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Mirrors
biopet.biopet
Commits
c066cf08
Commit
c066cf08
authored
Mar 29, 2017
by
Peter van 't Hof
Browse files
Removing sample and library queries and use the cache
parent
59100477
Changes
11
Hide whitespace changes
Inline
Side-by-side
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp
View file @
c066cf08
#import(nl.lumc.sasc.biopet.utils.summary.db.Schema._)
#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._)
...
...
@@ -16,8 +17,13 @@
<%@ var showTable: Boolean = true %>
<%@ var showIntro: Boolean = true%>
<%@ var runId: Int %>
<%@ var allSamples: Seq[Sample] %>
<%@ var allLibraries: Seq[Library] %>
#{
val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
val samples = sampleId match {
case Some(id) => allSamples.filter(_.id == id).toList
case _ => allSamples.toList
}
}#
#if (showIntro)
<br/>
...
...
@@ -74,12 +80,12 @@
val libs: List[Option[Int]] = (libId, sampleLevel) match {
case (_, true) => List(None)
case (Some(_), _) => List(libId)
case _ =>
Await.result(summary.getLibraries(
sampleId =
Some(
sample.id)
, runId = Some(runId)), Duration.Inf)
.map(x => Some(x.id)).toList
case _ =>
allLibraries.filter(_.
sampleId =
=
sample.id).map(x => Some(x.id)).toList
}
}#
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a></td>
#for (libId <- libs)
#{ val libName = libId.map(l =>
Await.result(summary.getLibraryName(l), Duration.Inf)
) }#
#{ val libName = libId.map(l =>
allLibraries.find(_.id == l).get.name
) }#
#if (libs.head != libId) <tr> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
#{
...
...
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp
View file @
c066cf08
...
...
@@ -2,9 +2,8 @@
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %>
<%@ var rootPath: String %>
<%@ var sampleId: Option[String] %>
<%@ var libId: Option[String] = None %>
<%@ var sampleId: Option[Int] %>
<%@ var libId: Option[Int] = None %>
<table class="table">
<tbody>
<tr><th>Pipeline</th><td>BamMetrics</td></tr>
...
...
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/clipping.ssp
View file @
c066cf08
#import(nl.lumc.sasc.biopet.utils.summary.db.Schema._)
#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._)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
<%@ var summary: SummaryDb %>
...
...
@@ -17,10 +16,14 @@
<%@ var showIntro: Boolean = true%>
<%@ var runId: Int %>
<%@ var fields: List[String] = List("min", "max", "mean", "median", "modal")%>
<%@ var allSamples: Seq[Sample] %>
<%@ var allLibraries: Seq[Library] %>
#{
val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
val samples = sampleId match {
case Some(id) => allSamples.filter(_.id == id).toList
case _ => allSamples.toList
}
}#
#if (showIntro)
<br/>
<div class="row">
...
...
@@ -74,12 +77,12 @@
val libs: List[Option[Int]] = (libId, sampleLevel) match {
case (_, true) => List(None)
case (Some(_), _) => List(libId)
case _ =>
Await.result(summary.getLibraries(
sampleId =
Some(
sample.id)
, runId = Some(runId)), Duration.Inf)
.map(x => Some(x.id)).toList
case _ =>
allLibraries.filter(_.
sampleId =
=
sample.id).map(x => Some(x.id)).toList
}
}#
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a></td>
#for (libId <- libs)
#{ val libName = libId.map(l =>
Await.result(summary.getLibraryName(l), Duration.Inf)
) }#
#{ val libName = libId.map(l =>
allLibraries.find(_.id == l).get.name
) }#
#if (libs.head != libId) <tr> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
#{
...
...
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp
View file @
c066cf08
#import(nl.lumc.sasc.biopet.utils.IoUtils)
#import(org.apache.commons.io.FileUtils)
#import(nl.lumc.sasc.biopet.utils.summary.db.Schema._)
#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._)
...
...
@@ -18,11 +19,14 @@
<%@ var target: Option[String] %>
<%@ var runId: Int %>
<%@ var fields: List[String] = List("mean", "median", "max", "horizontal", "frac_min_10x", "frac_min_20x", "frac_min_30x", "frac_min_40x", "frac_min_50x") %>
<%@ var allSamples: Seq[Sample] %>
<%@ var allLibraries: Seq[Library] %>
#{
val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
val samples = sampleId match {
case Some(id) => allSamples.filter(_.id == id).toList
case _ => allSamples.toList
}
}#
<table class="table">
<thead><tr>
<th>sample</th>
...
...
