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biopet.biopet
Commits
003136c0
Commit
003136c0
authored
Apr 07, 2017
by
Peter van 't Hof
Browse files
Fix compile issues
parent
06e9f248
Changes
2
Hide whitespace changes
Inline
Side-by-side
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
View file @
003136c0
...
...
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.core.report
import
java.io._
import
nl.lumc.sasc.biopet.core.ToolCommandFunction
import
nl.lumc.sasc.biopet.utils.summary.db.Schema.
{
Library
,
Module
,
Pipeline
,
Sample
}
import
nl.lumc.sasc.biopet.utils.summary.db.Schema.
{
Library
,
Module
,
Pipeline
,
Sample
,
Run
}
import
nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
import
nl.lumc.sasc.biopet.utils.
{
IoUtils
,
Logging
,
ToolCommand
}
import
org.broadinstitute.gatk.utils.commandline.Input
...
...
@@ -39,7 +39,7 @@ trait ReportBuilderExtension extends ToolCommandFunction {
/** Report builder object */
def
builder
:
ReportBuilder
def
toolObject
=
builder
def
toolObject
:
ReportBuilder
=
builder
@Input
(
required
=
true
)
var
summaryDbFile
:
File
=
_
...
...
@@ -112,20 +112,24 @@ trait ReportBuilder extends ToolCommand {
private
var
setSummary
:
SummaryDb
=
_
/** Retrival of summary, read only */
final
def
summary
=
setSummary
final
def
summary
:
SummaryDb
=
setSummary
private
var
setRunId
:
Int
=
0
final
def
runId
=
setRunId
final
def
runId
:
Int
=
setRunId
private
var
_setRun
:
Run
=
_
final
def
run
:
Run
=
_setRun
private
var
_setPipelines
=
Seq
[
Pipeline
]()
final
def
pipelines
=
_setPipelines
final
def
pipelines
:
Seq
[
Pipeline
]
=
_setPipelines
private
var
_setModules
=
Seq
[
Module
]()
final
def
modules
=
_setModules
final
def
modules
:
Seq
[
Module
]
=
_setModules
private
var
_setSamples
=
Seq
[
Sample
]()
final
def
samples
=
_setSamples
final
def
samples
:
Seq
[
Sample
]
=
_setSamples
private
var
_setLibraries
=
Seq
[
Library
]()
final
def
libraries
=
_setLibraries
final
def
libraries
:
Seq
[
Library
]
=
_setLibraries
/** default args that are passed to all page withing the report */
def
pageArgs
:
Map
[
String
,
Any
]
=
Map
()
...
...
@@ -134,13 +138,13 @@ trait ReportBuilder extends ToolCommand {
private
var
total
=
0
private
var
_sampleId
:
Option
[
Int
]
=
None
protected
[
report
]
def
sampleId
=
_sampleId
protected
[
report
]
def
sampleId
:
Option
[
Int
]
=
_sampleId
private
var
_libId
:
Option
[
Int
]
=
None
protected
[
report
]
def
libId
=
_libId
protected
[
report
]
def
libId
:
Option
[
Int
]
=
_libId
case
class
ExtFile
(
resourcePath
:
String
,
targetPath
:
String
)
def
extFiles
=
List
(
def
extFiles
:
List
[
ExtFile
]
=
List
(
"css/bootstrap_dashboard.css"
,
"css/bootstrap.min.css"
,
"css/bootstrap-theme.min.css"
,
...
...
@@ -181,6 +185,7 @@ trait ReportBuilder extends ToolCommand {
case
_
=>
}
_setRun
=
Await
.
result
(
summary
.
getRuns
(
runId
=
Some
(
runId
)),
Duration
.
Inf
).
head
_setPipelines
=
Await
.
result
(
summary
.
getPipelines
(
runId
=
Some
(
runId
)),
Duration
.
Inf
)
_setModules
=
Await
.
result
(
summary
.
getModules
(
runId
=
Some
(
runId
)),
Duration
.
Inf
)
_setSamples
=
Await
.
result
(
summary
.
getSamples
(
runId
=
Some
(
runId
),
sampleId
=
sampleId
),
Duration
.
Inf
)
...
...
@@ -240,6 +245,7 @@ trait ReportBuilder extends ToolCommand {
val
rootPath
=
"./"
+
Array
.
fill
(
path
.
size
)(
"../"
).
mkString
val
pageArgs
=
args
++
page
.
args
++
Map
(
"page"
->
page
,
"run"
->
run
,
"path"
->
path
,
"outputDir"
->
pageOutputDir
,
"rootPath"
->
rootPath
,
...
...
flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFastQcPlot.ssp
View file @
003136c0
#import(nl.lumc.sasc.biopet.utils.summary.db.Schema.Run)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
...
...
@@ -7,9 +8,9 @@
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(org.apache.commons.io.FileUtils)
#import(java.io.File)
#import(nl.lumc.sasc.biopet.core.report.ReportBuilder.ec)
<%@ var summary: SummaryDb %>
<%@ var runId: Int %>
<%@ var run: Run %>
<%@ var sampleId: Option[Int] %>
<%@ var libId: Option[Int] %>
<%@ var plot: String %>
...
...
@@ -17,7 +18,6 @@
#{
val settings = summary.getSettingKeys(runId, "flexiprep", NoModule, SampleId(sampleId.get), LibraryId(libId.get), keyValues = Map(
"skip_trim" -> List("skip_trim"), "skip_clip" -> List("skip_clip"), "paired" -> List("paired")))
val run = Await.result(summary.getRuns(runId = Some(runId)).map(_.head), Duration.Inf)
val paired: Boolean = settings("paired") == Some(true)
val skipClip: Boolean = settings("skip_clip") == Some(true)
...
...
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