Skip to content
GitLab
Projects
Groups
Snippets
Help
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
B
biopet.biopet
Project overview
Project overview
Details
Activity
Releases
Repository
Repository
Files
Commits
Branches
Tags
Contributors
Graph
Compare
CI / CD
CI / CD
Pipelines
Jobs
Schedules
Operations
Operations
Environments
Analytics
Analytics
CI / CD
Repository
Value Stream
Members
Members
Collapse sidebar
Close sidebar
Activity
Graph
Jobs
Commits
Open sidebar
Mirrors
biopet.biopet
Commits
c066cf08
Commit
c066cf08
authored
Mar 29, 2017
by
Peter van 't Hof
Browse files
Options
Browse Files
Download
Email Patches
Plain Diff
Removing sample and library queries and use the cache
parent
59100477
Changes
11
Hide whitespace changes
Inline
Side-by-side
Showing
11 changed files
with
78 additions
and
59 deletions
+78
-59
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp
...umc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp
+9
-3
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp
...lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp
+2
-3
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/clipping.ssp
...ces/nl/lumc/sasc/biopet/pipelines/bammetrics/clipping.ssp
+9
-6
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp
...c/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp
+8
-4
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp
...s/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp
+9
-6
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp
.../lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp
+9
-7
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp
...nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp
+9
-6
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp
...nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp
+9
-6
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
...c/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
+1
-3
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/librariesList.ssp
...sources/nl/lumc/sasc/biopet/core/report/librariesList.ssp
+10
-8
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/samplesList.ssp
...resources/nl/lumc/sasc/biopet/core/report/samplesList.ssp
+3
-7
No files found.
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._)
#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.SummaryDb.Implicts._)
...
@@ -16,8 +17,13 @@
...
@@ -16,8 +17,13 @@
<%@ var showTable: Boolean = true %>
<%@ var showTable: Boolean = true %>
<%@ var showIntro: Boolean = true%>
<%@ var showIntro: Boolean = true%>
<%@ var runId: Int %>
<%@ 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)
#if (showIntro)
<br/>
<br/>
...
@@ -74,12 +80,12 @@
...
@@ -74,12 +80,12 @@
val libs: List[Option[Int]] = (libId, sampleLevel) match {
val libs: List[Option[Int]] = (libId, sampleLevel) match {
case (_, true) => List(None)
case (_, true) => List(None)
case (Some(_), _) => List(libId)
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>
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a></td>
#for (libId <- libs)
#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 (libs.head != libId) <tr> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #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 @@
...
@@ -2,9 +2,8 @@
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %>
<%@ var summary: Summary %>
<%@ var rootPath: String %>
<%@ var rootPath: String %>
<%@ var sampleId: Option[String] %>
<%@ var sampleId: Option[Int] %>
<%@ var libId: Option[String] = None %>
<%@ var libId: Option[Int] = None %>
<table class="table">
<table class="table">
<tbody>
<tbody>
<tr><th>Pipeline</th><td>BamMetrics</td></tr>
<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._)
#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.SummaryDb.Implicts._)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#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(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
#import(java.io.File)
<%@ var summary: SummaryDb %>
<%@ var summary: SummaryDb %>
...
@@ -17,10 +16,14 @@
...
@@ -17,10 +16,14 @@
<%@ var showIntro: Boolean = true%>
<%@ var showIntro: Boolean = true%>
<%@ var runId: Int %>
<%@ var runId: Int %>
<%@ var fields: List[String] = List("min", "max", "mean", "median", "modal")%>
<%@ 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)
#if (showIntro)
<br/>
<br/>
<div class="row">
<div class="row">
...
@@ -74,12 +77,12 @@
...
@@ -74,12 +77,12 @@
val libs: List[Option[Int]] = (libId, sampleLevel) match {
val libs: List[Option[Int]] = (libId, sampleLevel) match {
case (_, true) => List(None)
case (_, true) => List(None)
case (Some(_), _) => List(libId)
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>
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a></td>
#for (libId <- libs)
#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 (libs.head != libId) <tr> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #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(nl.lumc.sasc.biopet.utils.IoUtils)
#import(org.apache.commons.io.FileUtils)
#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._)
#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.SummaryDb.Implicts._)
...
@@ -18,11 +19,14 @@
...
@@ -18,11 +19,14 @@
<%@ var target: Option[String] %>
<%@ var target: Option[String] %>
<%@ var runId: Int %>
<%@ 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 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">
<table class="table">
<thead><tr>
<thead><tr>
<th>sample</th>
<th>sample</th>
...
@@ -36,7 +40,7 @@
...
@@ -36,7 +40,7 @@
val libs: List[Option[Int]] = (libId, sampleLevel) match {
val libs: List[Option[Int]] = (libId, sampleLevel) match {
case (_, true) => List(None)
case (_, true) => List(None)
case (Some(_), _) => List(libId)
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>
<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._)
#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.SummaryDb.Implicts._)
#import(nl.lumc.sasc.biopet.utils.summary.db.Schema._)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#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(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
#import(java.io.File)
<%@ var summary: SummaryDb %>
<%@ var summary: SummaryDb %>
...
@@ -18,10 +17,14 @@
...
@@ -18,10 +17,14 @@
<%@ var showTable: Boolean = true %>
<%@ var showTable: Boolean = true %>
<%@ var showIntro: Boolean = true%>
<%@ var showIntro: Boolean = true%>
<%@ var runId: Int %>
<%@ 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)
#if (showIntro)
<br/>
<br/>
<div class="row">
<div class="row">
...
@@ -76,12 +79,12 @@
...
