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biopet.biopet
Commits
8a5bf774
Commit
8a5bf774
authored
Aug 31, 2015
by
Sander Bollen
Browse files
SummaryToTsvTest
parent
d1bd5949
Changes
6
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Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala
View file @
8a5bf774
...
...
@@ -44,7 +44,7 @@ object SamplesTsvToJson extends ToolCommand {
println
(
jsonString
)
}
def
mapFromFile
(
inputFile
:
File
)
:
Map
[
String
,
Any
]
=
{
def
mapFromFile
(
inputFile
:
File
)
:
Map
[
String
,
Any
]
=
{
val
reader
=
Source
.
fromFile
(
inputFile
)
val
lines
=
reader
.
getLines
().
toList
.
filter
(!
_
.
isEmpty
)
val
header
=
lines
.
head
.
split
(
"\t"
)
...
...
@@ -78,7 +78,7 @@ object SamplesTsvToJson extends ToolCommand {
librariesValues
.
foldLeft
(
Map
[
String
,
Any
]())((
acc
,
kv
)
=>
mergeMaps
(
acc
,
kv
))
}
def
stringFromInputs
(
inputs
:
List
[
File
])
:
String
=
{
def
stringFromInputs
(
inputs
:
List
[
File
])
:
String
=
{
val
map
=
inputs
.
map
(
f
=>
mapFromFile
(
f
)).
foldLeft
(
Map
[
String
,
Any
]())((
acc
,
kv
)
=>
mergeMaps
(
acc
,
kv
))
mapToJson
(
map
).
spaces2
}
...
...
public/biopet-framework/src/test/resources/test.summary.json
0 → 100644
View file @
8a5bf774
{
"samples"
:
{
"016"
:
{
"libraries"
:
{
"L001"
:
{
"flexiprep"
:
{
"settings"
:
{
"skip_trim"
:
false
,
"skip_clip"
:
false
,
"paired"
:
true
}
}
}
}
}
}
}
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/MpileupToVcfTest.scala
View file @
8a5bf774
...
...
@@ -13,7 +13,6 @@ import org.testng.annotations.Test
import
scala.collection.JavaConversions._
/**
* Created by ahbbollen on 27-8-15.
*/
...
...
@@ -52,7 +51,7 @@ class MpileupToVcfTest extends TestNGSuite with MockitoSugar with Matchers {
@Test
def
extraValidateOutVcf
()
=
{
val
tmp
=
File
.
createTempFile
(
"mpileup"
,
".vcf"
)
val
args
=
Array
(
"-I"
,
pileup
,
"--sample"
,
"test"
,
"-o"
,
tmp
.
getAbsolutePath
,
"--minDP"
,
"1"
,
"--minAP"
,
"1"
)
val
args
=
Array
(
"-I"
,
pileup
,
"--sample"
,
"test"
,
"-o"
,
tmp
.
getAbsolutePath
,
"--minDP"
,
"1"
,
"--minAP"
,
"1"
)
main
(
args
)
val
vcfReader
=
new
VCFFileReader
(
tmp
,
false
)
...
...
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/PrefixFastqTest.scala
View file @
8a5bf774
...
...
@@ -11,7 +11,6 @@ import org.testng.annotations.Test
import
scala.collection.JavaConversions._
/**
* Created by ahbbollen on 28-8-15.
*/
...
...
@@ -41,7 +40,7 @@ class PrefixFastqTest extends TestNGSuite with MockitoSugar with Matchers {
val
reader
=
new
FastqReader
(
temp
)
for
(
read
<-
reader
.
iterator
()){
for
(
read
<-
reader
.
iterator
())
{
read
.
getReadString
.
startsWith
(
"AAA"
)
shouldBe
true
}
}
...
...
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJsonTest.scala
View file @
8a5bf774
...
...
@@ -8,7 +8,6 @@ import org.scalatest.mock.MockitoSugar
import
org.scalatest.testng.TestNGSuite
import
org.testng.annotations.Test
/**
* Created by ahbbollen on 28-8-15.
*/
...
...
@@ -28,22 +27,22 @@ class SamplesTsvToJsonTest extends TestNGSuite with MockitoSugar with Matchers {
@Test
def
testNoSampleColumn
()
=
{
val
tsv
=
resourcePath
(
"/no_sample.tsv"
)
val
thrown
=
the
[
IllegalStateException
]
thrownBy
main
(
Array
(
"-i"
,
tsv
))
thrown
.
getMessage
should
equal
(
"Sample column does not exist in: "
+
tsv
)
val
thrown
=
the
[
IllegalStateException
]
thrownBy
main
(
Array
(
"-i"
,
tsv
))
thrown
.
getMessage
should
equal
(
"Sample column does not exist in: "
+
tsv
)
}
@Test
def
testNumberInLibs
=
{
val
tsv
=
resourcePath
(
"/number.tsv"
)
val
thrown
=
the
[
IllegalStateException
]
thrownBy
main
(
Array
(
"-i"
,
tsv
))
thrown
.
