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biopet.biopet
Commits
f8558f74
Commit
f8558f74
authored
Apr 10, 2017
by
Peter van 't Hof
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Updated some comments
parent
2129bb4f
Changes
4
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4 changed files
with
35 additions
and
37 deletions
+35
-37
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
...c/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
+13
-16
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilder.scala
...mc/sasc/biopet/core/report/MultisampleReportBuilder.scala
+16
-16
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
...scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
+4
-2
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
...umc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
+2
-3
No files found.
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @
f8558f74
...
@@ -44,27 +44,24 @@ object BammetricsReport extends ReportBuilder {
...
@@ -44,27 +44,24 @@ object BammetricsReport extends ReportBuilder {
def
pipelineName
=
"bammetrics"
def
pipelineName
=
"bammetrics"
/** Root page for single BamMetrcis report */
/** Root page for single BamMetrcis report */
def
indexPage
:
Future
[
ReportPage
]
=
Future
{
def
indexPage
:
Future
[
ReportPage
]
=
val
bamMetricsPage
=
Await
.
result
(
this
.
bamMetricsPage
(
summary
,
sampleId
,
libId
),
Duration
.
Inf
)
bamMetricsPage
(
summary
,
sampleId
,
libId
).
map
{
bamMetricsPage
=>
ReportPage
(
bamMetricsPage
.
subPages
:::
List
(
ReportPage
(
bamMetricsPage
.
subPages
:::
List
(
"Versions"
->
Future
(
ReportPage
(
List
(),
List
(
"Executables"
->
ReportSection
(
"/nl/lumc/sasc/biopet/core/report/executables.ssp"
"Versions"
->
Future
(
ReportPage
(
List
(),
List
(
"Executables"
->
ReportSection
(
"/nl/lumc/sasc/biopet/core/report/executables.ssp"
)),
Map
())),
)),
Map
())),
"Files"
->
filesPage
(
sampleId
,
libId
)
"Files"
->
filesPage
(
sampleId
,
libId
)
),
List
(
),
List
(
"Report"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp"
)
"Report"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp"
)
)
:::
bamMetricsPage
.
sections
,
)
:::
bamMetricsPage
.
sections
,
Map
()
Map
()
)
)
}
}
/** Generates a page with alignment stats */
/** Generates a page with alignment stats */
def
bamMetricsPage
(
summary
:
SummaryDb
,
def
bamMetricsPage
(
summary
:
SummaryDb
,
sampleId
:
Option
[
Int
],
sampleId
:
Option
[
Int
],
libId
:
Option
[
Int
],
libId
:
Option
[
Int
],
metricsTag
:
String
=
"bammetrics"
)
:
Future
[
ReportPage
]
=
Future
{
metricsTag
:
String
=
"bammetrics"
)
:
Future
[
ReportPage
]
=
Future
{
//val pipelineId: Int = summary.getPipelineId(runId, metricsTag).map(_.get)
val
wgsExecuted
=
summary
.
getStatsSize
(
runId
,
metricsTag
,
"wgs"
,
sample
=
sampleId
.
map
(
SampleId
),
library
=
libId
.
map
(
LibraryId
))
>=
1
val
wgsExecuted
=
summary
.
getStatsSize
(
runId
,
metricsTag
,
"wgs"
,
sample
=
sampleId
.
map
(
SampleId
),
library
=
libId
.
map
(
LibraryId
))
>=
1
val
rnaExecuted
=
summary
.
getStatsSize
(
runId
,
metricsTag
,
"rna"
,
sample
=
sampleId
.
map
(
SampleId
),
library
=
libId
.
map
(
LibraryId
))
>=
1
val
rnaExecuted
=
summary
.
getStatsSize
(
runId
,
metricsTag
,
"rna"
,
sample
=
sampleId
.
map
(
SampleId
),
library
=
libId
.
map
(
LibraryId
))
>=
1
...
@@ -86,7 +83,7 @@ object BammetricsReport extends ReportBuilder {
...
