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biopet.biopet
Commits
8427c6a6
Commit
8427c6a6
authored
Dec 10, 2015
by
Peter van 't Hof
Browse files
Fixed unit testing
parent
d03a8edd
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala
View file @
8427c6a6
...
...
@@ -58,14 +58,13 @@ class GearsSingleTest(val testset: String) extends TestNGSuite with Matchers {
for
(
fromBam
<-
startFromBam
;
pair
<-
paired
;
hasOutputName
<-
hasOutputNames
;
hasFileExtension
<-
hasFileExtensions
)
yield
Array
(
testset
,
fromBam
,
pair
,
hasOutputName
,
hasFileExtension
)
hasOutputName
<-
hasOutputNames
)
yield
Array
(
testset
,
fromBam
,
pair
,
hasOutputName
)
}
@Test
(
dataProvider
=
"gearsOptions"
)
def
testGears
(
testset
:
String
,
fromBam
:
Boolean
,
paired
:
Boolean
,
hasOutputName
:
Boolean
,
hasFileExtension
:
Boolean
)
=
{
hasOutputName
:
Boolean
)
=
{
val
map
=
ConfigUtils
.
mergeMaps
(
Map
(
"output_dir"
->
GearsSingleTest
.
outputDir
),
Map
(
GearsSingleTest
.
executables
.
toSeq
:
_
*
))
...
...
@@ -73,10 +72,10 @@ class GearsSingleTest(val testset: String) extends TestNGSuite with Matchers {
val
gears
:
GearsSingle
=
initPipeline
(
map
)
if
(
fromBam
)
{
gears
.
bamFile
=
if
(
hasFileExtension
)
Some
(
GearsSingleTest
.
bam
)
else
Some
(
GearsSingleTest
.
bam_noext
)
gears
.
bamFile
=
Some
(
GearsSingleTest
.
bam
)
}
else
{
gears
.
fastqR1
=
if
(
hasFileExtension
)
Some
(
GearsSingleTest
.
r1
)
else
Some
(
GearsSingleTest
.
r1_noext
)
gears
.
fastqR2
=
if
(
paired
)
if
(
hasFileExtension
)
Some
(
GearsSingleTest
.
r2
)
else
Some
(
GearsSingleTest
.
r2_noext
)
else
None
gears
.
fastqR1
=
Some
(
GearsSingleTest
.
r1
)
gears
.
fastqR2
=
if
(
paired
)
Some
(
GearsSingleTest
.
r2
)
else
None
}
if
(
hasOutputName
)
gears
.
outputName
=
"test"
...
...
@@ -87,12 +86,7 @@ class GearsSingleTest(val testset: String) extends TestNGSuite with Matchers {
gears
.
outputName
shouldBe
"test"
}
else
{
// in the following cases the filename should have been determined by the filename
if
(
hasFileExtension
)
{
gears
.
outputName
shouldBe
(
if
(
fromBam
)
"bamfile"
else
"R1"
)
}
else
{
// no real use-case for this one, have this is for sanity check
gears
.
outputName
shouldBe
(
if
(
fromBam
)
"bamfile"
else
"R1"
)
}
gears
.
outputName
shouldBe
(
if
(
fromBam
)
"bamfile"
else
"R1"
)
}
// SamToFastq should have started if it was started from bam
...
...
@@ -121,17 +115,11 @@ object GearsSingleTest {
val
bam
=
new
File
(
outputDir
,
"input"
+
File
.
separator
+
"bamfile.bam"
)
Files
.
touch
(
bam
)
val
r1_noext
=
new
File
(
outputDir
,
"input"
+
File
.
separator
+
"R1"
)
Files
.
touch
(
r1_noext
)
val
r2_noext
=
new
File
(
outputDir
,
"input"
+
File
.
separator
+
"R2"
)
Files
.
touch
(
r2_noext
)
val
bam_noext
=
new
File
(
outputDir
,
"input"
+
File
.
separator
+
"bamfile"
)
Files
.
touch
(
bam_noext
)
val
executables
=
Map
(
"kraken"
->
Map
(
"exe"
->
"test"
,
"db"
->
"test"
),
"krakenreport"
->
Map
(
"exe"
->
"test"
,
"db"
->
"test"
),
"sambamba"
->
Map
(
"exe"
->
"test"
),
"samtools"
->
Map
(
"exe"
->
"test"
),
"md5sum"
->
Map
(
"exe"
->
"test"
)
)
}
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