From 95882d8efc6d1a12e5dbc5ce48f65a392b3a5fba Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 4 Feb 2016 17:56:40 +0100
Subject: [PATCH] Added more methods to test
---
.../pipelines/gears/GearsSingleTest.scala | 51 +++++++++++++------
1 file changed, 36 insertions(+), 15 deletions(-)
diff --git a/public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala b/public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala
index b5bb39b2f..957e64fbf 100644
--- a/public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala
+++ b/public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala
@@ -36,7 +36,7 @@ import org.testng.annotations._
* Created by wyleung on 10/22/15.
*/
-class GearsSingleTest(val testset: String) extends TestNGSuite with Matchers {
+class GearsSingleTest extends TestNGSuite with Matchers {
def initPipeline(map: Map[String, Any]): GearsSingle = {
new GearsSingle {
override def configName = "gears"
@@ -50,22 +50,33 @@ class GearsSingleTest(val testset: String) extends TestNGSuite with Matchers {
@DataProvider(name = "gearsOptions")
def gearsOptions = {
- val startFromBam = Array(true, false)
- val paired = Array(true, false)
- val hasOutputNames = Array(true, false)
- val hasFileExtensions = Array(true, false)
+ val bool = Array(true, false)
for (
- fromBam <- startFromBam;
- pair <- paired;
- hasOutputName <- hasOutputNames
- ) yield Array(testset, fromBam, pair, hasOutputName)
+ fromBam <- bool;
+ pair <- bool;
+ hasOutputName <- bool;
+ kraken <- bool;
+ qiimeClosed <- bool;
+ qiimeRtax <- bool;
+ seqCount <- bool
+ ) yield Array("", fromBam, pair, hasOutputName, kraken, qiimeClosed, qiimeRtax, seqCount)
}
@Test(dataProvider = "gearsOptions")
- def testGears(testset: String, fromBam: Boolean, paired: Boolean,
- hasOutputName: Boolean) = {
+ def testGears(dummy: String,
+ fromBam: Boolean,
+ paired: Boolean,
+ hasOutputName: Boolean,
+ kraken: Boolean,
+ qiimeClosed: Boolean,
+ qiimeRtax: Boolean,
+ seqCount: Boolean) = {
val map = ConfigUtils.mergeMaps(Map(
+ "gears_use_kraken" -> kraken,
+ "gear_use_qiime_rtax" -> qiimeRtax,
+ "gear_use_qiime_closed" -> qiimeClosed,
+ "gear_use_seq_count" -> seqCount,
"output_dir" -> GearsSingleTest.outputDir
), Map(GearsSingleTest.executables.toSeq: _*))
@@ -93,9 +104,9 @@ class GearsSingleTest(val testset: String) extends TestNGSuite with Matchers {
gears.functions.count(_.isInstanceOf[SamtoolsView]) shouldBe (if (fromBam) 1 else 0)
gears.functions.count(_.isInstanceOf[SamToFastq]) shouldBe (if (fromBam) 1 else 0)
- gears.functions.count(_.isInstanceOf[Kraken]) shouldBe 1
- gears.functions.count(_.isInstanceOf[KrakenReport]) shouldBe 1
- gears.functions.count(_.isInstanceOf[KrakenReportToJson]) shouldBe 1
+ gears.functions.count(_.isInstanceOf[Kraken]) shouldBe (if (kraken) 1 else 0)
+ gears.functions.count(_.isInstanceOf[KrakenReport]) shouldBe (if (kraken) 1 else 0)
+ gears.functions.count(_.isInstanceOf[KrakenReportToJson]) shouldBe (if (kraken) 1 else 0)
}
// remove temporary run directory all tests in the class have been run
@@ -120,6 +131,16 @@ object GearsSingleTest {
"krakenreport" -> Map("exe" -> "test", "db" -> "test"),
"sambamba" -> Map("exe" -> "test"),
"samtools" -> Map("exe" -> "test"),
- "md5sum" -> Map("exe" -> "test")
+ "md5sum" -> Map("exe" -> "test"),
+ "assigntaxonomy" -> Map("exe" -> "test"),
+ "pickclosedreferenceotus" -> Map("exe" -> "test"),
+ "pickotus" -> Map("exe" -> "test"),
+ "pickrepset" -> Map("exe" -> "test"),
+ "splitlibrariesfastq" -> Map("exe" -> "test"),
+ "flash" -> Map("exe" -> "test"),
+ "fastqc" -> Map("exe" -> "test"),
+ "seqtk" -> Map("exe" -> "test"),
+ "sickle" -> Map("exe" -> "test"),
+ "cutadapt" -> Map("exe" -> "test")
)
}
--
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