@@ -86,7 +83,7 @@ object BammetricsReport extends ReportBuilder {
ReportPage
(
ReportPage
(
if
(
targets
.
isEmpty
)
List
()
if
(
targets
.
isEmpty
)
List
()
else
List
(
"Targets"
->
Future
(
ReportPage
(
else
List
(
"Targets"
->
Future
.
successful
(
ReportPage
(
List
(),
List
(),
targets
.
map
(
t
=>
t
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp"
,
Map
(
"target"
->
Some
(
t
)))),
targets
.
map
(
t
=>
t
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp"
,
Map
(
"target"
->
Some
(
t
)))),
Map
()))),
Map
()))),
...
...
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilder.scala
View file @
f8558f74
...
@@ -41,28 +41,28 @@ trait MultisampleReportBuilder extends ReportBuilder {
...
@@ -41,28 +41,28 @@ trait MultisampleReportBuilder extends ReportBuilder {
}
}
/** Generate the samples page including a single sample page for each sample in the summary */
/** Generate the samples page including a single sample page for each sample in the summary */
def
generateSamplesPage
(
args
:
Map
[
String
,
Any
])
:
Future
[
ReportPage
]
=
Future
{
def
generateSamplesPage
(
args
:
Map
[
String
,
Any
])
:
Future
[
ReportPage
]
=
val
samples
=
Await
.
result
(
summary
.
getSamples
(
runId
=
Some
(
runId
)),
Duration
.
Inf
)
summary
.
getSamples
(
runId
=
Some
(
runId
)).
map
{
samples
=>
val
samplePages
=
samples
.
map
(
_
.
id
)
val
samplePages
=
samples
.
map
(
_
.
id
)
.
map
(
sampleId
=>
sampleId
->
samplePage
(
sampleId
,
args
++
Map
(
"sampleId"
->
Some
(
sampleId
)))
.
map
(
sampleId
=>
sampleId
->
samplePage
(
sampleId
,
args
++
Map
(
"sampleId"
->
Some
(
sampleId
)))
.
map
(
x
=>
x
.
copy
(
subPages
=
x
.
subPages
:::
"Files"
->
filesPage
(
sampleId
,
None
)
::
Nil
)))
.
map
(
x
=>
x
.
copy
(
subPages
=
x
.
subPages
:::
"Files"
->
filesPage
(
sampleId
,
None
)
::
Nil
)))
.
toList
.
toList
ReportPage
(
samplePages
.
map
(
x
=>
samples
.
find
(
_
.
id
==
x
.
_1
).
get
.
name
->
x
.
_2
),
samplesSections
,
args
)
ReportPage
(
samplePages
.
map
(
x
=>
samples
.
find
(
_
.
id
==
x
.
_1
).
get
.
name
->
x
.
_2
),
samplesSections
,
args
)
}
}
/** Generate the libraries page for a single sample with a subpage for eacht library */
/** Generate the libraries page for a single sample with a subpage for eacht library */
def
generateLibraryPage
(
args
:
Map
[
String
,
Any
])
:
Future
[
ReportPage
]
=
Future
{
def
generateLibraryPage
(
args
:
Map
[
String
,
Any
])
:
Future
[
ReportPage
]
=
{
val
sampleId
=
args
(
"sampleId"
)
match
{
val
sampleId
=
args
(
"sampleId"
)
match
{
case
Some
(
x
:
Int
)
=>
x
case
Some
(
x
:
Int
)
=>
x
case
None
=>
throw
new
IllegalStateException
(
"Sample not found"
)
case
None
=>
throw
new
IllegalStateException
(
"Sample not found"
)
}
}
val
libraries
=
Await
.
result
(
summary
.
getLibraries
(
runId
=
Some
(
runId
),
sampleId
=
Some
(
sampleId
)),
Duration
.
Inf
)
summary
.
getLibraries
(
runId
=
Some
(
runId
),
sampleId
=
Some
(
sampleId
)).
map
{
libraries
=>
val
libPages
=
libraries
.
map
(
_
.
id
)
val
libPages
=
libraries
.
map
(
_
.
id
)
.
map
(
libId
=>
libId
->
libraryPage
(
sampleId
,
libId
,
args
++
Map
(
"libId"
->
Some
(
libId
))
)
.
map
(
libId
=>
libId
->
libraryPage
(
sampleId
,
libId
,
args
++
Map
(
"libId"
->
Some
(
libId
)))
.
map
(
x
=>
x
.
copy
(
subPages
=
x
.
subPages
:::
"Files"
->
filesPage
(
sampleId
,
libId
)
::
Nil
)))
.
map
(
x
=>
x
.
copy
(
subPages
=
x
.
subPages
:::
"Files"
->
filesPage
(
sampleId
,
libId
)
::
Nil
)))
.
toList
.
toList
ReportPage
(
libPages
.
map
(
x
=>
libraries
.
find
(
_
.
id
==
x
.
