Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
443efddc
Commit
443efddc
authored
Dec 07, 2016
by
Peter van 't Hof
Browse files
Adding some colors
parent
da2d54ee
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/PipelineStatus.scala
View file @
443efddc
...
...
@@ -50,6 +50,13 @@ object PipelineStatus extends ToolCommand {
val
jobs
=
ConfigUtils
.
any2map
(
deps
(
"jobs"
)).
map
(
x
=>
x
.
_1
->
new
Job
(
x
.
_1
,
ConfigUtils
.
any2map
(
x
.
_2
)))
val
jobDone
=
jobsDone
(
jobs
)
val
jobFailed
=
jobsFailed
(
jobs
)
val
jobsRunning
=
jobs
.
filterNot
(
x
=>
jobDone
(
x
.
_1
))
.
filterNot
(
x
=>
jobFailed
(
x
.
_1
))
.
filter
(
_
.
_2
.
stdoutFile
.
exists
()).
map
(
_
.
_1
).
toList
val
jobsDeps
=
jobs
.
map
(
x
=>
x
.
_1
->
(
x
.
_2
.
dependsOnJobs
match
{
case
l
:
List
[
_
]
=>
l
.
map
(
_
.
toString
)
case
_
=>
throw
new
IllegalStateException
(
"Value 'depends_on_jobs' is not a list"
)
...
...
@@ -57,8 +64,8 @@ object PipelineStatus extends ToolCommand {
val
jobsWriter
=
new
PrintWriter
(
new
File
(
outputDir
,
s
"jobs.json"
))
jobsWriter
.
println
(
ConfigUtils
.
mapToJson
(
jobsDeps
).
spaces2
)
jobsWriter
.
close
()
writeGraphvizFile
(
jobsDeps
,
new
File
(
outputDir
,
s
"jobs.gv"
))
writeGraphvizFile
(
compressOnType
(
jobsDeps
),
new
File
(
outputDir
,
s
"compress.jobs.gv"
))
writeGraphvizFile
(
jobsDeps
,
new
File
(
outputDir
,
s
"jobs.gv"
)
,
jobDone
,
jobFailed
,
jobsRunning
,
jobs
)
writeGraphvizFile
(
compressOnType
(
jobsDeps
),
new
File
(
outputDir
,
s
"compress.jobs.gv"
)
,
jobDone
,
jobFailed
,
jobsRunning
,
jobs
)
val
mainJobs
=
jobs
.
filter
(
_
.
_2
.
mainJob
==
true
).
map
{
case
(
name
,
job
)
=>
...
...
@@ -68,8 +75,8 @@ object PipelineStatus extends ToolCommand {
val
mainJobsWriter
=
new
PrintWriter
(
new
File
(
outputDir
,
s
"main_jobs.json"
))
mainJobsWriter
.
println
(
ConfigUtils
.
mapToJson
(
mainJobs
).
spaces2
)
mainJobsWriter
.
close
()
writeGraphvizFile
(
mainJobs
,
new
File
(
outputDir
,
s
"main_jobs.gv"
))
writeGraphvizFile
(
compressOnType
(
mainJobs
),
new
File
(
outputDir
,
s
"compress.main_jobs.gv"
))
writeGraphvizFile
(
mainJobs
,
new
File
(
outputDir
,
s
"main_jobs.gv"
)
,
jobDone
,
jobFailed
,
jobsRunning
,
jobs
)
writeGraphvizFile
(
compressOnType
(
mainJobs
),
new
File
(
outputDir
,
s
"compress.main_jobs.gv"
)
,
jobDone
,
jobFailed
,
jobsRunning
,
jobs
)
//print(jobsDone(jobs).mkString("\n"))
...
...
@@ -100,19 +107,48 @@ object PipelineStatus extends ToolCommand {
set
.
groupBy
(
_
.
_1
).
map
(
x
=>
x
.
_1
->
x
.
_2
.
map
(
_
.
_2
).
toList
)
}
def
writeGraphvizFile
(
jobs
:
Map
[
String
,
List
[
String
]],
outputFile
:
File
)
:
Unit
=
{
def
writeGraphvizFile
(
jobsDeps
:
Map
[
String
,
List
[
String
]],
outputFile
:
File
,
jobDone
:
Map
[
String
,
Boolean
],
jobFailed
:
Map
[
String
,
Boolean
],
jobsRunning
:
List
[
String
],
jobs
:
Map
[
String
,
Job
])
:
Unit
=
{
val
writer
=
new
PrintWriter
(
outputFile
)
writer
.
println
(
"digraph graphname {"
)
jobs
.
foreach
{
case
(
a
,
b
)
=>
b
.
foreach
(
c
=>
writer
.
println
(
s
" $c -> $a;"
))
}
jobDone
.
filter
(
x
=>
jobsDeps
.
contains
(
x
.
_1
))
.
filter
(
_
.
_2
)
.
foreach
(
x
=>
writer
.
println
(
s
" ${x._1} [color = green]"
))
jobFailed
.
filter
(
x
=>
jobsDeps
.
contains
(
x
.
_1
))
.
filter
(
_
.
_2
)
.
foreach
(
x
=>
writer
.
println
(
s
" ${x._1} [color = red]"
))
jobsReadyStart
(
jobs
,
jobDone
)
.
filter
(
jobsDeps
.
contains
)
.
filterNot
(
jobDone
)
.
filterNot
(
jobsRunning
.
contains
)
.
foreach
(
x
=>
writer
.
println
(
s
" $x [color = orange]"
))
jobsRunning
.
filter
(
jobsDeps
.
contains
)
.
foreach
(
x
=>
writer
.
println
(
s
" $x [color = blue]"
))
jobsDeps
.
foreach
{
case
(
a
,
b
)
=>
b
.
foreach
(
c
=>
writer
.
println
(
s
" $c -> $a;"
))
}
writer
.
println
(
"}"
)
writer
.
close
()
}
def
jobsReadyStart
(
jobs
:
Map
[
String
,
Job
],
jobsDone
:
Map
[
String
,
Boolean
])
:
List
[
String
]
=
{
jobs
.
filter
(
_
.
_2
.
dependsOnJobs
.
forall
(
jobsDone
)).
map
(
_
.
_1
).
toList
}
def
jobsDone
(
jobs
:
Map
[
String
,
Job
])
:
Map
[
String
,
Boolean
]
=
{
val
f
=
jobs
.
map
(
x
=>
x
.
_1
->
x
.
_2
.
isDone
)
f
.
map
(
x
=>
x
.
_1
->
Await
.
result
(
x
.
_2
,
Duration
.
Inf
))
}
def
jobsFailed
(
jobs
:
Map
[
String
,
Job
])
:
Map
[
String
,
Boolean
]
=
{
val
f
=
jobs
.
map
(
x
=>
x
.
_1
->
x
.
_2
.
isFailed
)
f
.
map
(
x
=>
x
.
_1
->
Await
.
result
(
x
.
_2
,
Duration
.
Inf
))
}
class
Job
(
val
name
:
String
,
map
:
Map
[
String
,
Any
])
{
def
doneAtStart
:
Boolean
=
ConfigUtils
.
any2boolean
(
map
(
"done_at_start"
))
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment