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biopet.biopet
Commits
96367c05
Commit
96367c05
authored
Dec 09, 2016
by
Peter van 't Hof
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Only compress plots by default
parent
ab606fff
Changes
1
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1 changed file
with
17 additions
and
11 deletions
+17
-11
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/PipelineStatus.scala
.../main/scala/nl/lumc/sasc/biopet/core/PipelineStatus.scala
+17
-11
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biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/PipelineStatus.scala
View file @
96367c05
...
...
@@ -18,7 +18,8 @@ object PipelineStatus extends ToolCommand {
outputDir
:
File
=
null
,
follow
:
Boolean
=
false
,
refreshTime
:
Int
=
30
,
plots
:
Boolean
=
true
)
extends
AbstractArgs
complate_plots
:
Boolean
=
false
,
compressPlots
:
Boolean
=
true
)
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
opt
[
File
](
'd'
,
"pipelineDir"
)
required
()
maxOccurs
1
valueName
"<file>"
action
{
(
x
,
c
)
=>
...
...
@@ -36,9 +37,12 @@ object PipelineStatus extends ToolCommand {
opt
[
Int
](
"refresh"
)
maxOccurs
1
action
{
(
x
,
c
)
=>
c
.
copy
(
refreshTime
=
x
)
}
text
"Time to check again, default set on 30 seconds"
opt
[
Unit
](
"skipPlots"
)
maxOccurs
1
action
{
(
x
,
c
)
=>
c
.
copy
(
plots
=
false
)
}
text
"This will follow a run"
opt
[
Unit
](
"complete_plots"
)
maxOccurs
1
action
{
(
x
,
c
)
=>
c
.
copy
(
complate_plots
=
true
)
}
text
"Add complete plots, this is disabled because of preformence"
opt
[
Unit
](
"skipCompressPlots"
)
maxOccurs
1
action
{
(
x
,
c
)
=>
c
.
copy
(
compressPlots
=
false
)
}
text
"Disable default plots"
}
def
main
(
args
:
Array
[
String
])
:
Unit
=
{
...
...
@@ -49,7 +53,8 @@ object PipelineStatus extends ToolCommand {
val
depsFile
=
cmdArgs
.
depsFile
.
getOrElse
(
getDepsFileFromDir
(
cmdArgs
.
pipelineDir
))
val
deps
=
readDepsFile
(
depsFile
)
writePipelineStatus
(
deps
,
cmdArgs
.
outputDir
,
follow
=
cmdArgs
.
follow
,
refreshTime
=
cmdArgs
.
refreshTime
,
plots
=
cmdArgs
.
plots
)
writePipelineStatus
(
deps
,
cmdArgs
.
outputDir
,
follow
=
cmdArgs
.
follow
,
refreshTime
=
cmdArgs
.
refreshTime
,
plots
=
cmdArgs
.
complate_plots
,
compressPlots
=
cmdArgs
.
compressPlots
)
logger
.
info
(
"Done"
)
}
...
...
@@ -80,7 +85,8 @@ object PipelineStatus extends ToolCommand {
alreadyFailed
:
Set
[
String
]
=
Set
(),
follow
:
Boolean
=
false
,
refreshTime
:
Int
=
30
,
plots
:
Boolean
=
true
)
:
Unit
=
{
plots
:
Boolean
=
false
,
compressPlots
:
Boolean
=
true
)
:
Unit
=
{
val
jobDone
=
jobsDone
(
deps
)
val
jobFailed
=
jobsFailed
(
deps
,
jobDone
)
...
...
@@ -95,8 +101,8 @@ object PipelineStatus extends ToolCommand {
val
jobsWriter
=
new
PrintWriter
(
new
File
(
outputDir
,
s
"jobs.json"
))
jobsWriter
.
println
(
ConfigUtils
.
mapToJson
(
jobsDeps
).
spaces2
)
jobsWriter
.
close
()
futures
:+=
writeGraphvizFile
(
jobsDeps
,
new
File
(
outputDir
,
s
"jobs.gv"
),
jobDone
,
jobFailed
,
jobsStart
,
deps
,
plots
)
futures
:+=
writeGraphvizFile
(
compressOnType
(
jobsDeps
),
new
File
(
outputDir
,
s
"compress.jobs.gv"
),
jobDone
,
jobFailed
,
jobsStart
,
deps
,
p
lots
)
futures
:+=
writeGraphvizFile
(
jobsDeps
,
new
File
(
outputDir
,
s
"jobs.gv"
),
jobDone
,
jobFailed
,
jobsStart
,
deps
,
plots
,
plots
)
futures
:+=
writeGraphvizFile
(
compressOnType
(
jobsDeps
),
new
File
(
outputDir
,
s
"compress.jobs.gv"
),
jobDone
,
jobFailed
,
jobsStart
,
deps
,
compressPlots
,
compressP
lots
)
val
mainJobs
=
deps
.
jobs
.
filter
(
_
.
_2
.
mainJob
==
true
).
map
{
case
(
name
,
job
)
=>
...
...
@@ -106,8 +112,8 @@ object PipelineStatus extends ToolCommand {
val
mainJobsWriter
=
new
PrintWriter
(
new
File
(
outputDir
,
s
"main_jobs.json"
))
mainJobsWriter
.
println
(
ConfigUtils
.
mapToJson
(
mainJobs
).
spaces2
)
mainJobsWriter
.
close
()
futures
:+=
writeGraphvizFile
(
mainJobs
,
new
File
(
outputDir
,
s
"main_jobs.gv"
),
jobDone
,
jobFailed
,
jobsStart
,
deps
,
plots
)
futures
:+=
writeGraphvizFile
(
compressOnType
(
mainJobs
),
new
File
(
outputDir
,
s
"compress.main_jobs.gv"
),
jobDone
,
jobFailed
,
jobsStart
,
deps
,
p
lots
)
futures
:+=
writeGraphvizFile
(
mainJobs
,
new
File
(
outputDir
,
s
"main_jobs.gv"
),
jobDone
,
jobFailed
,
jobsStart
,
deps
,
plots
,
plots
)
futures
:+=
writeGraphvizFile
(
compressOnType
(
mainJobs
),
new
File
(
outputDir
,
s
"compress.main_jobs.gv"
),
jobDone
,
jobFailed
,
jobsStart
,
deps
,
compressPlots
,
compressP
lots
)
val
totalJobs
=
deps
.
jobs
.
size
val
totalStart
=
jobsStart
.
size
...
...
@@ -156,7 +162,7 @@ object PipelineStatus extends ToolCommand {
jobFailed
:
Set
[
String
],
jobsStart
:
Set
[
String
],
deps
:
Deps
,
png
:
Boolean
=
true
,
svg
:
Boolean
=
fals
e
)
:
Future
[
Unit
]
=
Future
{
png
:
Boolean
=
true
,
svg
:
Boolean
=
tru
e
)
:
Future
[
Unit
]
=
Future
{
val
writer
=
new
PrintWriter
(
outputFile
)
writer
.
println
(
"digraph graphname {"
)
jobDone
...
...
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