From 280f922d8cc2d5cc71a4251935bd336ca2a2df28 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Mon, 16 Feb 2015 11:59:45 +0100
Subject: [PATCH] Use unique and transient temp directory for each pipeline
test
---
.../sasc/biopet/pipelines/carp/CarpTest.scala | 18 ++++++++++++-----
.../pipelines/flexiprep/FlexiprepTest.scala | 20 +++++++++++++------
.../pipelines/mapping/MappingTest.scala | 18 ++++++++++++-----
3 files changed, 40 insertions(+), 16 deletions(-)
diff --git a/public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala b/public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
index da63e765d..fd57a752a 100644
--- a/public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
+++ b/public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
@@ -2,15 +2,18 @@ package nl.lumc.sasc.biopet.pipelines.carp
import java.io.File
+import com.google.common.io.Files
+import org.apache.commons.io.FileUtils
+import org.broadinstitute.gatk.queue.QSettings
+import org.testng.annotations.{ AfterClass, Test, DataProvider }
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+
import nl.lumc.sasc.biopet.core.config.Config
import nl.lumc.sasc.biopet.extensions.bwa.BwaMem
import nl.lumc.sasc.biopet.extensions.macs2.Macs2CallPeak
import nl.lumc.sasc.biopet.extensions.picard.{ MergeSamFiles, SortSam }
import nl.lumc.sasc.biopet.utils.ConfigUtils
-import org.broadinstitute.gatk.queue.QSettings
-import org.testng.annotations.{ Test, DataProvider }
-import org.scalatest.Matchers
-import org.scalatest.testng.TestNGSuite
/**
* Created by pjvan_thof on 2/13/15.
@@ -69,10 +72,15 @@ class CarpTest extends TestNGSuite with Matchers {
carp.functions.count(_.isInstanceOf[Macs2CallPeak]) shouldBe (numberSamples + (if (threatment) 1 else 0))
}
}
+
+ // remove temporary run directory all tests in the class have been run
+ @AfterClass def removeTempOutputDir() = {
+ FileUtils.deleteDirectory(CarpTest.outputDir)
+ }
}
object CarpTest {
- val outputDir = System.getProperty("java.io.tmpdir") + File.separator + "flexiprep"
+ val outputDir = Files.createTempDir()
val excutables = Map(
"reference" -> "test",
diff --git a/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala b/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
index 1fcaab37b..7f6c81a34 100644
--- a/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
+++ b/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
@@ -2,15 +2,17 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
import java.io.File
+import com.google.common.io.Files
+import org.apache.commons.io.FileUtils
+import org.broadinstitute.gatk.queue.QSettings
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.{ AfterClass, DataProvider, Test }
+
import nl.lumc.sasc.biopet.core.config.Config
import nl.lumc.sasc.biopet.extensions.{ Gzip, Zcat }
import nl.lumc.sasc.biopet.tools.FastqSync
import nl.lumc.sasc.biopet.utils.ConfigUtils
-import org.broadinstitute.gatk.queue.QSettings
-import org.broadinstitute.gatk.queue.function.QFunction
-import org.scalatest.Matchers
-import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{ DataProvider, Test }
/**
* Created by pjvan_thof on 2/11/15.
@@ -67,9 +69,15 @@ class FlexiprepTest extends TestNGSuite with Matchers {
flexiprep.functions.count(_.isInstanceOf[Sickle]) shouldBe (if (skipTrim) 0 else 1)
flexiprep.functions.count(_.isInstanceOf[Gzip]) shouldBe (if (paired) 2 else 1)
}
+
+ // remove temporary run directory all tests in the class have been run
+ @AfterClass def removeTempOutputDir() = {
+ FileUtils.deleteDirectory(FlexiprepTest.outputDir)
+ }
}
+
object FlexiprepTest {
- val outputDir = System.getProperty("java.io.tmpdir") + File.separator + "flexiprep"
+ val outputDir = Files.createTempDir()
val excutables = Map(
"seqstat" -> Map("exe" -> "test"),
diff --git a/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala b/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
index 43085064c..19b773aba 100644
--- a/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
+++ b/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
@@ -2,6 +2,13 @@ package nl.lumc.sasc.biopet.pipelines.mapping
import java.io.File
+import com.google.common.io.Files
+import org.apache.commons.io.FileUtils
+import org.broadinstitute.gatk.queue.QSettings
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.{ AfterClass, DataProvider, Test }
+
import nl.lumc.sasc.biopet.core.config.Config
import nl.lumc.sasc.biopet.extensions.bwa.{ BwaSamse, BwaSampe, BwaAln, BwaMem }
import nl.lumc.sasc.biopet.extensions.picard.{ MergeSamFiles, AddOrReplaceReadGroups, MarkDuplicates, SortSam }
@@ -12,10 +19,6 @@ import nl.lumc.sasc.biopet.pipelines.flexiprep.Sickle
import nl.lumc.sasc.biopet.pipelines.flexiprep._
import nl.lumc.sasc.biopet.tools.FastqSync
import nl.lumc.sasc.biopet.utils.ConfigUtils
-import org.broadinstitute.gatk.queue.QSettings
-import org.scalatest.Matchers
-import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{ DataProvider, Test }
/**
* Created by pjvan_thof on 2/12/15.
@@ -94,10 +97,15 @@ class MappingTest extends TestNGSuite with Matchers {
mapping.functions.count(_.isInstanceOf[MergeSamFiles]) shouldBe (if (skipMarkDuplicate && chunks > 1) 1 else 0)
mapping.functions.count(_.isInstanceOf[MarkDuplicates]) shouldBe (if (skipMarkDuplicate) 0 else 1)
}
+
+ // remove temporary run directory all tests in the class have been run
+ @AfterClass def removeTempOutputDir() = {
+ FileUtils.deleteDirectory(MappingTest.outputDir)
+ }
}
object MappingTest {
- val outputDir = System.getProperty("java.io.tmpdir") + File.separator + "flexiprep"
+ val outputDir = Files.createTempDir()
val excutables = Map(
"reference" -> "test",
--
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