@@ -36,7 +40,7 @@
val libs: List[Option[Int]] = (libId, sampleLevel) match {
case (_, true) => List(None)
case (Some(_), _) => List(libId)
case _ =>
Await.result(summary.getLibraries(
sampleId =
Some(
sample.id)
, runId = Some(runId)), Duration.Inf)
.map(x => Some(x.id)).toList
case _ =>
allLibraries.filter(_.
sampleId =
=
sample.id).map(x => Some(x.id)).toList
}
}#
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a></td>
...
...
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp
View file @
c066cf08
#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._)
#import(nl.lumc.sasc.biopet.utils.summary.db.Schema._)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
<%@ var summary: SummaryDb %>
...
...
@@ -18,10 +17,14 @@
<%@ var showTable: Boolean = true %>
<%@ var showIntro: Boolean = true%>
<%@ var runId: Int %>
<%@ var allSamples: Seq[Sample] %>
<%@ var allLibraries: Seq[Library] %>
#{
val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
val samples = sampleId match {
case Some(id) => allSamples.filter(_.id == id).toList
case _ => allSamples.toList
}
}#
#if (showIntro)
<br/>
<div class="row">
...
...
@@ -76,12 +79,12 @@
val libs: List[Option[Int]] = (libId, sampleLevel) match {
case (_, true) => List(None)
case (Some(_), _) => List(libId)
case _ =>
Await.result(summary.getLibraries(
sampleId =
Some(
sample.id)
, runId = Some(runId)), Duration.Inf)
.map(x => Some(x.id)).toList
case _ =>
allLibraries.filter(_.
sampleId =
=
sample.id).map(x => Some(x.id)).toList
}
}#
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a></td>
#for (libId <- libs)
#{ val libName = libId.map(l =>
Await.result(summary.getLibraryName(l), Duration.Inf)
) }#
#{ val libName = libId.map(l =>
allLibraries.find(_.id == l).get.name
) }#
#if (libs.head != libId) <tr> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
#{
...
...
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp
View file @
c066cf08
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#import(nl.lumc.sasc.biopet.utils.summary.db.Schema._)
#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)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
<%@ var summary: SummaryDb %>
...
...
@@ -17,11 +16,14 @@
<%@ var showIntro: Boolean = true%>
<%@ var runId: Int %>
<%@ var fields: List[String] = List("min", "max", "mean", "median", "modal")%>
<%@ var allSamples: Seq[Sample] %>
<%@ var allLibraries: Seq[Library] %>
#{
val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
val samples = sampleId match {
case Some(id) => allSamples.filter(_.id == id).toList
case _ => allSamples.toList
}
}#
#if (showIntro)
<br/>
<div class="row">
...
...
@@ -75,12 +77,12 @@
val libs: List[Option[Int]] = (libId, sampleLevel) match {
case (_, true) => List(None)
case (Some(_), _) => List(libId)
case _ =>
Await.result(summary.getLibraries(
sampleId =
Some(
sample.id)
, runId = Some(runId)), Duration.Inf)
.map(x => Some(x.id)).toList
case _ =>
allLibraries.filter(_.
sampleId =
=
sample.id).map(x => Some(x.id)).toList
}
}#
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a></td>
#for (libId <- libs)
#{ val libName = libId.map(l =>
Await.result(summary.getLibraryName(l), Duration.Inf)
) }#
#{ val libName = libId.map(l =>
allLibraries.find(_.id == l).get.name
) }#
#if (libs.head != libId) <tr> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
#{
...
...
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp
View file @
c066cf08
#import(nl.lumc.sasc.biopet.utils.summary.db.Schema._)
#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._)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
<%@ var summary: SummaryDb %>
...
...
@@ -18,10 +17,14 @@
<%@ var showTable: Boolean = true %>
<%@ var showIntro: Boolean = true%>
<%@ var runId: Int %>
<%@ var allSamples: Seq[Sample] %>
<%@ var allLibraries: Seq[Library] %>
#{
val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
val samples = sampleId match {
case Some(id) => allSamples.filter(_.id == id).toList
case _ => allSamples.toList
}
}#
#if (showIntro)
<br/>
<div class="row">
...
...
@@ -66,12 +69,12 @@
val libs: List[Option[Int]] = (libId, sampleLevel) match {
case (_, true) => List(None)
case (Some(_), _) => List(libId)
case _ =>
Await.result(summary.getLibraries(
sampleId =
Some(
sample.id)
, runId = Some(runId)), Duration.Inf)
.map(x => Some(x.id)).toList
case _ =>
allLibraries.filter(_.
sampleId =
=
sample.id).map(x => Some(x.id)).toList
}
}#
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
#for (libId <- libs)
#{ val libName = libId.map(l =>
Await.result(summary.getLibraryName(l), Duration.Inf)
) }#
#{ val libName = libId.map(l =>
allLibraries.find(_.id == l).get.name
) }#
#if (libs.head != libId) <tr> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
#{
...
