Commit f7166e18 authored by Peter van 't Hof's avatar Peter van 't Hof

Fixed unit tests for shiva

parent b3adee75
......@@ -38,7 +38,6 @@ class KopisuTest extends TestNGSuite with Matchers {
new Kopisu() {
override def configNamespace = "kopisu"
override def globalConfig = new Config(ConfigUtils.mergeMaps(map, KopisuTest.config(dir)))
outputDir = dir
qSettings = new QSettings
qSettings.runName = "test"
}
......
......@@ -38,10 +38,10 @@ import scala.collection.mutable.ListBuffer
* Created by pjvan_thof on 3/2/15.
*/
class ShivaSvCallingTest extends TestNGSuite with Matchers {
def initPipeline(map: Map[String, Any], outputDir: File): ShivaSvCalling = {
def initPipeline(map: Map[String, Any], dir: File): ShivaSvCalling = {
new ShivaSvCalling {
override def configNamespace = "shivasvcalling"
override def globalConfig = new Config(ConfigUtils.mergeMaps(map, ShivaSvCallingTest.config(outputDir)))
override def globalConfig = new Config(ConfigUtils.mergeMaps(map, ShivaSvCallingTest.config(dir)))
qSettings = new QSettings
qSettings.runName = "test"
}
......
......@@ -193,7 +193,7 @@ object ShivaTest {
private def copyFile(name: String): Unit = {
val is = getClass.getResourceAsStream("/" + name)
val os = new FileOutputStream(new File(outputDir, name))
val os = new FileOutputStream(new File(inputDir, name))
org.apache.commons.io.IOUtils.copy(is, os)
os.close()
}
......
......@@ -44,10 +44,10 @@ import scala.collection.mutable.ListBuffer
* Created by pjvan_thof on 3/2/15.
*/
trait ShivaVariantcallingTestTrait extends TestNGSuite with Matchers {
def initPipeline(map: Map[String, Any], outputDir: File): ShivaVariantcalling = {
def initPipeline(map: Map[String, Any], dir: File): ShivaVariantcalling = {
new ShivaVariantcalling() {
override def configNamespace = "shivavariantcalling"
override def globalConfig = new Config(ConfigUtils.mergeMaps(map, ShivaVariantcallingTest.config(outputDir)))
override def globalConfig = new Config(ConfigUtils.mergeMaps(map, ShivaVariantcallingTest.config(dir)))
qSettings = new QSettings
qSettings.runName = "test"
}
......
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