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biopet.biopet
Commits
ce94a022
Commit
ce94a022
authored
Apr 12, 2017
by
Peter van 't Hof
Browse files
Fixing capture of failures
parent
916fe0d4
Changes
11
Hide whitespace changes
Inline
Side-by-side
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
View file @
ce94a022
...
...
@@ -224,10 +224,11 @@ trait ReportBuilder extends ToolCommand {
def
wait
(
futures
:
List
[
Future
[
Any
]])
:
Unit
=
{
try
{
Await
.
re
ady
(
Future
.
sequence
(
futures
),
Duration
.
fromNanos
(
30000000000L
))
Await
.
re
sult
(
Future
.
sequence
(
futures
),
Duration
.
fromNanos
(
30000000000L
))
}
catch
{
case
e
:
TimeoutException
=>
}
val
dones
=
futures
.
filter
(
_
.
isCompleted
)
val
notDone
=
futures
.
filter
(!
_
.
isCompleted
)
done
+=
futures
.
size
-
notDone
.
size
if
(
notDone
.
nonEmpty
)
{
...
...
@@ -236,8 +237,11 @@ trait ReportBuilder extends ToolCommand {
}
}
//jobsFutures.foreach(f => f.onFailure{ case e => throw new RuntimeException(e) })
wait
(
jobsFutures
)
Await
.
ready
(
baseFilesFuture
,
Duration
.
Inf
)
Await
.
result
(
Future
.
sequence
(
jobsFutures
),
Duration
.
Inf
)
Await
.
result
(
baseFilesFuture
,
Duration
.
Inf
)
logger
.
info
(
s
"Done, $done pages generated"
)
}
...
...
@@ -262,7 +266,7 @@ trait ReportBuilder extends ToolCommand {
pageFuture
:
Future
[
ReportPage
],
outputDir
:
File
,
path
:
List
[
String
]
=
Nil
,
args
:
Map
[
String
,
Any
]
=
Map
())
:
List
[
Future
[
_
]]
=
{
args
:
Map
[
String
,
Any
]
=
Map
())
:
List
[
Future
[
ReportPage
]]
=
{
val
pageOutputDir
=
new
File
(
outputDir
,
path
.
mkString
(
File
.
separator
))
def
pageArgs
(
page
:
ReportPage
)
=
{
...
...
@@ -301,6 +305,7 @@ trait ReportBuilder extends ToolCommand {
writer
.
close
()
logger
.
info
(
s
"Done rendering: $file"
)
page
}
renderFuture
::
Await
.
result
(
subPageJobs
,
Duration
.
Inf
)
...
...
carp/src/main/resources/nl/lumc/sasc/biopet/pipelines/carp/carpFront.ssp
View file @
ce94a022
#import(nl.lumc.sasc.biopet.utils.summary.db.Schema.Run)
#import(nl.lumc.sasc.biopet.utils.summary.db.Schema.Sample)
<%@ var run: Run %>
<%@ var allSamples:
List
[Sample] %>
<%@ var allSamples:
Seq
[Sample] %>
<table class="table">
<tbody>
<tr><th>Pipeline</th><td>Carp</td></tr>
...
...
flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp
View file @
ce94a022
...
...
@@ -19,8 +19,8 @@
<%@ var showTable: Boolean = true %>
<%@ var showIntro: Boolean = true %>
<%@ var multisample: Boolean = true %>
<%@ var allSamples:
List
[Sample] %>
<%@ var allLibraries:
List
[Library] %>
<%@ var allSamples:
Seq
[Sample] %>
<%@ var allLibraries:
Seq
[Library] %>
#{
val samples = sampleId.map(id => allSamples.filter(_.id == id)).getOrElse(allSamples)
val libraries = libId.map(id => allLibraries.filter(_.id == id)).getOrElse(allLibraries)
...
...
flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFront.ssp
View file @
ce94a022
...
...
@@ -4,8 +4,8 @@
<%@ var sampleId: Option[Int] %>
<%@ var libId: Option[Int] %>
<%@ var run: Run %>
<%@ var allSamples:
List
[Sample] %>
<%@ var allLibraries:
List
[Library] %>
<%@ var allSamples:
Seq
[Sample] %>
<%@ var allLibraries:
Seq
[Library] %>
<table class="table">
<tbody>
<tr><th>Pipeline</th><td>Flexiprep</td></tr>
...
