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biopet.biopet
Commits
b1191ca3
Commit
b1191ca3
authored
Jan 26, 2017
by
Peter van 't Hof
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Try setup with sqlite
parent
e34fe3a1
Changes
3
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3 changed files
with
31 additions
and
7 deletions
+31
-7
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SummaryToSqlite.scala
...ain/scala/nl/lumc/sasc/biopet/tools/SummaryToSqlite.scala
+10
-4
biopet-utils/pom.xml
biopet-utils/pom.xml
+8
-3
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/db/Samples.scala
.../scala/nl/lumc/sasc/biopet/utils/summary/db/Samples.scala
+13
-0
No files found.
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/
JsonToHdf5
.scala
→
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/
SummaryToSqlite
.scala
View file @
b1191ca3
...
...
@@ -2,14 +2,16 @@ package nl.lumc.sasc.biopet.tools
import
java.io.File
import
ncsa.hdf.
`object`
.
h5
.
H5File
import
nl.lumc.sasc.biopet.tools.GvcfToBed.Args
import
slick.driver.H2Driver.api._
import
scala.concurrent.ExecutionContext.Implicits.global
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
ToolCommand
}
/**
* Created by pjvanthof on 26/01/2017.
*/
object
JsonToHdf5
extends
ToolCommand
{
object
SummaryToSqlite
extends
ToolCommand
{
case
class
Args
(
inputJson
:
File
=
null
,
outputHdf5
:
File
=
null
)
extends
AbstractArgs
...
...
@@ -29,8 +31,12 @@ object JsonToHdf5 extends ToolCommand {
val
jsonMap
=
ConfigUtils
.
fileToConfigMap
(
cmdArgs
.
inputJson
)
val
hdf5
=
new
H5File
(
cmdArgs
.
outputHdf5
.
getAbsolutePath
)
val
db
=
Database
.
forURL
(
s
"jdbc:sqlite:${cmdArgs.outputHdf5.getAbsolutePath}"
,
driver
=
"org.sqlite.JDBC"
)
try
{
}
finally
db
.
close
}
}
biopet-utils/pom.xml
View file @
b1191ca3
...
...
@@ -31,9 +31,14 @@
<dependencies>
<dependency>
<groupId>
org.hdfgroup
</groupId>
<artifactId>
hdf-java
</artifactId>
<version>
2.6.1
</version>
<groupId>
com.typesafe.slick
</groupId>
<artifactId>
slick_2.10
</artifactId>
<version>
3.1.1
</version>
</dependency>
<dependency>
<groupId>
org.slf4j
</groupId>
<artifactId>
slf4j-nop
</artifactId>
<version>
1.6.4
</version>
</dependency>
<dependency>
<groupId>
colt
</groupId>
...
...
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/db/Samples.scala
0 → 100644
View file @
b1191ca3
package
nl.lumc.sasc.biopet.utils.summary.db
import
slick.driver.H2Driver.api._
/**
* Created by pjvan_thof on 26-1-17.
*/
class
Samples
(
tag
:
Tag
)
extends
Table
[(
Int
,
String
)](
tag
,
"SUPPLIERS"
)
{
def
sampleId
=
column
[
Int
](
"sampleId"
,
O
.
PrimaryKey
)
// This is the primary key column
def
sampleName
=
column
[
String
](
"sampleName"
)
// Every table needs a * projection with the same type as the table's type parameter
def
*
=
(
sampleId
,
sampleName
)
}
\ No newline at end of file
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