Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
71957bc9
Commit
71957bc9
authored
Jul 14, 2017
by
Peter van 't Hof
Browse files
Put back type changes
parent
caf71f04
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/db/Schema.scala
View file @
71957bc9
...
...
@@ -17,7 +17,6 @@ package nl.lumc.sasc.biopet.utils.summary.db
import
java.sql.Date
import
slick.driver.H2Driver.api._
import
slick.lifted.
{
Index
,
MappedProjection
}
/**
* Created by pjvan_thof on 27-1-17.
...
...
@@ -31,73 +30,69 @@ object Schema {
commitHash
:
String
,
creationDate
:
Date
)
class
Runs
(
tag
:
Tag
)
extends
Table
[
Run
](
tag
,
"Runs"
)
{
def
id
:
Rep
[
Int
]
=
column
[
Int
](
"id"
,
O
.
PrimaryKey
)
def
runName
:
Rep
[
String
]
=
column
[
String
](
"runName"
)
def
outputDir
:
Rep
[
String
]
=
column
[
String
](
"outputDir"
)
def
version
:
Rep
[
String
]
=
column
[
String
](
"version"
)
def
commitHash
:
Rep
[
String
]
=
column
[
String
](
"commitHash"
)
def
creationDate
:
Rep
[
Date
]
=
column
[
Date
](
"creationDate"
)
def
*
:
MappedProjection
[
Run
,
(
Int
,
String
,
String
,
String
,
String
,
Date
)]
=
def
id
=
column
[
Int
](
"id"
,
O
.
PrimaryKey
)
def
runName
=
column
[
String
](
"runName"
)
def
outputDir
=
column
[
String
](
"outputDir"
)
def
version
=
column
[
String
](
"version"
)
def
commitHash
=
column
[
String
](
"commitHash"
)
def
creationDate
=
column
[
Date
](
"creationDate"
)
def
*
=
(
id
,
runName
,
outputDir
,
version
,
commitHash
,
creationDate
)
<>
(
Run
.
tupled
,
Run
.
unapply
)
}
val
runs
:
TableQuery
[
Runs
]
=
TableQuery
[
Runs
]
val
runs
=
TableQuery
[
Runs
]
case
class
Sample
(
id
:
Int
,
name
:
String
,
runId
:
Int
,
tags
:
Option
[
String
])
class
Samples
(
tag
:
Tag
)
extends
Table
[
Sample
](
tag
,
"Samples"
)
{
def
id
:
Rep
[
Int
]
=
column
[
Int
](
"id"
,
O
.
PrimaryKey
)
def
name
:
Rep
[
String
]
=
column
[
String
](
"name"
)
def
runId
:
Rep
[
Int
]
=
column
[
Int
](
"runId"
)
def
tags
:
Rep
[
Option
[
String
]]
=
column
[
Option
[
String
]](
"tags"
)
def
id
=
column
[
Int
](
"id"
,
O
.
PrimaryKey
)
def
name
=
column
[
String
](
"name"
)
def
runId
=
column
[
Int
](
"runId"
)
def
tags
=
column
[
Option
[
String
]](
"tags"
)
def
*
:
MappedProjection
[
Sample
,
(
Int
,
String
,
Int
,
Option
[
String
])]
=
(
id
,
name
,
runId
,
tags
)
<>
(
Sample
.
tupled
,
Sample
.
unapply
)
def
*
=
(
id
,
name
,
runId
,
tags
)
<>
(
Sample
.
tupled
,
Sample
.
unapply
)
def
idx
:
Index
=
index
(
"idx_samples"
,
(
runId
,
name
),
unique
=
true
)
def
idx
=
index
(
"idx_samples"
,
(
runId
,
name
),
unique
=
true
)
}
val
samples
:
TableQuery
[
Samples
]
=
TableQuery
[
Samples
]
val
samples
=
TableQuery
[
Samples
]
case
class
Library
(
id
:
Int
,
name
:
String
,
runId
:
Int
,
sampleId
:
Int
,
tags
:
Option
[
String
])
class
Libraries
(
tag
:
Tag
)
extends
Table
[
Library
](
tag
,
"Libraries"
)
{
def
id
:
Rep
[
Int
]
=
column
[
Int
](
"id"
,
O
.
PrimaryKey
)
def
name
:
Rep
[
String
]
=
column
[
String
](
"name"
)
def
runId
:
Rep
[
Int
]
=
column
[
Int
](
"runId"
)
def
sampleId
:
Rep
[
Int
]
=
column
[
Int
](
"sampleId"
)
def
tags
:
Rep
[
Option
[
String
]]
=
column
[
Option
[
String
]](
"tags"
)
def
id
=
column
[
Int
](
"id"
,
O
.
