Commit b03d3473 authored by Sander Bollen's avatar Sander Bollen

fix tests

parent 8036de74
...@@ -15,10 +15,11 @@ ...@@ -15,10 +15,11 @@
package nl.lumc.sasc.biopet.core package nl.lumc.sasc.biopet.core
import java.io.File import java.io.File
import java.lang.IllegalStateException
import nl.lumc.sasc.biopet.core.MultiSampleQScript.Gender import nl.lumc.sasc.biopet.core.MultiSampleQScript.Gender
import nl.lumc.sasc.biopet.core.extensions.Md5sum import nl.lumc.sasc.biopet.core.extensions.Md5sum
import nl.lumc.sasc.biopet.utils.{ Logging, ConfigUtils } import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
import nl.lumc.sasc.biopet.utils.config.Config import nl.lumc.sasc.biopet.utils.config.Config
import org.broadinstitute.gatk.queue.QScript import org.broadinstitute.gatk.queue.QScript
import org.scalatest.Matchers import org.scalatest.Matchers
...@@ -119,6 +120,11 @@ class MultiSampleQScriptTest extends TestNGSuite with Matchers { ...@@ -119,6 +120,11 @@ class MultiSampleQScriptTest extends TestNGSuite with Matchers {
"Dash (-) and underscore (_) are permitted." "Dash (-) and underscore (_) are permitted."
} }
@Test
def testNoLibSample(): Unit = {
an [IllegalStateException] shouldBe thrownBy(MultiSampleQScriptTest(noLibSample :: Nil))
}
} }
object MultiSampleQScriptTest { object MultiSampleQScriptTest {
...@@ -153,10 +159,48 @@ object MultiSampleQScriptTest { ...@@ -153,10 +159,48 @@ object MultiSampleQScriptTest {
"lib1" -> Map("test" -> "4-1") "lib1" -> Map("test" -> "4-1")
)))) ))))
val child = Map("samples" -> Map("child" -> Map("tags" -> Map( val child = Map(
"gender" -> "male", "father" -> "father", "mother" -> "mother")))) "samples" -> Map(
val father = Map("samples" -> Map("father" -> Map("tags" -> Map("gender" -> "male")))) "child" -> Map(
val mother = Map("samples" -> Map("mother" -> Map("tags" -> Map("gender" -> "female")))) "tags" -> Map(
"gender" -> "male",
"father" -> "father",
"mother" -> "mother"
),
"libraries" -> Map(
"lib1" -> Map("test" -> "child-1")
)
)
)
)
val father = Map(
"samples" -> Map(
"father" -> Map(
"tags" -> Map("gender" -> "male"),
"libraries" -> Map(
"lib1" -> Map("test" -> "father-1")
)
)
)
)
val mother = Map(
"samples" -> Map(
"mother" -> Map(
"tags" -> Map("gender" -> "female"),
"libraries" -> Map(
"lib1" -> Map("test" -> "mother-1")
)
)
)
)
val noLibSample = Map(
"samples" -> Map(
"sample1" -> Map(
"tags" -> Map("gender" -> "female")
)
)
)
def apply(configs: List[Map[String, Any]], only: List[String] = Nil) = { def apply(configs: List[Map[String, Any]], only: List[String] = Nil) = {
new QScript with MultiSampleQScript { qscript => new QScript with MultiSampleQScript { qscript =>
......
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