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biopet.biopet
Commits
684fe7c8
Commit
684fe7c8
authored
Jan 14, 2016
by
Peter van 't Hof
Browse files
Adding tests for input files for summary
parent
645895a0
Changes
2
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Inline
Side-by-side
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
View file @
684fe7c8
...
...
@@ -184,6 +184,7 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
map
.
toMap
}
}
object
WriteSummary
{
/** Retrive checksum from file */
def
parseChecksum
(
checksumFile
:
File
)
:
String
=
{
...
...
public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScriptTest.scala
View file @
684fe7c8
...
...
@@ -2,6 +2,8 @@ package nl.lumc.sasc.biopet.core.summary
import
java.io.File
import
nl.lumc.sasc.biopet.core.BiopetQScript.InputFile
import
nl.lumc.sasc.biopet.core.extensions.Md5sum
import
nl.lumc.sasc.biopet.utils.config.
{
Config
,
Configurable
}
import
org.broadinstitute.gatk.queue.
{
QScript
,
QSettings
}
import
org.broadinstitute.gatk.queue.function.QFunction
...
...
@@ -32,6 +34,10 @@ class SummaryQScriptTest extends TestNGSuite with Matchers {
SummaryQScript
.
md5sumCache
.
toMap
shouldBe
Map
(
new
File
(
s
".${File.separator}bla"
)
->
new
File
(
s
".${File.separator}bla.md5"
))
script
.
functions
.
size
shouldBe
2
assert
(
script
.
functions
.
filter
(
_
.
isInstanceOf
[
Md5sum
])
.
map
(
_
.
asInstanceOf
[
Md5sum
])
.
exists
(
_
.
cmdLine
.
contains
(
" || "
)))
}
@Test
...
...
@@ -44,6 +50,10 @@ class SummaryQScriptTest extends TestNGSuite with Matchers {
SummaryQScript
.
md5sumCache
.
toMap
shouldBe
Map
(
new
File
(
s
".${File.separator}bla"
)
->
new
File
(
s
".${File.separator}bla.md5"
))
script
.
functions
.
size
shouldBe
2
assert
(
script
.
functions
.
filter
(
_
.
isInstanceOf
[
Md5sum
])
.
map
(
_
.
asInstanceOf
[
Md5sum
])
.
exists
(
_
.
cmdLine
.
contains
(
" || "
)))
}
@Test
...
...
@@ -58,9 +68,39 @@ class SummaryQScriptTest extends TestNGSuite with Matchers {
SummaryQScript
.
md5sumCache
.
toMap
shouldBe
Map
(
new
File
(
s
".${File.separator}bla"
)
->
new
File
(
s
".${File.separator}bla.md5"
))
script
.
functions
.
size
shouldBe
2
assert
(
script
.
functions
.
filter
(
_
.
isInstanceOf
[
Md5sum
])
.
map
(
_
.
asInstanceOf
[
Md5sum
])
.
exists
(
_
.
cmdLine
.
contains
(
" || "
)))
}
@Test
def
testInputFile
:
Unit
=
{
SummaryQScript
.
md5sumCache
.
clear
()
val
file
=
new
File
(
s
".${File.separator}bla"
)
val
script
=
makeQscript
()
script
.
addSummarizable
(
makeSummarizable
(
files
=
Map
(
"file"
->
file
,
"file2"
->
file
)),
"test"
)
script
.
summarizables
.
size
shouldBe
1
script
.
inputFiles
:+=
InputFile
(
file
,
Some
(
"md5sum"
))
script
.
inputFiles
:+=
InputFile
(
file
,
None
)
script
.
addSummaryJobs
()
SummaryQScript
.
md5sumCache
should
not
be
empty
SummaryQScript
.
md5sumCache
.
toMap
shouldBe
Map
(
new
File
(
s
".${File.separator}bla"
)
->
new
File
(
s
".${File.separator}bla.md5"
))
script
.
functions
.
size
shouldBe
3
assert
(
script
.
functions
.
filter
(
_
.
isInstanceOf
[
Md5sum
])
.
map
(
_
.
asInstanceOf
[
Md5sum
])
.
exists
(
_
.
cmdLine
.
contains
(
" || "
)))
}
@Test
def
testAddQscript
:
Unit
=
{
SummaryQScript
.
md5sumCache
.
clear
()
val
script
=
makeQscript
()
script
.
addSummaryQScript
(
script
)
script
.
summaryQScripts
.
head
shouldBe
script
}
}
object
SummaryQScriptTest
{
...
...
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