...
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp
View file @
c066cf08
#import(nl.lumc.sasc.biopet.utils.summary.db.Schema._)
#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._)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
<%@ var summary: SummaryDb %>
...
...
@@ -17,10 +16,14 @@
<%@ var showIntro: Boolean = true%>
<%@ var runId: Int %>
<%@ var fields: List[String] = List("mean_coverage", "pct_5x", "pct_10x", "pct_15x", "pct_20x", "pct_25x", "pct_30x", "pct_40x", "pct_50x", "pct_60x", "pct_70x", "pct_80x", "pct_90x", "pct_100x")%>
<%@ var allSamples: Seq[Sample] %>
<%@ var allLibraries: Seq[Library] %>
#{
val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
val samples = sampleId match {
case Some(id) => allSamples.filter(_.id == id).toList
case _ => allSamples.toList
}
}#
#if (showIntro)
<br/>
<div class="row">
...
...
@@ -65,12 +68,12 @@
val libs: List[Option[Int]] = (libId, sampleLevel) match {
case (_, true) => List(None)
case (Some(_), _) => List(libId)
case _ =>
Await.result(summary.getLibraries(
sampleId =
Some(
sample.id)
, runId = Some(runId)), Duration.Inf)
.map(x => Some(x.id)).toList
case _ =>
allLibraries.filter(_.
sampleId =
=
sample.id).map(x => Some(x.id)).toList
}
}#
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a></td>
#for (libId <- libs)
#{ val libName = libId.map(l =>
Await.result(summary.getLibraryName(l), Duration.Inf)
) }#
#{ val libName = libId.map(l =>
allLibraries.find(_.id == l).get.name
) }#
#if (libs.head != libId) <tr> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
#{
...
...
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @
c066cf08
...
...
@@ -48,9 +48,7 @@ object BammetricsReport extends ReportBuilder {
ReportPage
(
bamMetricsPage
.
subPages
:::
List
(
"Versions"
->
ReportPage
(
List
(),
List
(
"Executables"
->
ReportSection
(
"/nl/lumc/sasc/biopet/core/report/executables.ssp"
)),
Map
()),
"Files"
->
ReportPage
(
List
(),
List
(
"Input fastq files"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/bammetricsInputFile.ssp"
)
),
Map
())
"Files"
->
ReportPage
(
List
(),
List
(),
Map
())
),
List
(
"Report"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp"
)
)
:::
bamMetricsPage
.
sections
,
...
...
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/librariesList.ssp
View file @
c066cf08
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration)
<%@ var summary: SummaryDb %>
#import(nl.lumc.sasc.biopet.utils.summary.db.Schema._)
<%@ var rootPath: String %>
<%@ var sampleId: Option[Int] = None %>
<%@ var runId: Int %>
<%@ var allLibraries: Seq[Library] %>
<%@ var allSamples: Seq[Sample] %>
<table class="table">
<thead><tr><th>Libraries</th></tr></thead>
<tbody>
#for (lib <- Await.result(summary.getLibraries(runId = Some(runId)), Duration.Inf))
<tr><td><a href="${rootPath}Samples/${Await.result(summary.getSampleName(lib.sampleId), Duration.Inf)}/Libraries/${lib.name}/index.html">${lib}</a></td></tr>
#{ val libs = sampleId match {
case Some(id) => allLibraries.filter(_.sampleId == id)
case _ => allLibraries
} }#
#for (lib <- libs)
#{ val sampleName: String = allSamples.find(_.id == lib.sampleId).get.name }#
<tr><td><a href="${rootPath}Samples/${sampleName}/Libraries/${lib.name}/index.html">${lib}</a></td></tr>
#end
</tbody>
</table>
\ No newline at end of file
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/samplesList.ssp
View file @
c066cf08
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration)
<%@ var summary: SummaryDb %>
#import(nl.lumc.sasc.biopet.utils.summary.db.Schema._)
<%@ var rootPath: String %>
<%@ var
runId: Int
%>
<%@ var
allSamples: Seq[Sample]
%>
<table class="table sortable-theme-bootstrap" data-sortable>
<thead><tr><th data-sorted="true" data-sorted-direction="ascending">Sample</th></tr></thead>
<tbody>
#for (sample <-
Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
)
#for (sample <-
allSamples
)
<tr><td><a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a></td></tr>
#end
</tbody>
...
...
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