PrimaryKey
)
def
name
=
column
[
String
](
"name"
)
def
runId
=
column
[
Int
](
"runId"
)
def
sampleId
=
column
[
Int
](
"sampleId"
)
def
tags
=
column
[
Option
[
String
]](
"tags"
)
def
*
:
MappedProjection
[
Library
,
(
Int
,
String
,
Int
,
Int
,
Option
[
String
])]
=
(
id
,
name
,
runId
,
sampleId
,
tags
)
<>
(
Library
.
tupled
,
Library
.
unapply
)
def
*
=
(
id
,
name
,
runId
,
sampleId
,
tags
)
<>
(
Library
.
tupled
,
Library
.
unapply
)
def
idx
:
Index
=
index
(
"idx_libraries"
,
(
runId
,
sampleId
,
name
),
unique
=
true
)
def
idx
=
index
(
"idx_libraries"
,
(
runId
,
sampleId
,
name
),
unique
=
true
)
}
val
libraries
:
TableQuery
[
Libraries
]
=
TableQuery
[
Libraries
]
val
libraries
=
TableQuery
[
Libraries
]
case
class
Pipeline
(
id
:
Int
,
name
:
String
,
runId
:
Int
)
class
Pipelines
(
tag
:
Tag
)
extends
Table
[
Pipeline
](
tag
,
"PipelineNames"
)
{
def
id
:
Rep
[
Int
]
=
column
[
Int
](
"id"
,
O
.
PrimaryKey
)
def
name
:
Rep
[
String
]
=
column
[
String
](
"name"
)
def
runId
:
Rep
[
Int
]
=
column
[
Int
](
"runId"
)
def
id
=
column
[
Int
](
"id"
,
O
.
PrimaryKey
)
def
name
=
column
[
String
](
"name"
)
def
runId
=
column
[
Int
](
"runId"
)
def
*
:
MappedProjection
[
Pipeline
,
(
Int
,
String
,
Int
)]
=
(
id
,
name
,
runId
)
<>
(
Pipeline
.
tupled
,
Pipeline
.
unapply
)
def
*
=
(
id
,
name
,
runId
)
<>
(
Pipeline
.
tupled
,
Pipeline
.
unapply
)
def
idx
:
Index
=
index
(
"idx_pipeline_names"
,
(
name
,
runId
),
unique
=
true
)
def
idx
=
index
(
"idx_pipeline_names"
,
(
name
,
runId
),
unique
=
true
)
}
val
pipelines
:
TableQuery
[
Pipelines
]
=
TableQuery
[
Pipelines
]
val
pipelines
=
TableQuery
[
Pipelines
]
case
class
Module
(
id
:
Int
,
name
:
String
,
runId
:
Int
,
pipelineId
:
Int
)
class
Modules
(
tag
:
Tag
)
extends
Table
[
Module
](
tag
,
"ModuleNames"
)
{
def
id
:
Rep
[
Int
]
=
column
[
Int
](
"id"
,
O
.
PrimaryKey
)
def
name
:
Rep
[
String
]
=
column
[
String
](
"name"
)
def
runId
:
Rep
[
Int
]
=
column
[
Int
](
"runId"
)
def
pipelineId
:
Rep
[
Int
]
=
column
[
Int
](
"pipelineId"
)
def
id
=
column
[
Int
](
"id"
,
O
.
PrimaryKey
)
def
name
=
column
[
String
](
"name"
)
def
runId
=
column
[
Int
](
"runId"
)
def
pipelineId
=
column
[
Int
](
"pipelineId"
)
def
*
:
MappedProjection
[
Module
,
(
Int
,
String
,
Int
,
Int
)]
=
(
id
,
name
,
runId
,
pipelineId
)
<>
(
Module
.
tupled
,
Module
.
unapply
)
def
*
=
(
id
,
name
,
runId
,
pipelineId
)
<>
(
Module
.
tupled
,
Module
.
unapply
)
def
idx
:
Index
=
index
(
"idx_module_names"
,
(
name
,
runId
,
pipelineId
),
unique
=
true
)
def
idx
=
index
(
"idx_module_names"
,
(
name
,
runId
,
pipelineId
),
unique
=
true
)
}
val
modules
:
TableQuery
[
Modules
]
=
TableQuery
[
Modules
]
val
modules
=
TableQuery
[
Modules
]
case
class
Stat
(
runId
:
Int
,
pipelineId
:
Int
,
...
...
@@ -106,20 +101,19 @@ object Schema {
library
:
Option
[
Int
],
content
:
String
)
class
Stats
(
tag
:
Tag
)
extends
Table
[
Stat
](
tag
,
"Stats"
)
{
def
runId
:
Rep
[
Int
]
=
column
[
Int
](
"runId"
)
def
pipelineId
:
Rep
[
Int
]
=
column
[
Int
](
"pipelineId"
)
def
moduleId
:
Rep
[
Option
[
Int
]]
=
column
[
Option
[
Int
]](
"moduleId"
)
def
sampleId
:
Rep
[
Option
[
Int
]]
=
column
[
Option
[
Int
]](
"sampleId"
)
def
libraryId
:
Rep
[
Option
[
Int
]]
=
column
[
Option
[
Int
]](
"libraryId"
)
def
content
:
Rep
[
String
]
=
column
[
String
](
"content"
)
def
*
:
MappedProjection
[
Stat
,
(
Int
,
Int
,
Option
[
Int
]
,
Option
[
Int
]
,
Option
[
Int
]
,
String
)]
=
def
runId
=
column
[
Int
](
"runId"
)
def
pipelineId
=
column
[
Int
](
"pipelineId"
)
def
moduleId
=
column
[
Option
[
Int
]](
"moduleId"
)
def
sampleId
=
column
[
Option
[
Int
]](
"sampleId"
)
def
libraryId
=
column
[
Option
[
Int
]](
"libraryId"
)
def
content
=
column
[
String
](
"content"
)
def
*
=
(
runId
,
pipelineId
,
moduleId
,
sampleId
,
libraryId
,
content
)
<>
(
Stat
.
tupled
,
Stat
.
unapply
)
def
idx
:
Index
=
index
(
"idx_stats"
,
(
runId
,
pipelineId
,
moduleId
,
sampleId
,
libraryId
),
unique
=
true
)
def
idx
=
index
(
"idx_stats"
,
(
runId
,
pipelineId
,
moduleId
,
sampleId
,
libraryId
),
unique
=
true
)
}
val
stats
:
TableQuery
[
Stats
]
=
TableQuery
[
Stats
]
val
stats
=
TableQuery
[
Stats
]
case
class
Setting
(
runId
:
Int
,
pipelineId
:
Int
,
...
...
@@ -128,20 +122,20 @@ object Schema {
library
:
Option
[
Int
],
content
:
String
)
class
Settings
(
tag
:
Tag
)
extends
Table
[
Setting
](
tag
,
"Settings"
)
{
def
runId
:
Rep
[
Int
]
=
column
[
Int
](
"runId"
)
def
pipelineId
:
Rep
[
Int
]
=
column
[
Int
](
"pipelineId"
)
def
moduleId
:
Rep
[
Option
[
Int
]]
=
column
[
Option
[
Int
]](
"moduleId"
)
def
sampleId
:
Rep
[
Option
[
Int
]]
=
column
[
Option
[
Int
]](
"sampleId"
)
def
libraryId
:
Rep
[
Option
[
Int
]]
=
column
[
Option
[
Int
]](
"libraryId"
)
def
content
:
Rep
[
String
]
=
column
[
String
](
"content"
)
def
*
:
MappedProjection
[
Setting
,
(
Int
,
Int
,
Option
[
Int
]
,
Option
[
Int
]
,
Option
[
Int
]
,
String
)]
=
def
runId
=
column
[
Int
](
"runId"
)
def
pipelineId
=
column
[
Int
](
"pipelineId"
)
def
moduleId
=
column
[
Option
[
Int
]](
"moduleId"
)
def
sampleId
=
column
[
Option
[
Int
]](
"sampleId"
)
def
libraryId
=
column
[
Option
[
Int
]](
"libraryId"
)
def
content
=
column
[
String
](
"content"
)
def
*
=
(
runId
,
pipelineId
,
moduleId
,
sampleId
,
libraryId
,
content
)
<>
(
Setting
.
tupled
,
Setting
.
unapply
)
def
idx
:
Index
=
def
idx
=
index
(
"idx_settings"
,
(
runId
,
pipelineId
,
moduleId
,
sampleId
,
libraryId
),
unique
=
true
)
}
val
settings
:
TableQuery
[
Settings
]
=
TableQuery
[
Settings
]
val
settings
=
TableQuery
[
Settings
]
case
class
File
(
runId
:
Int
,
pipelineId
:
Int
,
...
...
@@ -154,26 +148,24 @@ object Schema {
link
:
Boolean
,
size
:
Long
)
class
Files
(
tag
:
Tag
)
extends
Table
[
File
](
tag
,
"Files"
)
{
def
runId
:
Rep
[
Int
]
=
column
[
Int
](
"runId"
)
def
pipelineId
:
Rep
[
Int
]
=
column
[
Int
](
"pipelineId"
)
def
moduleId
:
Rep
[
Option
[
Int
]]
=
column
[
Option
[
Int
]](
"moduleId"
)
def
sampleId
:
Rep
[
Option
[
Int
]]
=
column
[
Option
[
Int
]](
"sampleId"
)
def
libraryId
:
Rep
[
Option
[
Int
]]
=
column
[
Option
[
Int
]](
"libraryId"
)
def
key
:
Rep
[
String
]
=
column
[
String
](
"key"
)
def
path
:
Rep
[
String
]
=
column
[
String
](
"path"
)
// This should be relative to the outputDir
def
md5
:
Rep
[
String
]
=
column
[
String
](
"md5"
)
def
link
:
Rep
[
Boolean
]
=
column
[
Boolean
](
"link"
,
O
.
