From 10342ec527ae42c2cd3a16217c7de6ba7c9cfd1a Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Fri, 13 May 2016 15:00:56 +0200
Subject: [PATCH] Extended tests.
---
.../extensions/clever/CleverFixVCFTest.scala | 48 +++++++++++++++++++
1 file changed, 48 insertions(+)
diff --git a/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/clever/CleverFixVCFTest.scala b/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/clever/CleverFixVCFTest.scala
index 6592a920e..114fcf22d 100644
--- a/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/clever/CleverFixVCFTest.scala
+++ b/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/clever/CleverFixVCFTest.scala
@@ -1,14 +1,27 @@
package nl.lumc.sasc.biopet.extensions.clever
+import java.io.File
+import java.nio.file.Paths
+
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.Test
+import scala.io.Source
/**
* Created by wyleung on 13-5-16.
*/
class CleverFixVCFTest extends TestNGSuite with Matchers {
+ /** Returns the absolute path to test resource directory as a File object */
+ private[clever] val resourceDir: File = new File(Paths.get(getClass.getResource(".").toURI).toString)
+
+ /** Given a resource file name, returns the the absolute path to it as a File object */
+ private[clever] def resourceFile(p: String): File = new File(resourceDir, p)
+
+ val rawCleverVCF = resourceFile("test.clever.vcf")
+ val expectedCleverVCF = resourceFile("expectedresult.clever.vcf")
+
@Test
def replacementSucces = {
CleverFixVCF.replaceHeaderLine(
@@ -31,4 +44,39 @@ class CleverFixVCFTest extends TestNGSuite with Matchers {
) should equal(vcfRecordExpected + "\n")
}
+ @Test
+ def mainTest = {
+ val output = File.createTempFile("clever", ".test.vcf")
+ output.deleteOnExit()
+
+ val result = CleverFixVCF.main(Array(
+ "-i", rawCleverVCF.getAbsolutePath,
+ "-o", output.getAbsolutePath,
+ "-s", "testsample"
+ ))
+
+ val exp = Source.fromFile(expectedCleverVCF).getLines()
+ val obs = Source.fromFile(output).getLines()
+
+ (exp zip obs).foreach(_ match {
+ case (a,b) => {
+ a shouldEqual(b)
+ }
+ case _ =>
+ })
+ }
+
+ @Test
+ def javaCommand = {
+ val output = File.createTempFile("clever", ".test.vcf")
+ output.deleteOnExit()
+ val cfvcf = new CleverFixVCF(null)
+ cfvcf.input = rawCleverVCF
+ cfvcf.output = output
+ cfvcf.sampleName = "testsample"
+
+ cfvcf.cmdLine should include ("'-s' 'testsample'")
+ cfvcf.cmdLine should include (s"'-i' '${rawCleverVCF}'")
+ cfvcf.cmdLine should include (s"'-o' '${output}'")
+ }
}
--
GitLab