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biopet.biopet
Commits
a327c58d
Commit
a327c58d
authored
Feb 10, 2017
by
Peter van 't Hof
Browse files
Add sampleId and libId for single sample pipelines
parent
b2475ba7
Changes
1
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Inline
Side-by-side
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
View file @
a327c58d
...
...
@@ -56,13 +56,23 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
}
def
init
()
:
Unit
=
{
val
db
=
SummaryDb
.
openSqliteSummary
(
qscript
.
summaryDbFile
)
if
(
qscript
==
root
)
{
// This initialize the database
qscript
match
{
case
s
:
MultiSampleQScript
=>
s
.
initSummaryDb
case
t
:
SampleLibraryTag
=>
t
.
sampleId
.
foreach
{
case
sampleName
=>
val
sampleId
=
Await
.
result
(
db
.
getSamples
(
name
=
Some
(
sampleName
),
runId
=
Some
(
qscript
.
summaryRunId
)).
map
(
_
.
headOption
.
map
(
_
.
id
)),
Duration
.
Inf
).
getOrElse
{
Await
.
result
(
db
.
createSample
(
sampleName
,
qscript
.
summaryRunId
),
Duration
.
Inf
)
}
t
.
libId
.
foreach
{
libName
=>
val
libId
=
Await
.
result
(
db
.
getSamples
(
name
=
Some
(
libName
),
runId
=
Some
(
qscript
.
summaryRunId
),
sampleId
=
Some
(
sampleId
)).
map
(
_
.
headOption
.
map
(
_
.
id
)),
Duration
.
Inf
).
getOrElse
{
Await
.
result
(
db
.
createLibrary
(
libName
,
qscript
.
summaryRunId
,
sampleId
),
Duration
.
Inf
)
}
}
}
case
_
=>
qscript
.
summaryRunId
}
}
val
db
=
SummaryDb
.
openSqliteSummary
(
qscript
.
summaryDbFile
)
val
pipelineId
=
Await
.
result
(
db
.
createPipeline
(
qscript
.
summaryName
,
qscript
.
summaryRunId
),
Duration
.
Inf
)
qscript
.
summarizables
.
map
(
x
=>
Await
.
result
(
db
.
createModule
(
x
.
_1
.
_1
,
qscript
.
summaryRunId
,
pipelineId
),
Duration
.
Inf
))
db
.
close
()
...
...
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