Skip to content
Snippets Groups Projects
Commit b7c5a56c authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Add job check to unit tests

parent 3152e5fc
No related branches found
No related tags found
No related merge requests found
......@@ -2,17 +2,20 @@ package nl.lumc.sasc.biopet.pipelines.carp
import java.io.File
import nl.lumc.sasc.biopet.core.config.{ConfigValueIndex, Config}
import nl.lumc.sasc.biopet.core.config.Config
import nl.lumc.sasc.biopet.extensions.bwa.BwaMem
import nl.lumc.sasc.biopet.extensions.macs2.Macs2CallPeak
import nl.lumc.sasc.biopet.extensions.picard.{ MergeSamFiles, SortSam }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.queue.QSettings
import org.testng.annotations.{DataProvider, Test}
import org.testng.annotations.{Test, DataProvider}
import org.scalatest.Assertions._
import org.testng.annotations.{ Test, DataProvider }
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
/**
* Created by pjvan_thof on 2/13/15.
*/
class CarpTest {
class CarpTest extends TestNGSuite with Matchers {
def initPipeline(map: Map[String, Any]): Carp = {
new Carp() {
override def configName = "carp"
......@@ -26,12 +29,11 @@ class CarpTest {
def carpOptions = {
val bool = Array(true, false)
for (s1 <- bool; s2 <- bool; s3 <- bool; t <- bool; c <- bool) yield
Array("", s1, s2, s3, t, c)
for (s1 <- bool; s2 <- bool; s3 <- bool; t <- bool; c <- bool) yield Array("", s1, s2, s3, t, c)
}
@Test(dataProvider = "carpOptions")
def testCarp(f:String, sample1:Boolean, sample2:Boolean, sample3:Boolean, threatment:Boolean, control:Boolean): Unit = {
def testCarp(f: String, sample1: Boolean, sample2: Boolean, sample3: Boolean, threatment: Boolean, control: Boolean): Unit = {
val map = {
var m = ConfigUtils.mergeMaps(Map("output_dir" -> CarpTest.outputDir
), CarpTest.excutables)
......@@ -55,8 +57,16 @@ class CarpTest {
} else { // When samples are correct
val carp = initPipeline(map)
carp.script()
val numberLibs = (if (sample1) 1 else 0) + (if (sample2) 1 else 0) + (if (sample3) 2 else 0) +
(if (threatment) 1 else 0) + (if (control) 1 else 0)
val numberSamples = (if (sample1) 1 else 0) + (if (sample2) 1 else 0) + (if (sample3) 1 else 0) +
(if (threatment) 1 else 0) + (if (control) 1 else 0)
carp.functions.count(_.isInstanceOf[BwaMem]) shouldBe numberLibs
carp.functions.count(_.isInstanceOf[SortSam]) shouldBe numberLibs
carp.functions.count(_.isInstanceOf[MergeSamFiles]) shouldBe (if (sample3) 1 else 0)
carp.functions.count(_.isInstanceOf[Macs2CallPeak]) shouldBe (numberSamples + (if (threatment) 1 else 0))
}
}
}
......@@ -76,7 +86,7 @@ object CarpTest {
)
val sample1 = Map(
"samples" -> Map( "sample1" -> Map( "libraries" -> Map(
"samples" -> Map("sample1" -> Map("libraries" -> Map(
"lib1" -> Map(
"R1" -> "1_1_R1.fq",
"R2" -> "1_1_R2.fq"
......@@ -85,16 +95,16 @@ object CarpTest {
)))
val sample2 = Map(
"samples" -> Map( "sample2" -> Map( "libraries" -> Map(
"samples" -> Map("sample2" -> Map("libraries" -> Map(
"lib1" -> Map(
"R1" -> "2_1_R1.fq",
"R2" -> "2_1_R2.fq"
)
)
)))
)))
val sample3 = Map(
"samples" -> Map( "sample3" -> Map( "libraries" -> Map(
"samples" -> Map("sample3" -> Map("libraries" -> Map(
"lib1" -> Map(
"R1" -> "3_1_R1.fq",
"R2" -> "3_1_R2.fq"
......@@ -107,7 +117,7 @@ object CarpTest {
)))
val threatment1 = Map(
"samples" -> Map( "threatment" -> Map( "control" -> "control1","libraries" -> Map(
"samples" -> Map("threatment" -> Map("control" -> "control1", "libraries" -> Map(
"lib1" -> Map(
"R1" -> "threatment_1_R1.fq",
"R2" -> "threatment_1_R2.fq"
......@@ -116,7 +126,7 @@ object CarpTest {
)))
val control1 = Map(
"samples" -> Map( "control1" -> Map( "libraries" -> Map(
"samples" -> Map("control1" -> Map("libraries" -> Map(
"lib1" -> Map(
"R1" -> "control_1_R1.fq",
"R2" -> "control_1_R2.fq"
......
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment