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biopet.biopet
Commits
da319f92
Commit
da319f92
authored
Jan 28, 2017
by
Peter van 't Hof
Browse files
Added settings
parent
004bd645
Changes
2
Hide whitespace changes
Inline
Side-by-side
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SummaryToSqlite.scala
View file @
da319f92
...
...
@@ -54,7 +54,7 @@ object SummaryToSqlite extends ToolCommand {
(
runs
.
schema
++
samples
.
schema
++
samplesRuns
.
schema
++
libraries
.
schema
++
librariesRuns
.
schema
++
pipelineNames
.
schema
++
moduleNames
.
schema
++
stats
.
schema
++
moduleNames
.
schema
++
stats
.
schema
++
settings
.
schema
++
files
.
schema
++
executables
.
schema
).
create
)
val
setupFuture
=
db
.
run
(
setup
)
...
...
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/db/Schema.scala
View file @
da319f92
...
...
@@ -84,11 +84,25 @@ object Schema {
def
*
=
(
pipelineId
,
runId
,
moduleId
,
sampleId
,
libraryId
,
stats
,
schema
)
def
idx
=
index
(
"idx_stats"
,
(
pipelineId
,
runId
,
sampleId
,
libraryId
),
unique
=
true
)
def
idx
=
index
(
"idx_stats"
,
(
pipelineId
,
runId
,
moduleId
,
sampleId
,
libraryId
),
unique
=
true
)
}
val
stats
=
TableQuery
[
Stats
]
class
Settings
(
tag
:
Tag
)
extends
Table
[(
Int
,
Int
,
Option
[
Int
]
,
Option
[
Int
]
,
Option
[
Int
]
,
Blob
,
Option
[
String
])](
tag
,
"Settings"
)
{
def
pipelineId
=
column
[
Int
](
"pipelineId"
)
def
runId
=
column
[
Int
](
"runId"
)
def
moduleId
=
column
[
Option
[
Int
]](
"moduleId"
)
def
sampleId
=
column
[
Option
[
Int
]](
"sampleId"
)
def
libraryId
=
column
[
Option
[
Int
]](
"libraryId"
)
def
stats
=
column
[
Blob
](
"stats"
)
def
schema
=
column
[
Option
[
String
]](
"schema"
)
def
*
=
(
pipelineId
,
runId
,
moduleId
,
sampleId
,
libraryId
,
stats
,
schema
)
def
idx
=
index
(
"idx_settings"
,
(
pipelineId
,
runId
,
moduleId
,
sampleId
,
libraryId
),
unique
=
true
)
}
val
settings
=
TableQuery
[
Settings
]
class
Files
(
tag
:
Tag
)
extends
Table
[(
Int
,
Int
,
Option
[
Int
]
,
Option
[
Int
]
,
Option
[
Int
]
,
String
,
String
)](
tag
,
"Files"
)
{
def
pipelineId
=
column
[
Int
](
"pipelineId"
)
def
runId
=
column
[
Int
](
"runId"
)
...
...
@@ -104,12 +118,17 @@ object Schema {
}
val
files
=
TableQuery
[
Files
]
class
Executables
(
tag
:
Tag
)
extends
Table
[(
Int
,
Int
)](
tag
,
"Executables"
)
{
class
Executables
(
tag
:
Tag
)
extends
Table
[(
Int
,
String
,
Option
[
String
]
,
Option
[
String
]
,
Option
[
String
]
,
Option
[
String
]
)](
tag
,
"Executables"
)
{
def
runId
=
column
[
Int
](
"runId"
)
def
moduleId
=
column
[
Int
](
"moduleId"
)
//TODO: add fields
def
toolName
=
column
[
String
](
"toolName"
)
def
version
=
column
[
Option
[
String
]](
"version"
)
def
javaVersion
=
column
[
Option
[
String
]](
"javaVersion"
)
def
exeMd5
=
column
[
Option
[
String
]](
"exeMd5"
)
def
javaMd5
=
column
[
Option
[
String
]](
"javaMd5"
)
def
*
=
(
runId
,
toolName
,
version
,
javaVersion
,
exeMd5
,
javaMd5
)
def
*
=
(
runId
,
moduleId
)
def
idx
=
index
(
"idx_executables"
,
(
runId
,
toolName
),
unique
=
true
)
}
val
executables
=
TableQuery
[
Executables
]
}
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