DownloadGenomesTest.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.generateindexes

import com.google.common.io.Files
import nl.lumc.sasc.biopet.utils.ConfigUtils
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 13-5-16.
 */
class DownloadGenomesTest extends TestNGSuite with Matchers {
  def initPipeline(map: Map[String, Any]): DownloadGenomes = {
    new DownloadGenomes() {
      override def configNamespace = "generateindexes"
      override def globalConfig = new Config(ConfigUtils.mergeMaps(map, DownloadGenomesTest.config))
      qSettings = new QSettings
      qSettings.runName = "test"
    }
  }

  @Test
  def testNoFastaUri(): Unit = {
    val pipeline = initPipeline(Map())
    pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("" -> "")))
    an[IllegalArgumentException] should be thrownBy pipeline.script()
  }

  @Test
  def testNcbiAssembly(): Unit = {
    val pipeline = initPipeline(Map())
    pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("ncbi_assembly_id" -> "id")))
    pipeline.script()
  }

  @Test
  def testSingleFasta(): Unit = {
    val pipeline = initPipeline(Map())
    pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri")))
    pipeline.script()
  }

  @Test
  def testMultiFasta(): Unit = {
    val pipeline = initPipeline(Map())
    pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> List("uri", "uri2", "uri3.gz"))))
    pipeline.script()
  }

  @Test
  def testSingleDbsnp(): Unit = {
    val pipeline = initPipeline(Map("download_annotations" -> true))
    pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri",
      "dbsnp" -> Map("version" -> Map("vcf_uri" -> "uri.vcf.gz")))))
    pipeline.script()
  }

  @Test
  def testContigMapDbsnp(): Unit = {
    val pipeline = initPipeline(Map("download_annotations" -> true))
    pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri",
      "dbsnp" -> Map("version" -> Map("vcf_uri" -> "uri.vcf.gz", "contig_map" -> Map("1" -> "chr1"))))))
    pipeline.script()
  }

  @Test
  def testUnzippedContigMapDbsnp(): Unit = {
    val pipeline = initPipeline(Map("download_annotations" -> true))
    pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri",
      "dbsnp" -> Map("version" -> Map("vcf_uri" -> "uri.vcf", "contig_map" -> Map("1" -> "chr1"))))))
    pipeline.script()
  }

  @Test
  def testSingleUnzippedDbsnp(): Unit = {
    val pipeline = initPipeline(Map("download_annotations" -> true))
    pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri",
      "dbsnp" -> Map("version" -> Map(("vcf_uri" -> "uri.vcf"))))))
    pipeline.script()
  }

  @Test
  def testMultiDbsnp(): Unit = {
    val pipeline = initPipeline(Map("download_annotations" -> true))
    pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri",
      "dbsnp" -> Map("version" -> Map("vcf_uri" -> List("uri.vcf.gz", "uri2.vcf.gz"))))))
    pipeline.script()
  }

  @Test
  def testVep(): Unit = {
    val pipeline = initPipeline(Map("download_annotations" -> true))
    pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri",
      "vep" -> Map("version" -> Map("cache_uri" -> "something/human_vep_80_hg19.tar.gz")))))
    pipeline.script()
  }

  @Test
  def testGtfZipped(): Unit = {
    val pipeline = initPipeline(Map("download_annotations" -> true))
    pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri",
      "gene_annotation" -> Map("version" -> Map("gtf_uri" -> "bla.gf.gz")))))
    pipeline.script()
  }

  @Test
  def testGtf(): Unit = {
    val pipeline = initPipeline(Map("download_annotations" -> true))
    pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri",
      "gene_annotation" -> Map("version" -> Map("gtf_uri" -> "bla.gf")))))
    pipeline.script()
  }

  @Test
  def testGff(): Unit = {
    val pipeline = initPipeline(Map("download_annotations" -> true))
    pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri",
      "gene_annotation" -> Map("version" -> Map("gff_uri" -> "bla.gf")))))
    pipeline.script()
  }

}

object DownloadGenomesTest {
  val outputDir = Files.createTempDir()
  outputDir.deleteOnExit()

  val config = Map("output_dir" -> outputDir,
    "bwa" -> Map("exe" -> "test"),
    "star" -> Map("exe" -> "test"),
    "hisat2build" -> Map("exe" -> "test"),
    "bowtiebuild" -> Map("exe" -> "test"),
    "bowtie2build" -> Map("exe" -> "test"),
    "gmapbuild" -> Map("exe" -> "test"),
    "samtools" -> Map("exe" -> "test"),
    "md5sum" -> Map("exe" -> "test"),
    "gatk_jar" -> "test",
    "tabix" -> Map("exe" -> "test"),
    "gffread" -> Map("exe" -> "test")
  )
}