From 0086a0a5459988ee2647db802601c061390be95c Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 21 Jun 2016 13:17:56 +0200
Subject: [PATCH] Fixed test
---
.../biopet/pipelines/gentrap/GentrapTest.scala | 17 +++++++++++------
1 file changed, 11 insertions(+), 6 deletions(-)
diff --git a/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala b/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
index 34e093691..45878efa4 100644
--- a/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
+++ b/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
@@ -14,9 +14,10 @@
*/
package nl.lumc.sasc.biopet.pipelines.gentrap
-import java.io.{File, FileOutputStream}
+import java.io.{ File, FileOutputStream }
import com.google.common.io.Files
+import nl.lumc.sasc.biopet.core.{ BiopetFifoPipe, BiopetPipe }
import nl.lumc.sasc.biopet.extensions._
import nl.lumc.sasc.biopet.extensions.gmap.Gsnap
import nl.lumc.sasc.biopet.extensions.hisat.Hisat2
@@ -26,7 +27,7 @@ import nl.lumc.sasc.biopet.utils.config.Config
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{DataProvider, Test}
+import org.testng.annotations.{ DataProvider, Test }
abstract class GentrapTestAbstract(val expressionMeasure: String, val aligner: Option[String]) extends TestNGSuite with Matchers {
@@ -114,7 +115,11 @@ abstract class GentrapTestAbstract(val expressionMeasure: String, val aligner: O
val gentrap: Gentrap = initPipeline(config)
gentrap.script()
- val functions = gentrap.functions.groupBy(_.getClass)
+ val functions = gentrap.functions.flatMap {
+ case f: BiopetFifoPipe => f.pipesJobs
+ case f: BiopetPipe => f.pipesJobs
+ case f => List(f)
+ }.groupBy(_.getClass)
val numSamples = sampleConfig("samples").size
if (expMeasures.contains("fragments_per_gene"))
@@ -151,15 +156,15 @@ abstract class GentrapTestAbstract(val expressionMeasure: String, val aligner: O
val alignerClass = classMap.get(aligner.getOrElse("gsnap"))
- alignerClass.foreach(c => assert(gentrap.functions.exists(c.isInstance(_))))
- classMap.values.filterNot(Some(_) == alignerClass).foreach(x => assert(!gentrap.functions.exists(x.isInstance(_))))
+ alignerClass.foreach(c => assert(functions.keys.exists(_ == c)))
+ classMap.values.filterNot(Some(_) == alignerClass).foreach(x => assert(!functions.keys.exists(_ == x)))
}
}
class GentrapFragmentsPerGeneTest extends GentrapTestAbstract("fragments_per_gene", None)
//class GentrapFragmentsPerExonTest extends GentrapTestAbstract("fragments_per_exon", None)
-class GentrapBaseCountsTest extends GentrapTestAbstract("base_counts", Some("gsnap"))
+class GentrapBaseCountsTest extends GentrapTestAbstract("base_counts", None)
class GentrapCufflinksStrictTest extends GentrapTestAbstract("cufflinks_strict", None)
class GentrapCufflinksGuidedTest extends GentrapTestAbstract("cufflinks_guided", None)
class GentrapCufflinksBlindTest extends GentrapTestAbstract("cufflinks_blind", None)
--
GitLab