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biopet.biopet
Commits
412df3fe
Commit
412df3fe
authored
Apr 27, 2016
by
Peter van 't Hof
Browse files
Merge remote-tracking branch 'remotes/origin/develop' into feature-queue_licence
parents
49517b11
0232ff00
Changes
2
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biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
View file @
412df3fe
...
...
@@ -202,8 +202,16 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
/** Runs addAndTrackJobs method for each sample */
final
def
addSamplesJobs
()
{
logger
.
info
(
s
"Starting script for ${samples.size} samples"
)
var
count
=
0
if
(
onlySamples
.
isEmpty
||
samples
.
forall
(
x
=>
onlySamples
.
contains
(
x
.
_1
)))
{
samples
.
foreach
{
case
(
sampleId
,
sample
)
=>
sample
.
addAndTrackJobs
()
}
samples
.
foreach
{
case
(
sampleId
,
sample
)
=>
logger
.
info
(
s
"Starting script sample '$sampleId'"
)
sample
.
addAndTrackJobs
()
count
+=
1
logger
.
info
(
s
"Finish script for '$sampleId', samples done: $count / ${samples.size}"
)
}
logger
.
info
(
"Starting script for multisample jobs"
)
addMultiSampleJobs
()
}
else
onlySamples
.
foreach
(
sampleId
=>
samples
.
get
(
sampleId
)
match
{
case
Some
(
sample
)
=>
sample
.
addAndTrackJobs
()
...
...
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Config.scala
View file @
412df3fe
...
...
@@ -91,12 +91,12 @@ class Config(protected var _map: Map[String, Any],
else
_map
=
mergeMaps
(
valueMap
,
_map
)
}
protected
[
config
]
var
notFoundCache
:
Lis
t
[
ConfigValueIndex
]
=
Lis
t
()
protected
[
config
]
var
notFoundCache
:
Se
t
[
ConfigValueIndex
]
=
Se
t
()
protected
[
config
]
var
fixedCache
:
Map
[
ConfigValueIndex
,
ConfigValue
]
=
Map
()
protected
[
config
]
var
foundCache
:
Map
[
ConfigValueIndex
,
ConfigValue
]
=
Map
()
protected
[
config
]
var
defaultCache
:
Map
[
ConfigValueIndex
,
ConfigValue
]
=
Map
()
protected
[
config
]
def
clearCache
()
:
Unit
=
{
notFoundCache
=
Lis
t
()
notFoundCache
=
Se
t
()
foundCache
=
Map
()
defaultCache
=
Map
()
}
...
...
@@ -137,7 +137,7 @@ class Config(protected var _map: Map[String, Any],
foundCache
+=
(
requestedIndex
->
value
.
get
)
true
}
else
{
notFoundCache
+
:
=
requestedIndex
notFoundCache
+=
requestedIndex
false
}
}
...
...
@@ -220,7 +220,7 @@ class Config(protected var _map: Map[String, Any],
val
effectiveFound
=
convertIndexValuesToMap
(
foundCache
.
filter
(!
_
.
_2
.
default
).
toList
.
map
(
x
=>
(
x
.
_2
.
requestIndex
,
x
.
_2
.
value
)),
Some
(
false
))
val
effectiveFixed
=
convertIndexValuesToMap
(
fixedCache
.
filter
(!
_
.
_2
.
default
).
toList
.
map
(
x
=>
(
x
.
_2
.
requestIndex
,
x
.
_2
.
value
)),
Some
(
false
))
val
effectiveDefaultFound
=
convertIndexValuesToMap
(
defaultCache
.
filter
(
_
.
_2
.
default
).
toList
.
map
(
x
=>
(
x
.
_2
.
requestIndex
,
x
.
_2
.
value
)),
Some
(
false
))
val
notFound
=
convertIndexValuesToMap
(
notFoundCache
.
map
((
_
,
None
)),
Some
(
false
))
val
notFound
=
convertIndexValuesToMap
(
notFoundCache
.
toList
.
map
((
_
,
None
)),
Some
(
false
))
// Merged maps
val
fullEffective
=
ConfigUtils
.
mergeMaps
(
effectiveFound
,
effectiveDefaultFound
)
...
...
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