Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
bb9a3e4e
Commit
bb9a3e4e
authored
Mar 03, 2017
by
Peter van 't Hof
Browse files
Switch templates to scalaz
parent
18b8594a
Changes
9
Hide whitespace changes
Inline
Side-by-side
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp
View file @
bb9a3e4e
...
...
@@ -4,6 +4,8 @@
#import(scala.concurrent.duration.Duration)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
#import(scalaz._)
#import(Scalaz._)
<%@ var summary: SummaryDb %>
<%@ var sampleId: Option[Int] = None %>
<%@ var libId: Option[Int] = None %>
...
...
@@ -87,7 +89,7 @@
"Duplicates" -> List("flagstats", "Duplicates"),
"NotPrimaryAlignment" -> List("flagstats", "NotPrimaryAlignment")
)
val results = summary.getStatKeys(runId,
Right(
"bammetrics"
)
, Some(
Right(
"bamstats"
)
), sample = Some(
Left(
sample.id
)
), library = libId.map(
Left(_)
), keyValues = statsPaths)
val results = summary.getStatKeys(runId, "bammetrics"
.right
, Some("bamstats"
.right
), sample = Some(sample.id
.left
), library = libId.map(
_.left
), keyValues = statsPaths)
val total = results("All").getOrElse(0L).asInstanceOf[Long]
val mapped = results("Mapped").getOrElse(0L).asInstanceOf[Long]
val duplicates = results("Duplicates").getOrElse(0L).asInstanceOf[Long]
...
...
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/clipping.ssp
View file @
bb9a3e4e
...
...
@@ -4,6 +4,8 @@
#import(scala.concurrent.duration.Duration)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
#import(scalaz._)
#import(Scalaz._)
<%@ var summary: SummaryDb %>
<%@ var sampleId: Option[Int] = None %>
<%@ var libId: Option[Int] = None %>
...
...
@@ -82,7 +84,7 @@
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
#{
val statsPaths = fields.map(x => x -> List("clipping", "general", x)).toMap
val results = summary.getStatKeys(runId,
Right(
"bammetrics"
)
, Some(
Right(
"bamstats"
)
), sample = Some(
Left(
sample.id
)
), library = libId.map(
Left(_)
), keyValues = statsPaths)
val results = summary.getStatKeys(runId, "bammetrics"
.right
, Some("bamstats"
.right
), sample = Some(sample.id
.left
), library = libId.map(
_.left
), keyValues = statsPaths)
}#
#for (field <- fields)
<td>${results(field)}</td>
...
...
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp
View file @
bb9a3e4e
...
...
@@ -4,6 +4,8 @@
#import(scala.concurrent.duration.Duration)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
#import(scalaz._)
#import(Scalaz._)
<%@ var summary: SummaryDb %>
<%@ var sampleId: Option[Int] = None %>
<%@ var libId: Option[Int] = None %>
...
...
@@ -84,7 +86,7 @@
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
#{
val statsPaths = fields.map(x => x -> List("metrics", x.toUpperCase)).toMap
val results = summary.getStatKeys(runId,
Right(
"bammetrics"
), Some(Right
("CollectInsertSizeMetrics"
)
), sample = Some(
Left(
sample.id
)
), library = libId.map(
Left(_)
), keyValues = statsPaths)
val results = summary.getStatKeys(runId, "bammetrics"
.right, Some
("CollectInsertSizeMetrics"
.right
), sample = Some(sample.id
.left
), library = libId.map(
_.left
), keyValues = statsPaths)
}#
#for (field <- fields)
<td>${results(field)}</td>
...
...
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp
View file @
bb9a3e4e
...
...
@@ -4,6 +4,8 @@
#import(scala.concurrent.duration.Duration)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
#import(scalaz._)
#import(Scalaz._)
<%@ var summary: SummaryDb %>
<%@ var sampleId: Option[Int] = None %>
<%@ var libId: Option[Int] = None %>
...
...
@@ -83,7 +85,7 @@
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
#{
val statsPaths = fields.map(x => x -> List("mapping_quality", "general", x)).toMap
val results = summary.getStatKeys(runId,
Right(
"bammetrics"
)
, Some(
Right(
"bamstats"
)
), sample = Some(
Left(
sample.id
)
), library = libId.map(
Left(_)
), keyValues = statsPaths)
val results = summary.getStatKeys(runId, "bammetrics"
.right
, Some("bamstats"
.right
), sample = Some(sample.id
.left
), library = libId.map(
_.left
), keyValues = statsPaths)
}#
#for (field <- fields)
<td>${results(field)}</td>
...
...
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp
View file @
bb9a3e4e
...
...
@@ -4,6 +4,8 @@
#import(scala.concurrent.duration.Duration)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
#import(scalaz._)
#import(Scalaz._)
<%@ var summary: SummaryDb %>
<%@ var sampleId: Option[Int] = None %>
<%@ var libId: Option[Int] = None %>
...
