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biopet.biopet
Commits
7eab836c
Commit
7eab836c
authored
Feb 15, 2017
by
Peter van 't Hof
Browse files
Colapse all summaries into 1 connector
parent
1cf01f63
Changes
4
Hide whitespace changes
Inline
Side-by-side
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
View file @
7eab836c
...
...
@@ -272,7 +272,6 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
if
(!
libNamesOld
.
contains
(
libName
))
Await
.
result
(
db
.
createLibrary
(
libName
,
summaryRunId
,
sampleId
,
libraryTags
),
Duration
.
Inf
)
}
}
db
.
close
()
}
}
...
...
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
View file @
7eab836c
...
...
@@ -20,6 +20,8 @@ import nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.extensions.
{
CheckChecksum
,
Md5sum
}
import
nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
import
org.broadinstitute.gatk.queue.QScript
import
org.broadinstitute.gatk.queue.engine.JobRunInfo
import
org.broadinstitute.gatk.queue.function.QFunction
import
scala.collection.mutable
import
scala.concurrent.Await
...
...
@@ -198,6 +200,10 @@ trait SummaryQScript extends BiopetQScript { qscript: QScript =>
addedJobs
=
true
}
override
def
onExecutionDone
(
jobs
:
Map
[
QFunction
,
JobRunInfo
],
success
:
Boolean
)
=
{
SummaryDb
.
closeAll
()
}
}
object
SummaryQScript
{
...
...
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
View file @
7eab836c
...
...
@@ -75,7 +75,7 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
}
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
()
for
(
q
<-
qscript
.
summaryQScripts
)
deps
:+=
q
.
summaryFile
for
((
_
,
l
)
<-
qscript
.
summarizables
;
s
<-
l
)
{
...
...
@@ -179,8 +179,6 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
}
db
.
close
()
///////////////// OLD //////////////////
for
(((
name
,
sampleId
,
libraryId
),
summarizables
)
<-
qscript
.
summarizables
;
summarizable
<-
summarizables
)
{
summarizable
.
addToQscriptSummary
(
qscript
,
name
)
...
...
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/db/SummaryDb.scala
View file @
7eab836c
...
...
@@ -286,11 +286,20 @@ class SummaryDb(db: Database) extends Closeable {
}
object
SummaryDb
{
private
var
summaryConnections
=
Map
[
File
,
SummaryDb
]()
def
closeAll
()
:
Unit
=
{
summaryConnections
.
foreach
(
_
.
_2
.
close
())
}
def
openSqliteSummary
(
file
:
File
)
:
SummaryDb
=
{
val
exist
=
file
.
exists
()
val
db
=
Database
.
forURL
(
s
"jdbc:sqlite:${file.getAbsolutePath}"
,
driver
=
"org.sqlite.JDBC"
)
val
s
=
new
SummaryDb
(
db
)
if
(!
exist
)
s
.
createTables
()
s
if
(!
summaryConnections
.
contains
(
file
))
{
val
exist
=
file
.
exists
()
val
db
=
Database
.
forURL
(
s
"jdbc:sqlite:${file.getAbsolutePath}"
,
driver
=
"org.sqlite.JDBC"
)
val
s
=
new
SummaryDb
(
db
)
if
(!
exist
)
s
.
createTables
()
summaryConnections
+=
file
->
s
}
summaryConnections
(
file
)
}
}
\ No newline at end of file
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