_1
).
get
.
name
->
x
.
_2
),
librariesSections
,
args
)
ReportPage
(
libPages
.
map
(
x
=>
libraries
.
find
(
_
.
id
==
x
.
_1
).
get
.
name
->
x
.
_2
),
librariesSections
,
args
)
}
}
}
}
}
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
View file @
f8558f74
...
@@ -313,12 +313,14 @@ trait ReportBuilder extends ToolCommand {
...
@@ -313,12 +313,14 @@ trait ReportBuilder extends ToolCommand {
case
(
moduleId
,
files
)
=>
case
(
moduleId
,
files
)
=>
val
moduleName
:
Future
[
String
]
=
moduleId
match
{
val
moduleName
:
Future
[
String
]
=
moduleId
match
{
case
Some
(
id
)
=>
summary
.
getModuleName
(
pipelineId
,
id
).
map
(
_
.
getOrElse
(
"Pipeline"
))
case
Some
(
id
)
=>
summary
.
getModuleName
(
pipelineId
,
id
).
map
(
_
.
getOrElse
(
"Pipeline"
))
case
_
=>
Future
(
"Pipeline"
)
case
_
=>
Future
.
successful
(
"Pipeline"
)
}
}
moduleName
.
map
(
_
->
ReportSection
(
"/nl/lumc/sasc/biopet/core/report/files.ssp"
,
Map
(
"files"
->
files
)))
moduleName
.
map
(
_
->
ReportSection
(
"/nl/lumc/sasc/biopet/core/report/files.ssp"
,
Map
(
"files"
->
files
)))
}
}
val
moduleSectionsSorted
=
moduleSections
.
find
(
_
.
_1
==
"Pipeline"
)
++
moduleSections
.
filter
(
_
.
_1
!=
"Pipeline"
)
val
moduleSectionsSorted
=
moduleSections
.
find
(
_
.
_1
==
"Pipeline"
)
++
moduleSections
.
filter
(
_
.
_1
!=
"Pipeline"
)
summary
.
getPipelineName
(
pipelineId
=
pipelineId
).
map
(
_
.
get
->
Future
(
ReportPage
(
Nil
,
Await
.
result
(
Future
.
sequence
(
moduleSectionsSorted
),
Duration
.
Inf
).
toList
,
Map
())))
summary
.
getPipelineName
(
pipelineId
=
pipelineId
)
.
map
(
_
.
get
->
Future
.
sequence
(
moduleSectionsSorted
)
.
map
(
sections
=>
ReportPage
(
Nil
,
sections
.
toList
,
Map
())))
})
})
val
pipelineFiles
=
summary
.
getPipelineId
(
runId
,
pipelineName
)
val
pipelineFiles
=
summary
.
getPipelineId
(
runId
,
pipelineName
)
...
...
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
View file @
f8558f74
...
@@ -42,11 +42,10 @@ object FlexiprepReport extends ReportBuilder {
...
@@ -42,11 +42,10 @@ object FlexiprepReport extends ReportBuilder {
override
def
pageArgs
=
Map
(
"multisample"
->
false
)
override
def
pageArgs
=
Map
(
"multisample"
->
false
)
/** Index page for a flexiprep report */
/** Index page for a flexiprep report */
def
indexPage
:
Future
[
ReportPage
]
=
Future
{
def
indexPage
:
Future
[
ReportPage
]
=
this
.
flexiprepPage
.
map
{
flexiprepPage
=>
val
flexiprepPage
=
this
.
flexiprepPage
ReportPage
(
Nil
,
List
(
ReportPage
(
Nil
,
List
(
"Report"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFront.ssp"
)
"Report"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFront.ssp"
)
)
:::
Await
.
result
(
flexiprepPage
,
Duration
.
Inf
)
.
sections
,
)
:::
flexiprepPage
.
sections
,
Map
()
Map
()
)
)
}
}
...
...
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