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biopet.biopet
Commits
8449e73b
Commit
8449e73b
authored
Mar 08, 2016
by
Peter van 't Hof
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Fix threading issue in unit tests
parent
610e9327
Changes
4
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4 changed files
with
14 additions
and
17 deletions
+14
-17
public/biopet-tools-extensions/src/test/scala/VcfFilterTest.scala
...iopet-tools-extensions/src/test/scala/VcfFilterTest.scala
+4
-6
public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/Rscript.scala
...ain/scala/nl/lumc/sasc/biopet/utils/rscript/Rscript.scala
+1
-1
public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
...a/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
+7
-10
public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
...sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
+2
-0
No files found.
public/biopet-tools-extensions/src/test/scala/VcfFilterTest.scala
View file @
8449e73b
...
...
@@ -3,12 +3,11 @@ import java.io.File
import
nl.lumc.sasc.biopet.extensions.tools.VcfFilter
import
org.scalatest.Matchers
import
org.scalatest.testng.TestNGSuite
import
org.testng.annotations.
{
DataProvider
,
Test
}
import
org.testng.annotations.
{
DataProvider
,
Test
}
/**
* Created by ahbbollen on 2-3-16.
*/
* Created by ahbbollen on 2-3-16.
*/
class
VcfFilterTest
extends
TestNGSuite
with
Matchers
{
def
cmd
(
s
:
String
)
=
{
...
...
@@ -112,7 +111,7 @@ class VcfFilterTest extends TestNGSuite with Matchers {
}
if
(
minAlternateDepth
.
isDefined
)
{
cmdString
=
"--minAlternateDepth "
+
minAlternateDepth
.
getOrElse
(
""
)
::
cmdString
cmdString
=
"--minAlternateDepth "
+
minAlternateDepth
.
getOrElse
(
""
)
::
cmdString
}
if
(
minSamplesPass
.
isDefined
)
{
...
...
@@ -183,7 +182,6 @@ class VcfFilterTest extends TestNGSuite with Matchers {
cmdString
=
"--minQualScore "
+
minQualScore
.
getOrElse
(
""
)
::
cmdString
}
cmdString
.
foreach
(
x
=>
command
.
contains
(
x
)
shouldBe
true
)
}
...
...
public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/Rscript.scala
View file @
8449e73b
...
...
@@ -30,7 +30,7 @@ import scala.sys.process.{ Process, ProcessLogger }
trait
Rscript
extends
Configurable
{
protected
var
script
:
File
def
rscriptExecutable
:
String
=
config
(
"exe"
,
default
=
"Rscript"
,
submodule
=
"
R
script"
)
def
rscriptExecutable
:
String
=
config
(
"exe"
,
default
=
"Rscript"
,
submodule
=
"
r
script"
)
/** This is the defaul implementation, to add arguments override this */
def
cmd
:
Seq
[
String
]
=
Seq
(
rscriptExecutable
,
script
.
getAbsolutePath
)
...
...
public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
View file @
8449e73b
...
...
@@ -15,18 +15,17 @@
*/
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.extensions.tools.BaseCounter
import
nl.lumc.sasc.biopet.utils.config.Config
import
nl.lumc.sasc.biopet.extensions._
import
nl.lumc.sasc.biopet.extensions.tools.BaseCounter
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
org.apache.commons.io.FileUtils
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.
{
AfterClass
,
DataProvider
,
Test
}
import
org.testng.annotations.
{
DataProvider
,
Test
}
abstract
class
GentrapTestAbstract
(
val
expressionMeasure
:
String
)
extends
TestNGSuite
with
Matchers
{
...
...
@@ -143,10 +142,6 @@ abstract class GentrapTestAbstract(val expressionMeasure: String) extends TestNG
}
}
// remove temporary run directory all tests in the class have been run
@AfterClass
def
removeTempOutputDir
()
=
{
FileUtils
.
deleteDirectory
(
GentrapTest
.
outputDir
)
}
}
class
GentrapFragmentsPerGeneTest
extends
GentrapTestAbstract
(
"fragments_per_gene"
)
...
...
@@ -158,6 +153,7 @@ class GentrapCufflinksBlindTest extends GentrapTestAbstract("cufflinks_blind")
object
GentrapTest
{
val
outputDir
=
Files
.
createTempDir
()
outputDir
.
deleteOnExit
()
new
File
(
outputDir
,
"input"
).
mkdirs
()
def
inputTouch
(
name
:
String
)
:
String
=
{
val
file
=
new
File
(
outputDir
,
"input"
+
File
.
separator
+
name
)
...
...
@@ -182,7 +178,8 @@ object GentrapTest {
"annotation_gtf"
->
(
outputDir
+
File
.
separator
+
"ref.fa"
),
"annotation_bed"
->
(
outputDir
+
File
.
separator
+
"ref.fa"
),
"annotation_refflat"
->
(
outputDir
+
File
.
separator
+
"ref.fa"
),
"varscan_jar"
->
"test"
"varscan_jar"
->
"test"
,
"rscript"
->
Map
(
"exe"
->
"test"
)
)
++
Seq
(
// fastqc executables
"fastqc"
,
"seqtk"
,
"sickle"
,
"cutadapt"
,
...
...
public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
View file @
8449e73b
...
...
@@ -133,6 +133,8 @@ object ShivaVariantcallingTest {
"md5sum"
->
Map
(
"exe"
->
"test"
),
"bgzip"
->
Map
(
"exe"
->
"test"
),
"tabix"
->
Map
(
"exe"
->
"test"
),
"rscript"
->
Map
(
"exe"
->
"test"
),
"exe"
->
"test"
,
"varscan_jar"
->
"test"
)
}
\ No newline at end of file
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