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biopet.biopet
Commits
49a89abd
Commit
49a89abd
authored
Jan 10, 2017
by
Peter van 't Hof
Browse files
Testing intermediates
parent
e687d703
Changes
2
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Inline
Side-by-side
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/PipelineStatus.scala
View file @
49a89abd
...
...
@@ -151,7 +151,7 @@ object PipelineStatus extends ToolCommand {
(
compressedName
(
job
).
_1
,
compressedName
(
dep
).
_1
)
}
// This will collapse a Set[(String, String)] to a Map[String, List[String]]
set
.
groupBy
(
_
.
_1
).
map
(
x
=>
x
.
_1
->
x
.
_2
.
map
(
_
.
_2
).
toList
)
set
.
groupBy
(
_
.
_1
).
map
(
x
=>
x
.
_1
->
x
.
_2
.
map
(
_
.
_2
).
toList
)
++
jobs
.
filter
(
_
.
_2
.
isEmpty
).
map
(
job
=>
compressedName
(
job
.
_1
).
_1
->
Nil
)
}
def
compressedName
(
jobName
:
String
)
=
jobName
match
{
...
...
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/PipelineStatusTest.scala
View file @
49a89abd
...
...
@@ -50,21 +50,33 @@ class PipelineStatusTest extends TestNGSuite with Matchers {
require
(
jobsGvLines
.
exists
(
_
.
contains
(
"cat_1 -> gzip_1"
)))
require
(
jobsGvLines
.
exists
(
_
.
contains
(
"gzip_1 -> zcat_1"
)))
require
(
jobsGvLines
.
forall
(!
_
.
contains
(
"cat_1 -> zcat_1"
)))
require
(
jobsGvLines
.
exists
(
_
.
contains
(
"cat_1 [style = dashed]"
)))
require
(
jobsGvLines
.
forall
(!
_
.
contains
(
"gzip_1 [style = dashed]"
)))
require
(
jobsGvLines
.
forall
(!
_
.
contains
(
"zcat_1 [style = dashed]"
)))
val
mainJobsGvLines
=
getLinesFromFile
(
mainJobsGvFile
)
require
(
mainJobsGvLines
.
exists
(
_
.
contains
(
"cat_1 -> zcat_1"
)))
require
(
mainJobsGvLines
.
forall
(!
_
.
contains
(
"cat_1 -> gzip_1"
)))
require
(
mainJobsGvLines
.
forall
(!
_
.
contains
(
"gzip_1 -> zcat_1"
)))
require
(
mainJobsGvLines
.
exists
(
_
.
contains
(
"cat_1 [style = dashed]"
)))
require
(
mainJobsGvLines
.
forall
(!
_
.
contains
(
"gzip_1 [style = dashed]"
)))
require
(
mainJobsGvLines
.
forall
(!
_
.
contains
(
"zcat_1 [style = dashed]"
)))
val
compressJobsGvLines
=
getLinesFromFile
(
compressJobsGvFile
)
require
(
compressJobsGvLines
.
exists
(
_
.
contains
(
"cat -> gzip"
)))
require
(
compressJobsGvLines
.
exists
(
_
.
contains
(
"gzip -> zcat"
)))
require
(
compressJobsGvLines
.
forall
(!
_
.
contains
(
"cat -> zcat"
)))
require
(
compressJobsGvLines
.
exists
(
_
.
contains
(
"cat [style = dashed]"
)))
require
(
compressJobsGvLines
.
forall
(!
_
.
contains
(
"gzip [style = dashed]"
)))
require
(
compressJobsGvLines
.
forall
(!
_
.
contains
(
"zcat [style = dashed]"
)))
val
compressMainJobsGvLines
=
getLinesFromFile
(
compressMainJobsGvFile
)
require
(
compressMainJobsGvLines
.
exists
(
_
.
contains
(
"cat -> zcat"
)))
require
(
compressMainJobsGvLines
.
forall
(!
_
.
contains
(
"cat -> gzip"
)))
require
(
compressMainJobsGvLines
.
forall
(!
_
.
contains
(
"gzip -> zcat"
)))
require
(
compressMainJobsGvLines
.
exists
(
_
.
contains
(
"cat [style = dashed]"
)))
require
(
compressMainJobsGvLines
.
forall
(!
_
.
contains
(
"gzip [style = dashed]"
)))
require
(
compressMainJobsGvLines
.
forall
(!
_
.
contains
(
"zcat [style = dashed]"
)))
}
...
...
@@ -143,7 +155,7 @@ object PipelineStatusTest {
| "depends_on_jobs" : [
| "cat_1"
| ],
| "intermediate" :
tru
e,
| "intermediate" :
fals
e,
| "done_files" : [
| "$outputDir/.file.out.gz.done",
| "$outputDir/..file.out.gz.Gzip.out.done"
...
...
@@ -173,7 +185,7 @@ object PipelineStatusTest {
| "depends_on_jobs" : [
|
| ],
| "intermediate" :
fals
e,
| "intermediate" :
tru
e,
| "done_files" : [
| "$outputDir/.file.out.done",
| "$outputDir/..file.out.Cat.out.done"
...
...
@@ -192,7 +204,7 @@ object PipelineStatusTest {
| ],
| "exists_at_start" : false,
| "pipeline_input" : false,
| "intermediate" :
fals
e
| "intermediate" :
tru
e
| },
| {
| "output_jobs" : [
...
...
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