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biopet.biopet
Commits
17328f96
Commit
17328f96
authored
Mar 07, 2017
by
Peter van 't Hof
Browse files
Adding pipe executables again
parent
d76d8c9c
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
View file @
17328f96
...
...
@@ -166,15 +166,21 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
db
.
createOrUpdateSetting
(
qscript
.
summaryRunId
,
pipelineId
,
None
,
None
,
None
,
ConfigUtils
.
mapToJson
(
q
.
summarySettings
).
nospaces
)
}
(
for
(
f
<-
qscript
.
functions
.
par
)
yield
f
match
{
case
f
:
BiopetJavaCommandLineFunction
with
Version
=>
Some
(
db
.
createOrUpdateExecutable
(
qscript
.
summaryRunId
,
f
.
configNamespace
,
f
.
getVersion
,
f
.
getJavaVersion
,
javaMd5
=
BiopetCommandLineFunction
.
executableMd5Cache
.
get
(
f
.
executable
),
jarPath
=
Option
(
f
.
jarFile
).
map
(
_
.
getAbsolutePath
)))
case
f
:
BiopetCommandLineFunction
with
Version
=>
Some
(
db
.
createOrUpdateExecutable
(
qscript
.
summaryRunId
,
f
.
configNamespace
,
f
.
getVersion
,
Option
(
f
.
executable
)))
case
f
:
Configurable
with
Version
=>
Some
(
db
.
createOrUpdateExecutable
(
qscript
.
summaryRunId
,
f
.
configNamespace
,
f
.
getVersion
))
case
_
=>
None
val
pipeFunctions
=
(
for
(
f
<-
qscript
.
functions
)
yield
f
match
{
case
f
:
BiopetCommandLineFunction
=>
f
.
pipesJobs
case
_
=>
Nil
}).
flatten
(
for
(
f
<-
qscript
.
functions
++
pipeFunctions
)
yield
{
f
match
{
case
f
:
BiopetJavaCommandLineFunction
with
Version
=>
List
(
db
.
createOrUpdateExecutable
(
qscript
.
summaryRunId
,
f
.
configNamespace
,
f
.
getVersion
,
f
.
getJavaVersion
,
javaMd5
=
BiopetCommandLineFunction
.
executableMd5Cache
.
get
(
f
.
executable
),
jarPath
=
Option
(
f
.
jarFile
).
map
(
_
.
getAbsolutePath
)))
case
f
:
BiopetCommandLineFunction
with
Version
=>
List
(
db
.
createOrUpdateExecutable
(
qscript
.
summaryRunId
,
f
.
configNamespace
,
f
.
getVersion
,
Option
(
f
.
executable
)))
case
f
:
Configurable
with
Version
=>
List
(
db
.
createOrUpdateExecutable
(
qscript
.
summaryRunId
,
f
.
configNamespace
,
f
.
getVersion
))
case
_
=>
List
()
}
}).
flatten
.
foreach
(
Await
.
ready
(
_
,
Duration
.
Inf
))
}
...
...
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