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biopet.biopet
Commits
1a85e5ca
Commit
1a85e5ca
authored
Nov 18, 2016
by
Peter van 't Hof
Browse files
Added unit tests
parent
01d2c652
Changes
2
Hide whitespace changes
Inline
Side-by-side
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/ReferenceTest.scala
View file @
1a85e5ca
...
...
@@ -22,13 +22,12 @@ import nl.lumc.sasc.biopet.utils.config.{ Config, Configurable }
import
org.scalatest.Matchers
import
org.scalatest.mock.MockitoSugar
import
org.scalatest.testng.TestNGSuite
import
org.mockito.Mockito._
import
org.testng.annotations.Test
/**
* Created by pjvan_thof on 12/30/15.
*/
class
ReferenceTest
extends
TestNGSuite
with
Matchers
with
MockitoSugar
{
class
ReferenceTest
extends
TestNGSuite
with
Matchers
{
import
ReferenceTest._
...
...
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/annotation/AnnotationTest.scala
0 → 100644
View file @
1a85e5ca
package
nl.lumc.sasc.biopet.core.annotation
import
java.io.File
import
nl.lumc.sasc.biopet.core.BiopetQScript
import
nl.lumc.sasc.biopet.core.annotations.
{
AnnotationGff
,
AnnotationGtf
,
AnnotationRefFlat
}
import
nl.lumc.sasc.biopet.utils.Logging
import
nl.lumc.sasc.biopet.utils.config.Config
import
org.broadinstitute.gatk.queue.QScript
import
org.scalatest.Matchers
import
org.scalatest.testng.TestNGSuite
import
org.testng.annotations.Test
/**
* Created by pjvanthof on 18/11/2016.
*/
class
AnnotationTest
extends
TestNGSuite
with
Matchers
{
@Test
def
testAnnotationGtf
:
Unit
=
{
val
s1
=
new
AnnotationTest
.
Script
(
AnnotationTest
.
config
)
with
AnnotationGtf
s1
.
annotationGtf
shouldBe
new
File
(
""
)
an
[
IllegalStateException
]
shouldBe
thrownBy
(
Logging
.
checkErrors
())
val
s2
=
new
AnnotationTest
.
Script
(
AnnotationTest
.
config
++
Map
(
"species"
->
"s1"
,
"reference_name"
->
"g1"
))
with
AnnotationGtf
s2
.
annotationGtf
shouldBe
new
File
(
"no_set.gtf"
)
noException
should
be
thrownBy
(
Logging
.
checkErrors
())
val
s3
=
new
AnnotationTest
.
Script
(
AnnotationTest
.
config
++
Map
(
"species"
->
"s1"
,
"reference_name"
->
"g1"
,
"gene_annotation_name"
->
"set1"
))
with
AnnotationGtf
s3
.
annotationGtf
shouldBe
new
File
(
"set1.gtf"
)
noException
should
be
thrownBy
(
Logging
.
checkErrors
())
}
@Test
def
testAnnotationGff
:
Unit
=
{
val
s1
=
new
AnnotationTest
.
Script
(
AnnotationTest
.
config
)
with
AnnotationGff
s1
.
annotationGff
shouldBe
new
File
(
""
)
an
[
IllegalStateException
]
shouldBe
thrownBy
(
Logging
.
checkErrors
())
val
s2
=
new
AnnotationTest
.
Script
(
AnnotationTest
.
config
++
Map
(
"species"
->
"s1"
,
"reference_name"
->
"g1"
))
with
AnnotationGff
s2
.
annotationGff
shouldBe
new
File
(
"no_set.gff"
)
noException
should
be
thrownBy
(
Logging
.
checkErrors
())
val
s3
=
new
AnnotationTest
.
Script
(
AnnotationTest
.
config
++
Map
(
"species"
->
"s1"
,
"reference_name"
->
"g1"
,
"gene_annotation_name"
->
"set1"
))
with
AnnotationGff
s3
.
annotationGff
shouldBe
new
File
(
"set1.gff"
)
noException
should
be
thrownBy
(
Logging
.
checkErrors
())
}
@Test
def
testAnnotationRefFlat
:
Unit
=
{
val
s1
=
new
AnnotationTest
.
Script
(
AnnotationTest
.
config
)
with
AnnotationRefFlat
s1
.
annotationRefFlat
.
get
shouldBe
new
File
(
""
)
an
[
IllegalStateException
]
shouldBe
thrownBy
(
Logging
.
checkErrors
())
val
s2
=
new
AnnotationTest
.
Script
(
AnnotationTest
.
config
++
Map
(
"species"
->
"s1"
,
"reference_name"
->
"g1"
))
with
AnnotationRefFlat
s2
.
annotationRefFlat
.
get
shouldBe
new
File
(
"no_set.refFlat"
)
noException
should
be
thrownBy
(
Logging
.
checkErrors
())
val
s3
=
new
AnnotationTest
.
Script
(
AnnotationTest
.
config
++
Map
(
"species"
->
"s1"
,
"reference_name"
->
"g1"
,
"gene_annotation_name"
->
"set1"
))
with
AnnotationRefFlat
s3
.
annotationRefFlat
.
get
shouldBe
new
File
(
"set1.refFlat"
)
noException
should
be
thrownBy
(
Logging
.
checkErrors
())
}
}
object
AnnotationTest
{
class
Script
(
c
:
Map
[
String
,
Any
])
extends
QScript
with
BiopetQScript
{
override
def
globalConfig
:
Config
=
new
Config
(
c
)
val
root
=
null
/** Init for pipeline */
def
init
()
:
Unit
=
???
/** Pipeline itself */
def
biopetScript
()
:
Unit
=
???
}
val
config
:
Map
[
String
,
Any
]
=
Map
(
"references"
->
Map
(
"s1"
->
Map
(
"g1"
->
Map
(
"annotation_gtf"
->
"no_set.gtf"
,
"annotation_gff"
->
"no_set.gff"
,
"annotation_refflat"
->
"no_set.refFlat"
,
"gene_annotations"
->
Map
(
"set1"
->
Map
(
"annotation_gtf"
->
"set1.gtf"
,
"annotation_gff"
->
"set1.gff"
,
"annotation_refflat"
->
"set1.refFlat"
))
))))
}
\ No newline at end of file
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