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biopet.biopet
Commits
a5f4c0a0
Commit
a5f4c0a0
authored
Jan 28, 2017
by
Peter van 't Hof
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Adding method to create empty database
parent
da319f92
Changes
2
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2 changed files
with
24 additions
and
14 deletions
+24
-14
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SummaryToSqlite.scala
...ain/scala/nl/lumc/sasc/biopet/tools/SummaryToSqlite.scala
+2
-14
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/db/Schema.scala
...n/scala/nl/lumc/sasc/biopet/utils/summary/db/Schema.scala
+22
-0
No files found.
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SummaryToSqlite.scala
View file @
a5f4c0a0
...
...
@@ -2,6 +2,7 @@ package nl.lumc.sasc.biopet.tools
import
java.io.File
import
nl.lumc.sasc.biopet.utils.summary.db.Schema
import
slick.driver.H2Driver.api._
import
scala.concurrent.ExecutionContext.Implicits.global
...
...
@@ -45,21 +46,8 @@ object SummaryToSqlite extends ToolCommand {
}
else
throw
new
IllegalArgumentException
(
s
"Db already exist: ${cmdArgs.outputSqlite}"
)
}
val
db
=
Database
.
forURL
(
s
"jdbc:s
qlite
:${
cmdArgs.outputSqlite
.getAbsolutePath}"
,
driver
=
"org.sqlite.JDBC"
)
Schema
.
createEmptyS
qlite
(
cmdArgs
.
outputSqlite
)
try
{
import
nl.lumc.sasc.biopet.utils.summary.db.Schema._
val
setup
=
DBIO
.
seq
(
(
runs
.
schema
++
samples
.
schema
++
samplesRuns
.
schema
++
libraries
.
schema
++
librariesRuns
.
schema
++
pipelineNames
.
schema
++
moduleNames
.
schema
++
stats
.
schema
++
settings
.
schema
++
files
.
schema
++
executables
.
schema
).
create
)
val
setupFuture
=
db
.
run
(
setup
)
Await
.
result
(
setupFuture
,
Duration
.
Inf
)
}
finally
db
.
close
logger
.
info
(
"Done"
)
}
...
...
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/db/Schema.scala
View file @
a5f4c0a0
package
nl.lumc.sasc.biopet.utils.summary.db
import
java.io.File
import
java.sql.Blob
import
nl.lumc.sasc.biopet.utils.Logging
import
slick.driver.H2Driver.api._
import
scala.concurrent.Await
import
scala.concurrent.duration.Duration
/**
* Created by pjvan_thof on 27-1-17.
*/
...
...
@@ -131,4 +136,21 @@ object Schema {
def
idx
=
index
(
"idx_executables"
,
(
runId
,
toolName
),
unique
=
true
)
}
val
executables
=
TableQuery
[
Executables
]
def
createEmptySqlite
(
file
:
File
)
:
Unit
=
{
val
db
=
Database
.
forURL
(
s
"jdbc:sqlite:${file.getAbsolutePath}"
,
driver
=
"org.sqlite.JDBC"
)
try
{
val
setup
=
DBIO
.
seq
(
(
runs
.
schema
++
samples
.
schema
++
samplesRuns
.
schema
++
libraries
.
schema
++
librariesRuns
.
schema
++
pipelineNames
.
schema
++
moduleNames
.
schema
++
stats
.
schema
++
settings
.
schema
++
files
.
schema
++
executables
.
schema
).
create
)
val
setupFuture
=
db
.
run
(
setup
)
Await
.
result
(
setupFuture
,
Duration
.
Inf
)
}
finally
db
.
close
}
}
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