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biopet.biopet
Commits
211bcfda
Commit
211bcfda
authored
Nov 27, 2016
by
Peter van 't Hof
Browse files
Adding dot files to log folder
parent
40b3b42d
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala
View file @
211bcfda
...
...
@@ -39,7 +39,7 @@ object WriteDependencies extends Logging with Configurable {
case
f
=>
f
.
getClass
.
getSimpleName
}
cache
+=
baseName
->
(
cache
.
getOrElse
(
baseName
,
0
)
+
1
)
function
->
s
"$baseName
-
${cache(baseName)}"
function
->
s
"$
{
baseName
.replaceAll("
-
", "
_
")}_
${cache(baseName)}"
}).
toMap
}
...
...
@@ -115,7 +115,7 @@ object WriteDependencies extends Logging with Configurable {
case
_
=>
None
}),
"main_job"
->
(
f
match
{
case
cmd
:
BiopetCommandLineFunction
=>
cmd
.
mainFunction
case
_
:
WriteSummary
=>
true
case
s
:
WriteSummary
if
s.qscript.root
=
=
null
=>
true
case
_
=>
false
}),
"intermediate"
->
f
.
isIntermediate
,
"depends_on_intermediate"
->
f
.
inputs
.
exists
(
files
(
_
).
isIntermediate
),
...
...
@@ -136,10 +136,11 @@ object WriteDependencies extends Logging with Configurable {
)).
spaces2
)
writer
.
close
()
val
jobsDeps
=
jobs
.
map
(
x
=>
x
.
_1
->
(
x
.
_2
(
"depends_on_jobs"
)))
val
jobsDeps
=
jobs
.
map
(
x
=>
x
.
_1
->
(
x
.
_2
(
"depends_on_jobs"
)
.
asInstanceOf
[
List
[
String
]]
))
val
jobsWriter
=
new
PrintWriter
(
new
File
(
outputDir
,
s
"$prefix.jobs.json"
))
jobsWriter
.
println
(
ConfigUtils
.
mapToJson
(
jobsDeps
).
spaces2
)
jobsWriter
.
close
()
writeDotFile
(
jobsDeps
,
new
File
(
outputDir
,
s
"$prefix.jobs.dot"
))
val
mainJobs
=
jobs
.
filter
(
_
.
_2
(
"main_job"
)
==
true
).
map
{
case
(
name
,
job
)
=>
...
...
@@ -149,6 +150,7 @@ object WriteDependencies extends Logging with Configurable {
val
mainJobsWriter
=
new
PrintWriter
(
new
File
(
outputDir
,
s
"$prefix.main_jobs.json"
))
mainJobsWriter
.
println
(
ConfigUtils
.
mapToJson
(
mainJobs
).
spaces2
)
mainJobsWriter
.
close
()
writeDotFile
(
mainJobs
,
new
File
(
outputDir
,
s
"$prefix.main_jobs.dot"
))
logger
.
info
(
"done calculating dependencies"
)
}
...
...
@@ -165,4 +167,12 @@ object WriteDependencies extends Logging with Configurable {
}
}.
distinct
}
def
writeDotFile
(
jobs
:
Map
[
String
,
List
[
String
]],
outputFile
:
File
)
:
Unit
=
{
val
writer
=
new
PrintWriter
(
outputFile
)
writer
.
println
(
"digraph graphname {"
)
jobs
.
foreach
{
case
(
a
,
b
)
=>
b
.
foreach
(
c
=>
writer
.
println
(
s
" $c -> $a;"
))}
writer
.
println
(
"}"
)
writer
.
close
()
}
}
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