@@ -76,12 +79,12 @@
val libs: List[Option[Int]] = (libId, sampleLevel) match {
val libs: List[Option[Int]] = (libId, sampleLevel) match {
case (_, true) => List(None)
case (_, true) => List(None)
case (Some(_), _) => List(libId)
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>
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a></td>
#for (libId <- libs)
#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 (libs.head != libId) <tr> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #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.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._)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#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(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
#import(java.io.File)
<%@ var summary: SummaryDb %>
<%@ var summary: SummaryDb %>
...
@@ -17,11 +16,14 @@
...
@@ -17,11 +16,14 @@
<%@ var showIntro: Boolean = true%>
<%@ var showIntro: Boolean = true%>
<%@ var runId: Int %>
<%@ var runId: Int %>
<%@ var fields: List[String] = List("min", "max", "mean", "median", "modal")%>
<%@ 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)
#if (showIntro)
<br/>
<br/>
<div class="row">
<div class="row">
...
@@ -75,12 +77,12 @@
...
@@ -75,12 +77,12 @@
val libs: List[Option[Int]] = (libId, sampleLevel) match {
val libs: List[Option[Int]] = (libId, sampleLevel) match {
case (_, true) => List(None)
case (_, true) => List(None)
case (Some(_), _) => List(libId)
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>
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a></td>
#for (libId <- libs)
#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 (libs.head != libId) <tr> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #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._)
#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.SummaryDb.Implicts._)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#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(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
#import(java.io.File)
<%@ var summary: SummaryDb %>
<%@ var summary: SummaryDb %>
...
@@ -18,10 +17,14 @@
...
@@ -18,10 +17,14 @@
<%@ var showTable: Boolean = true %>
<%@ var showTable: Boolean = true %>
<%@ var showIntro: Boolean = true%>
<%@ var showIntro: Boolean = true%>
<%@ var runId: Int %>
<%@ 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)
#if (showIntro)
<br/>
<br/>
<div class="row">
<div class="row">
...
@@ -66,12 +69,12 @@
...
@@ -66,12 +69,12 @@
val libs: List[Option[Int]] = (libId, sampleLevel) match {
val libs: List[Option[Int]] = (libId, sampleLevel) match {
case (_, true) => List(None)
case (_, true) => List(None)
case (Some(_), _) => List(libId)
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>
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
#for (libId <- libs)
#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 (libs.head != libId) <tr> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #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._)
#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.SummaryDb.Implicts._)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#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(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
#import(java.io.File)
<%@ var summary: SummaryDb %>
<%@ var summary: SummaryDb %>
...
@@ -17,10 +16,14 @@
...
@@ -17,10 +16,14 @@
<%@ var showIntro: Boolean = true%>
<%@ var showIntro: Boolean = true%>
<%@ var runId: Int %>
<%@ 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 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)
#if (showIntro)
<br/>
<br/>
<div class="row">
<div class="row">
...
@@ -65,12 +68,12 @@
...
@@ -65,12 +68,12 @@
val libs: List[Option[Int]] = (libId, sampleLevel) match {
val libs: List[Option[Int]] = (libId, sampleLevel) match {
case (_, true) => List(None)
case (_, true) => List(None)
case (Some(_), _) => List(libId)
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>
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a></td>
#for (libId <- libs)
#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 (libs.head != libId) <tr> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #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 {
...
@@ -48,9 +48,7 @@ object BammetricsReport extends ReportBuilder {
ReportPage
(
bamMetricsPage
.
subPages
:::
List
(
ReportPage
(
bamMetricsPage
.
subPages
:::
List
(
"Versions"
->
ReportPage
(
List
(),
List
(
"Executables"
->
ReportSection
(
"/nl/lumc/sasc/biopet/core/report/executables.ssp"
"Versions"
->
ReportPage
(
List
(),
List
(
"Executables"
->
ReportSection
(
"/nl/lumc/sasc/biopet/core/report/executables.ssp"
)),
Map
()),
)),
Map
()),
"Files"
->
ReportPage
(
List
(),
List
(
"Files"
->
ReportPage
(
List
(),
List
(),
Map
())
"Input fastq files"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/bammetricsInputFile.ssp"
)
),
Map
())
),
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
,
...
...
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.utils.summary.db.Schema._)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration)
<%@ var summary: SummaryDb %>
<%@ var rootPath: String %>
<%@ var rootPath: String %>
<%@ var sampleId: Option[Int] = None %>
<%@ var sampleId: Option[Int] = None %>
<%@ var runId: Int %>
<%@ var allLibraries: Seq[Library] %>
<%@ var allSamples: Seq[Sample] %>
<table class="table">
<table class="table">
<thead><tr><th>Libraries</th></tr></thead>
<thead><tr><th>Libraries</th></tr></thead>
<tbody>
<tbody>
#for (lib <- Await.result(summary.getLibraries(runId = Some(runId)), Duration.Inf))
#{ val libs = sampleId match {
<tr><td><a href="${rootPath}Samples/${Await.result(summary.getSampleName(lib.sampleId), Duration.Inf)}/Libraries/${lib.name}/index.html">${lib}</a></td></tr>
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
#end
</tbody>
</tbody>
</table>
</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.utils.summary.db.Schema._)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration)
<%@ var summary: SummaryDb %>
<%@ var rootPath: String %>
<%@ var rootPath: String %>
<%@ var
runId: Int
%>
<%@ var
allSamples: Seq[Sample]
%>
<table class="table sortable-theme-bootstrap" data-sortable>
<table class="table sortable-theme-bootstrap" data-sortable>
<thead><tr><th data-sorted="true" data-sorted-direction="ascending">Sample</th></tr></thead>
<thead><tr><th data-sorted="true" data-sorted-direction="ascending">Sample</th></tr></thead>
<tbody>
<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">${sample.name}</a></td></tr>
<tr><td><a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a></td></tr>
#end
#end
</tbody>
</tbody>
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a 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