...
flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp
View file @
ce94a022
...
...
@@ -18,8 +18,8 @@
<%@ var showTable: Boolean = true %>
<%@ var showIntro: Boolean = true %>
<%@ var multisample: Boolean = true %>
<%@ var allSamples:
List
[Sample] %>
<%@ var allLibraries:
List
[Library] %>
<%@ var allSamples:
Seq
[Sample] %>
<%@ var allLibraries:
Seq
[Library] %>
#{
val samples = sampleId.map(id => allSamples.filter(_.id == id)).getOrElse(allSamples)
val libraries = libId.map(id => allLibraries.filter(_.id == id)).getOrElse(allLibraries)
...
...
gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsFront.ssp
View file @
ce94a022
#import(nl.lumc.sasc.biopet.utils.summary.db.Schema.Run)
#import(nl.lumc.sasc.biopet.utils.summary.db.Schema.Sample)
<%@ var run: Run %>
<%@ var allSamples:
List
[Sample] %>
<%@ var allSamples:
Seq
[Sample] %>
<table class="table">
<tbody>
<tr><th>Pipeline</th><td>Gears</td></tr>
...
...
gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/gentrapFront.ssp
View file @
ce94a022
#import(nl.lumc.sasc.biopet.utils.summary.db.Schema.Run)
#import(nl.lumc.sasc.biopet.utils.summary.db.Schema.Sample)
<%@ var run: Run %>
<%@ var allSamples:
List
[Sample] %>
<%@ var allSamples:
Seq
[Sample] %>
<table class="table">
<tbody>
<tr><th>Pipeline</th><td>Gentrap</td></tr>
...
...
mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/mappingFront.ssp
View file @
ce94a022
...
...
@@ -5,8 +5,6 @@
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration)
<%@ var summary: SummaryDb %>
<%@ var rootPath: String %>
<%@ var runId: Int %>
...
...
mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/multisampleMappingFront.ssp
View file @
ce94a022
...
...
@@ -11,7 +11,7 @@
<%@ var pipeline: String %>
<%@ var runId: Int %>
<%@ var run: Run %>
<%@ var allSamples:
List
[Sample] %>
<%@ var allSamples:
Seq
[Sample] %>
#{
val samples = allSamples
val settings = summary.getSettingKeys(runId, pipeline,
...
...
shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp
View file @
ce94a022
...
...
@@ -19,7 +19,7 @@
<%@ var target: Option[String] = None %>
<%@ var caller: String = "final" %>
<%@ var runId: Int %>
<%@ var allSamples:
List
[Sample] %>
<%@ var allSamples:
Seq
[Sample] %>
#{
val fields = List("Hom", "HomVar", "Het", "HomRef", "NoCall", "Variant", "Total")
...
...
shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp
View file @
ce94a022
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#import(nl.lumc.sasc.biopet.utils.summary.db.Schema.Run)
#import(nl.lumc.sasc.biopet.utils.summary.db.Schema.Sample)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
...
...
@@ -8,8 +9,8 @@
<%@ var summary: SummaryDb %>
<%@ var runId: Int %>
<%@ var run: Run %>
<%@ var allSamples: Seq[Sample] %>
#{
val samples = Await.result(summary.getSamples(Some(runId)), Duration.Inf)
val settings = summary.getSettingKeys(runId, run.name,
keyValues = Map(
"contigs" -> List("reference", "contigs"),
...
...
@@ -33,7 +34,7 @@
<td>${settings.get("variantcallers")}</td>
</tr>
<tr><th>Reference</th><td>${settings.get("species")} - ${settings.get("name")}</td></tr>
<tr><th>Number of samples</th><td>${
s
amples.size}</td></tr>
<tr><th>Number of samples</th><td>${
allS
amples.size}</td></tr>
<tr><th>Annotation</th><td>${settings.get("annotation")}</td></tr>
<tr><th>Multisample variantcalling</th><td>${settings.get("multisample_variantcalling")}</td></tr>
<tr><th>Sv calling</th><td>${settings.get("sv_calling")}</td></tr>
...
...
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