileUtils.deleteDirectory)
  }
}

object GwasTestTest {
  val vcfFile = File.createTempFile("gwas.", ".vcf")
  Files.touch(vcfFile)
  vcfFile.deleteOnExit()

  val phenotypeFile = File.createTempFile("gwas.", ".txt")
  phenotypeFile.deleteOnExit()

  val reference = new File(resourcePath("/fake_chrQ.fa"))

  private def resourcePath(p: String): String = {
    Paths.get(getClass.getResource(p).toURI).toString
  }

  def config(outputDir: File) = Map(
    "skip_write_dependencies" -> true,
    "reference_fasta" -> reference.toString,
    "phenotype_file" -> phenotypeFile.toString,
    "output_dir" -> outputDir,
    "snptest" -> Map("exe" -> "test"),
    "md5sum" -> Map("exe" -> "test"),
    "gatk_jar" -> "test"
  )

}