Default
(
false
))
def
size
:
Rep
[
Long
]
=
column
[
Long
](
"size"
)
def
*
:
MappedProjection
[
File
,
(
Int
,
Int
,
Option
[
Int
]
,
Option
[
Int
]
,
Option
[
Int
]
,
String
,
String
,
String
,
Boolean
,
Long
)]
=
def
runId
=
column
[
Int
](
"runId"
)
def
pipelineId
=
column
[
Int
](
"pipelineId"
)
def
moduleId
=
column
[
Option
[
Int
]](
"moduleId"
)
def
sampleId
=
column
[
Option
[
Int
]](
"sampleId"
)
def
libraryId
=
column
[
Option
[
Int
]](
"libraryId"
)
def
key
=
column
[
String
](
"key"
)
def
path
=
column
[
String
](
"path"
)
// This should be relative to the outputDir
def
md5
=
column
[
String
](
"md5"
)
def
link
=
column
[
Boolean
](
"link"
,
O
.
Default
(
false
))
def
size
=
column
[
Long
](
"size"
)
def
*
=
(
runId
,
pipelineId
,
moduleId
,
sampleId
,
libraryId
,
key
,
path
,
md5
,
link
,
size
)
<>
(
File
.
tupled
,
File
.
unapply
)
def
idx
:
Index
=
def
idx
=
index
(
"idx_files"
,
(
runId
,
pipelineId
,
moduleId
,
sampleId
,
libraryId
,
key
),
unique
=
true
)
}
val
files
:
TableQuery
[
Files
]
=
TableQuery
[
Files
]
val
files
=
TableQuery
[
Files
]
case
class
Executable
(
runId
:
Int
,
toolName
:
String
,
...
...
@@ -184,28 +176,20 @@ object Schema {
javaMd5
:
Option
[
String
]
=
None
,
jarPath
:
Option
[
String
]
=
None
)
class
Executables
(
tag
:
Tag
)
extends
Table
[
Executable
](
tag
,
"Executables"
)
{
def
runId
:
Rep
[
Int
]
=
column
[
Int
](
"runId"
)
def
toolName
:
Rep
[
String
]
=
column
[
String
](
"toolName"
)
def
version
:
Rep
[
Option
[
String
]]
=
column
[
Option
[
String
]](
"version"
)
def
path
:
Rep
[
Option
[
String
]]
=
column
[
Option
[
String
]](
"path"
)
def
javaVersion
:
Rep
[
Option
[
String
]]
=
column
[
Option
[
String
]](
"javaVersion"
)
def
exeMd5
:
Rep
[
Option
[
String
]]
=
column
[
Option
[
String
]](
"exeMd5"
)
def
javaMd5
:
Rep
[
Option
[
String
]]
=
column
[
Option
[
String
]](
"javaMd5"
)
def
jarPath
:
Rep
[
Option
[
String
]]
=
column
[
Option
[
String
]](
"jarPath"
)
def
*
:
MappedProjection
[
Executable
,
(
Int
,
String
,
Option
[
String
]
,
Option
[
String
]
,
Option
[
String
]
,
Option
[
String
]
,
Option
[
String
]
,
Option
[
String
])]
=
def
runId
=
column
[
Int
](
"runId"
)
def
toolName
=
column
[
String
](
"toolName"
)
def
version
=
column
[
Option
[
String
]](
"version"
)
def
path
=
column
[
Option
[
String
]](
"path"
)
def
javaVersion
=
column
[
Option
[
String
]](
"javaVersion"
)
def
exeMd5
=
column
[
Option
[
String
]](
"exeMd5"
)
def
javaMd5
=
column
[
Option
[
String
]](
"javaMd5"
)
def
jarPath
=
column
[
Option
[
String
]](
"jarPath"
)
def
*
=
(
runId
,
toolName
,
version
,
path
,
javaVersion
,
exeMd5
,
javaMd5
,
jarPath
)
<>
(
Executable
.
tupled
,
Executable
.
unapply
)
def
idx
:
Index
=
index
(
"idx_executables"
,
(
runId
,
toolName
),
unique
=
true
)
def
idx
=
index
(
"idx_executables"
,
(
runId
,
toolName
),
unique
=
true
)
}
val
executables
:
TableQuery
[
Executables
]
=
TableQuery
[
Executables
]
val
executables
=
TableQuery
[
Executables
]
}
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment