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biopet.biopet
Commits
051ca556
Commit
051ca556
authored
Nov 28, 2016
by
Peter van 't Hof
Browse files
Rename files
parent
168543b0
Changes
1
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Inline
Side-by-side
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala
View file @
051ca556
...
...
@@ -123,6 +123,9 @@ object WriteDependencies extends Logging with Configurable {
"output_used_by_jobs"
->
outputFiles
(
f
).
toList
.
flatMap
(
files
(
_
).
inputJobNames
).
distinct
,
"outputs"
->
outputFiles
(
f
).
toList
,
"inputs"
->
f
.
inputs
.
toList
,
"done_files"
->
f
.
doneOutputs
.
toList
,
"fail_files"
->
f
.
failOutputs
.
toList
,
"stdout_file"
->
f
.
jobOutputFile
,
"done_at_start"
->
f
.
isDone
,
"fail_at_start"
->
f
.
isFail
)
}.
toIterator
.
toMap
...
...
@@ -141,6 +144,7 @@ object WriteDependencies extends Logging with Configurable {
jobsWriter
.
println
(
ConfigUtils
.
mapToJson
(
jobsDeps
).
spaces2
)
jobsWriter
.
close
()
writeGraphvizFile
(
jobsDeps
,
new
File
(
outputDir
,
s
"$prefix.jobs.gv"
))
writeGraphvizFile
(
compressOnType
(
jobsDeps
),
new
File
(
outputDir
,
s
"$prefix.compress.jobs.gv"
))
val
mainJobs
=
jobs
.
filter
(
_
.
_2
(
"main_job"
)
==
true
).
map
{
case
(
name
,
job
)
=>
...
...
@@ -151,6 +155,7 @@ object WriteDependencies extends Logging with Configurable {
mainJobsWriter
.
println
(
ConfigUtils
.
mapToJson
(
mainJobs
).
spaces2
)
mainJobsWriter
.
close
()
writeGraphvizFile
(
mainJobs
,
new
File
(
outputDir
,
s
"$prefix.main_jobs.gv"
))
writeGraphvizFile
(
compressOnType
(
mainJobs
),
new
File
(
outputDir
,
s
"$prefix.compress.main_jobs.gv"
))
logger
.
info
(
"done calculating dependencies"
)
}
...
...
@@ -168,6 +173,18 @@ object WriteDependencies extends Logging with Configurable {
}.
distinct
}
val
numberRegex
=
"""(.*)_(\d*)$"""
.
r
def
compressOnType
(
jobs
:
Map
[
String
,
List
[
String
]])
:
Map
[
String
,
List
[
String
]]
=
{
val
set
=
for
((
job
,
deps
)
<-
jobs
.
toSet
;
dep
<-
deps
)
yield
{
job
match
{
case
numberRegex
(
name
,
number
)
=>
(
name
,
dep
match
{
case
numberRegex
(
name
,
number
)
=>
name
})
}
}
set
.
groupBy
(
_
.
_1
).
map
(
x
=>
x
.
_1
->
x
.
_2
.
map
(
_
.
_2
).
toList
)
}
def
writeGraphvizFile
(
jobs
:
Map
[
String
,
List
[
String
]],
outputFile
:
File
)
:
Unit
=
{
val
writer
=
new
PrintWriter
(
outputFile
)
writer
.
println
(
"digraph graphname {"
)
...
...
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