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biopet.biopet
Commits
21da59ab
Commit
21da59ab
authored
Jan 10, 2017
by
Peter van 't Hof
Browse files
Adding test for PipelineStatus
parent
e01e6050
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/PipelineStatusTest.scala
0 → 100644
View file @
21da59ab
package
nl.lumc.sasc.biopet.core
import
java.io.
{
File
,
PrintWriter
}
import
com.google.common.io.Files
import
org.scalatest.Matchers
import
org.scalatest.testng.TestNGSuite
import
org.testng.annotations.Test
/**
* Created by pjvan_thof on 10-1-17.
*/
class
PipelineStatusTest
extends
TestNGSuite
with
Matchers
{
@Test
def
testDefault
:
Unit
=
{
val
outputDir
=
Files
.
createTempDir
()
outputDir
.
deleteOnExit
()
PipelineStatusTest
.
writeDeps
(
outputDir
)
PipelineStatus
.
main
(
Array
(
"-o"
,
outputDir
.
toString
,
"-d"
,
outputDir
.
toString
))
}
@Test
def
testDepsFileArg
:
Unit
=
{
val
outputDir
=
Files
.
createTempDir
()
outputDir
.
deleteOnExit
()
val
depsfile
=
PipelineStatusTest
.
writeDeps
(
outputDir
)
PipelineStatus
.
main
(
Array
(
"-o"
,
outputDir
.
toString
,
"-d"
,
outputDir
.
toString
,
"--depsFile"
,
depsfile
.
toString
))
}
}
object
PipelineStatusTest
{
def
writeDeps
(
outputDir
:
File
)
:
File
=
{
require
(
outputDir
.
exists
())
val
depsFile
=
new
File
(
outputDir
,
".log/test.1234567890/graph/deps.json"
)
depsFile
.
getParentFile
.
mkdirs
()
val
writer
=
new
PrintWriter
(
depsFile
)
writer
.
println
(
defaultDeps
(
outputDir
))
writer
.
close
()
depsFile
}
def
defaultDeps
(
outputDir
:
File
)
=
s
"""
|{
| "jobs" : {
| "gzip_1" : {
| "fail_files" : [
| "$outputDir/.file.out.gz.fail",
| "$outputDir/..file.out.gz.Gzip.out.fail"
| ],
| "done_at_start" : false,
| "output_used_by_jobs" : [
|
| ],
| "outputs" : [
| "$outputDir/file.out.gz",
| "$outputDir/.file.out.gz.Gzip.out"
| ],
| "command" : "\n\n '/bin/gzip' -c '$outputDir/file.out' > '$outputDir/file.out.gz' ",
| "stdout_file" : "$outputDir/.file.out.gz.Gzip.out",
| "depends_on_intermediate" : false,
| "fail_at_start" : false,
| "inputs" : [
| "$outputDir/file.out"
| ],
| "depends_on_jobs" : [
| "cat_1"
| ],
| "intermediate" : false,
| "done_files" : [
| "$outputDir/.file.out.gz.done",
| "$outputDir/..file.out.gz.Gzip.out.done"
| ],
| "main_job" : true
| },
| "cat_1" : {
| "fail_files" : [
| "$outputDir/.file.out.fail",
| "$outputDir/..file.out.Cat.out.fail"
| ],
| "done_at_start" : false,
| "output_used_by_jobs" : [
| "gzip_1"
| ],
| "outputs" : [
| "$outputDir/file.out",
| "$outputDir/.file.out.Cat.out"
| ],
| "command" : "\n\n '/bin/cat' 'test.deps' > '$outputDir/file.out' ",
| "stdout_file" : "$outputDir/.file.out.Cat.out",
| "depends_on_intermediate" : false,
| "fail_at_start" : false,
| "inputs" : [
| "test.deps"
| ],
| "depends_on_jobs" : [
|
| ],
| "intermediate" : false,
| "done_files" : [
| "$outputDir/.file.out.done",
| "$outputDir/..file.out.Cat.out.done"
| ],
| "main_job" : true
| }
| },
| "files" : [
| {
| "output_jobs" : [
| "cat_1"
| ],
| "path" : "$outputDir/file.out",
| "input_jobs" : [
| "gzip_1"
| ],
| "exists_at_start" : false,
| "pipeline_input" : false,
| "intermediate" : false
| },
| {
| "output_jobs" : [
| "gzip_1"
| ],
| "path" : "$outputDir/.file.out.gz.Gzip.out",
| "input_jobs" : [
|
| ],
| "exists_at_start" : false,
| "pipeline_input" : false,
| "intermediate" : false
| },
| {
| "output_jobs" : [
| "gzip_1"
| ],
| "path" : "$outputDir/file.out.gz",
| "input_jobs" : [
|
| ],
| "exists_at_start" : false,
| "pipeline_input" : false,
| "intermediate" : false
| },
| {
| "output_jobs" : [
|
| ],
| "path" : "$outputDir/test.deps",
| "input_jobs" : [
| "cat_1"
| ],
| "exists_at_start" : false,
| "pipeline_input" : true,
| "intermediate" : false
| },
| {
| "output_jobs" : [
| "cat_1"
| ],
| "path" : "$outputDir/.file.out.Cat.out",
| "input_jobs" : [
|
| ],
| "exists_at_start" : false,
| "pipeline_input" : false,
| "intermediate" : false
| }
| ]
|}
"""
.
stripMargin
}
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