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biopet.biopet
Commits
6f7fe187
Commit
6f7fe187
authored
Jan 15, 2016
by
Peter van 't Hof
Browse files
Adding empty summary test
parent
58369dd0
Changes
2
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public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScriptTest.scala
View file @
6f7fe187
...
...
@@ -5,8 +5,7 @@ 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
import
org.broadinstitute.gatk.queue.QScript
import
org.scalatest.Matchers
import
org.scalatest.testng.TestNGSuite
import
org.testng.annotations.Test
...
...
public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala
0 → 100644
View file @
6f7fe187
package
nl.lumc.sasc.biopet.core.summary
import
java.io.File
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.utils.config.
{
Config
,
Configurable
}
import
nl.lumc.sasc.biopet.utils.summary.Summary
import
org.broadinstitute.gatk.queue.
{
QScript
,
QSettings
}
import
org.broadinstitute.gatk.queue.function.QFunction
import
org.scalatest.Matchers
import
org.scalatest.testng.TestNGSuite
import
WriteSummaryTest._
import
org.testng.annotations.Test
import
scala.io.Source
/**
* Created by pjvanthof on 15/01/16.
*/
class
WriteSummaryTest
extends
TestNGSuite
with
Matchers
{
def
testWrongRoot
:
Unit
=
{
intercept
[
IllegalArgumentException
]
{
makeWriter
(
null
)
}
}
@Test
def
testEmpty
:
Unit
=
{
val
qscript
=
makeQscript
()
val
writer
=
makeWriter
(
qscript
)
writer
.
freezeFieldValues
()
writer
.
run
()
val
summary
=
new
Summary
(
writer
.
out
)
summary
.
getValue
(
"test"
)
should
not
be
None
summary
.
getValue
(
"test"
,
"files"
)
shouldBe
Some
(
Map
(
"pipeline"
->
Map
()))
summary
.
getValue
(
"test"
,
"settings"
)
shouldBe
Some
(
Map
())
summary
.
getValue
(
"test"
,
"executables"
)
shouldBe
Some
(
Map
())
summary
.
getValue
(
"meta"
)
should
not
be
None
summary
.
getValue
(
"meta"
,
"pipeline_name"
)
shouldBe
Some
(
"test"
)
summary
.
getValue
(
"meta"
,
"last_commit_hash"
)
shouldBe
Some
(
nl
.
lumc
.
sasc
.
biopet
.
LastCommitHash
)
summary
.
getValue
(
"meta"
,
"pipeline_version"
)
shouldBe
Some
(
nl
.
lumc
.
sasc
.
biopet
.
Version
)
summary
.
getValue
(
"meta"
,
"output_dir"
)
shouldBe
Some
(
new
File
(
"."
).
getAbsolutePath
)
summary
.
getValue
(
"meta"
,
"summary_creation"
)
should
not
be
None
}
}
object
WriteSummaryTest
{
def
makeWriter
(
root
:
Configurable
,
c
:
Map
[
String
,
Any
]
=
Map
())
=
new
WriteSummary
(
root
)
{
override
def
globalConfig
=
new
Config
(
c
)
override
def
outputs
=
Seq
()
override
def
inputs
=
Seq
()
qSettings
=
new
QSettings
{
jobName
=
"test"
jobTempDir
=
Files
.
createTempDir
()
jobTempDir
.
deleteOnExit
()
jobPriority
=
Some
(
1
)
}
override
def
absoluteCommandDirectory
()
{}
}
def
makeQscript
(
settings
:
Map
[
String
,
Any
]
=
Map
(),
files
:
Map
[
String
,
File
]
=
Map
(),
c
:
Map
[
String
,
Any
]
=
Map
())
=
new
SummaryQScript
with
QScript
{
summaryName
=
"test"
outputDir
=
new
File
(
"."
).
getAbsoluteFile
override
def
globalConfig
=
new
Config
(
c
)
def
summarySettings
:
Map
[
String
,
Any
]
=
settings
def
summaryFiles
:
Map
[
String
,
File
]
=
files
val
tempFile
=
File
.
createTempFile
(
"summary"
,
".json"
)
tempFile
.
deleteOnExit
()
def
summaryFile
:
File
=
tempFile
def
init
()
:
Unit
=
???
def
biopetScript
()
:
Unit
=
???
def
root
:
Configurable
=
null
}
def
makeSummarizable
(
files
:
Map
[
String
,
File
]
=
Map
(),
stats
:
Map
[
String
,
Any
]
=
Map
())
=
new
Summarizable
{
def
summaryFiles
:
Map
[
String
,
File
]
=
files
def
summaryStats
:
Any
=
stats
}
}
\ No newline at end of file
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