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biopet.biopet
Commits
d609b6cb
Commit
d609b6cb
authored
Nov 26, 2016
by
Peter van 't Hof
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Added compress method
parent
00e96408
Changes
2
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2 changed files
with
29 additions
and
3 deletions
+29
-3
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+4
-1
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala
...in/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala
+25
-2
No files found.
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
d609b6cb
...
...
@@ -121,7 +121,10 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
}
})
WriteDependencies
.
writeDependencies
(
functions
,
new
File
(
outputDir
,
s
".log/${qSettings.runName}.deps.json"
))
WriteDependencies
.
writeDependencies
(
functions
,
new
File
(
outputDir
,
s
".log/${qSettings.runName}.deps.json"
),
Some
(
new
File
(
outputDir
,
s
".log/${qSettings.runName}.mainJobs.json"
))
)
Logging
.
checkErrors
()
logger
.
info
(
"Script complete without errors"
)
...
...
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala
View file @
d609b6cb
...
...
@@ -49,7 +49,7 @@ object WriteDependencies extends Logging with Configurable {
* @param functions This should be all functions that are given to the graph of Queue
* @param outputFile Json file to write dependencies to
*/
def
writeDependencies
(
functions
:
Seq
[
QFunction
],
outputFile
:
File
)
:
Unit
=
{
def
writeDependencies
(
functions
:
Seq
[
QFunction
],
outputFile
:
File
,
mainJobsFile
:
Option
[
File
]
=
None
)
:
Unit
=
{
logger
.
info
(
"Start calculating dependencies"
)
val
errorOnMissingInput
:
Boolean
=
config
(
"error_on_missing_input"
,
false
)
...
...
@@ -126,14 +126,37 @@ object WriteDependencies extends Logging with Configurable {
"fail_at_start"
->
f
.
isFail
)
}.
toIterator
.
toMap
mainJobsFile
.
foreach
{
file
=>
val
mainJobs
=
jobs
.
filter
(
_
.
_2
(
"main_job"
)
==
true
).
map
{
case
(
name
,
job
)
=>
name
->
(
job
+
(
"depends_on_jobs"
->
getMainDependencies
(
name
,
jobs
)))
}
val
writer
=
new
PrintWriter
(
file
)
writer
.
println
(
ConfigUtils
.
mapToJson
(
mainJobs
).
spaces2
)
writer
.
close
()
}
logger
.
info
(
s
"Writing dependencies to: $outputFile"
)
val
writer
=
new
PrintWriter
(
outputFile
)
writer
.
println
(
ConfigUtils
.
mapToJson
(
Map
(
"jobs"
->
jobs
.
toMap
,
"jobs"
->
jobs
,
"files"
->
files
.
values
.
par
.
map
(
_
.
getMap
).
toList
)).
spaces2
)
writer
.
close
()
logger
.
info
(
"done calculating dependencies"
)
}
def
getMainDependencies
(
jobName
:
String
,
jobsMap
:
Map
[
String
,
Map
[
String
,
Any
]])
:
List
[
String
]
=
{
val
job
=
jobsMap
(
jobName
)
val
dependencies
=
job
(
"depends_on_jobs"
)
match
{
case
l
:
List
[
_
]
=>
l
.
map
(
_
.
toString
)
}
dependencies
.
flatMap
{
dep
=>
jobsMap
(
dep
)(
"main_job"
)
match
{
case
true
=>
List
(
dep
)
case
false
=>
getMainDependencies
(
dep
,
jobsMap
)
}
}
}
}
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