getMessage
should
equal
(
"Sample or library may not start with a number"
)
val
thrown
=
the
[
IllegalStateException
]
thrownBy
main
(
Array
(
"-i"
,
tsv
))
thrown
.
getMessage
should
equal
(
"Sample or library may not start with a number"
)
}
@Test
def
testSampleIDs
=
{
val
tsv
=
resourcePath
(
"/same.tsv"
)
val
thrown
=
the
[
IllegalStateException
]
thrownBy
main
(
Array
(
"-i"
,
tsv
))
thrown
.
getMessage
should
equal
(
"Combination of Sample_ID_1 and Lib_ID_1 is found multiple times"
)
val
thrown
=
the
[
IllegalStateException
]
thrownBy
main
(
Array
(
"-i"
,
tsv
))
thrown
.
getMessage
should
equal
(
"Combination of Sample_ID_1 and Lib_ID_1 is found multiple times"
)
}
...
...
@@ -52,7 +51,7 @@ class SamplesTsvToJsonTest extends TestNGSuite with MockitoSugar with Matchers {
val
tsv
=
new
File
(
resourcePath
(
"/sample.tsv"
))
val
json
=
stringFromInputs
(
List
(
tsv
))
json
should
equal
(
json
should
equal
(
"""|{
| "samples" : {
| "Sample_ID_1" : {
...
...
@@ -73,6 +72,4 @@ class SamplesTsvToJsonTest extends TestNGSuite with MockitoSugar with Matchers {
|}"""
.
stripMargin
)
}
}
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala
0 → 100644
View file @
8a5bf774
package
nl.lumc.sasc.biopet.tools
import
java.io.File
import
java.nio.file.Paths
import
nl.lumc.sasc.biopet.tools.SamplesTsvToJson._
import
org.scalatest.Matchers
import
org.scalatest.mock.MockitoSugar
import
org.scalatest.testng.TestNGSuite
import
org.testng.annotations.Test
import
nl.lumc.sasc.biopet.core.summary.Summary
/**
* Created by ahbbollen on 31-8-15.
*/
class
SummaryToTsvTest
extends
TestNGSuite
with
MockitoSugar
with
Matchers
{
import
SummaryToTsv._
private
def
resourcePath
(
p
:
String
)
:
String
=
{
Paths
.
get
(
getClass
.
getResource
(
p
).
toURI
).
toString
}
@Test
def
testMain
=
{
val
tsv
=
resourcePath
(
"/test.summary.json"
)
noException
should
be
thrownBy
main
(
Array
(
"-s"
,
tsv
,
"-p"
,
"something=flexiprep:settings:skip_trim"
,
"-m"
,
"root"
))
noException
should
be
thrownBy
main
(
Array
(
"-s"
,
tsv
,
"-p"
,
"something=flexiprep:settings:skip_trim"
,
"-m"
,
"sample"
))
noException
should
be
thrownBy
main
(
Array
(
"-s"
,
tsv
,
"-p"
,
"something=flexiprep:settings:skip_trim"
,
"-m"
,
"lib"
))
}
@Test
def
testHeader
=
{
val
tsv
=
resourcePath
(
"/test.summary.json"
)
val
path
=
List
(
"something=flexiprep:settings:skip_trim"
)
val
paths
=
path
.
map
(
x
=>
{
val
split
=
x
.
split
(
"="
,
2
)
split
(
0
)
->
split
(
1
).
split
(
":"
)
}).
toMap
createHeader
(
paths
)
should
equal
(
"\tsomething"
)
}
@Test
def
testLine
=
{
val
tsv
=
resourcePath
(
"/test.summary.json"
)
val
path
=
List
(
"something=flexiprep:settings:skip_trim"
)
val
paths
=
path
.
map
(
x
=>
{
val
split
=
x
.
split
(
"="
,
2
)
split
(
0
)
->
split
(
1
).
split
(
":"
)
}).
toMap
val
summary
=
new
Summary
(
new
File
(
tsv
))
val
values
=
fetchValues
(
summary
,
paths
)
val
line
=
values
.
head
.
_2
.
keys
.
map
(
x
=>
createLine
(
paths
,
values
,
x
)).
head
line
should
equal
(
"value\t"
)
val
sample_values
=
fetchValues
(
summary
,
paths
,
true
,
false
)
val
sample_line
=
sample_values
.
head
.
_2
.
keys
.
map
(
x
=>
createLine
(
paths
,
sample_values
,
x
)).
head
sample_line
should
equal
(
"016\t"
)
val
lib_values
=
fetchValues
(
summary
,
paths
,
false
,
true
)
val
lib_line
=
lib_values
.
head
.
_2
.
keys
.
map
(
x
=>
createLine
(
paths
,
lib_values
,
x
)).
head
lib_line
should
equal
(
"016-L001\tfalse"
)
}
}
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