...
@@ -73,7 +75,7 @@
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
#{
val statsPaths = fields.map(x => x -> List("metrics", x)).toMap
val results = summary.getStatKeys(runId,
Right(
"bammetrics"
)
, Some(
Right("wgs")
), sample = Some(
Left(
sample.id
)
), library = libId.map(
Left(_)
), keyValues = statsPaths)
val results = summary.getStatKeys(runId, "bammetrics"
.right
, Some(
"wgs".right
), sample = Some(sample.id
.left
), library = libId.map(
_.left
), keyValues = statsPaths)
}#
#for (field <- fields)
<td>${results(field)}</td>
...
...
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/reference.ssp
View file @
bb9a3e4e
...
...
@@ -2,7 +2,8 @@
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration)
#import(scalaz._)
#import(Scalaz._)
<%@ var summary: SummaryDb %>
<%@ var rootPath: String %>
<%@ var pipeline: String %>
...
...
@@ -10,7 +11,7 @@
#{
val settings = summary.getSettingKeys(runId,
Right(
pipeline
)
,
val settings = summary.getSettingKeys(runId, pipeline
.right
,
keyValues = Map(
"contigs" -> List("reference", "contigs"),
"species" -> List("reference", "species"),
...
...
@@ -18,7 +19,7 @@
))
val contigs = settings.getOrElse("contigs", Some(Map())).getOrElse(Map()).asInstanceOf[Map[String, Map[String, Any]]]
val referenceFile = Await.result(summary.getFile(runId,
Right(
pipeline
)
, None, None, None, key = "referenceFasta"), Duration.Inf)
val referenceFile = Await.result(summary.getFile(runId, pipeline
.right
, None, None, None, key = "referenceFasta"), Duration.Inf)
}#
<table class="table">
...
...
flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp
View file @
bb9a3e4e
...
...
@@ -5,6 +5,8 @@
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport)
#import(java.io.File)
#import(scalaz._)
#import(Scalaz._)
<%@ var summary: SummaryDb %>
<%@ var runId: Int %>
<%@ var sampleId: Option[Int] = None %>
...
...
@@ -18,7 +20,7 @@
#{
val samples = Await.result(summary.getSamples(runId = Some(runId), sampleId = sampleId), Duration.Inf)
val libraries = Await.result(summary.getLibraries(runId = Some(runId), sampleId = sampleId), Duration.Inf)
val settings = summary.getSettingsForLibraries(runId,
Right(
"flexiprep"
)
, keyValues = Map(
val settings = summary.getSettingsForLibraries(runId, "flexiprep"
.right
, keyValues = Map(
"skip_trim" -> List("skip_trim"), "skip_clip" -> List("skip_clip"), "paired" -> List("paired")))
settings.count(_._2.getOrElse("skip_trim", None) == Some(true))
val trimCount = settings.count(_._2.getOrElse("skip_trim", None) == Some(true))
...
...
@@ -26,7 +28,7 @@
val librariesCount = libraries.size
val paired: Boolean = if (sampleId.isDefined && libId.isDefined)
summary.getSettingKeys(runId,
Right(
"flexiprep"
)
, None, sampleId.map(
Left(_)
), libId.map(
Left(_)
), keyValues = Map("paired" -> List("paired"))).getOrElse("paired", None) == Some(true)
summary.getSettingKeys(runId, "flexiprep"
.right
, None, sampleId.map(
_.left
), libId.map(
_.left
), keyValues = Map("paired" -> List("paired"))).getOrElse("paired", None) == Some(true)
else settings.count(_._2.getOrElse("paired", None) == Some(true)) >= 1
}#
#if (showIntro)
...
...
@@ -137,8 +139,8 @@
#if (read == "R2") </tr><tr> #end
#{
val statsPaths = Map("num_total" -> List("bases", "num_total"))
val seqstatStats = summary.getStatKeys(runId,
Right(
"flexiprep"
)
, Some(
Right
("seqstat_" + read)), sample = Some(
Left(
sample.id
)
), library = Some(
Left(
lib.id
)
), keyValues = statsPaths)
val seqstatQcStats = summary.getStatKeys(runId,
Right(
"flexiprep"
)
, Some(
Right
("seqstat_" + read + "_qc")), sample = Some(
Left(
sample.id
)
), library = Some(
Left(
lib.id
)
), keyValues = statsPaths)
val seqstatStats = summary.getStatKeys(runId, "flexiprep"
.right
, Some(("seqstat_" + read)
.right
), sample = Some(sample.id
.left
), library = Some(lib.id
.left
), keyValues = statsPaths)
val seqstatQcStats = summary.getStatKeys(runId, "flexiprep"
.right
, Some(("seqstat_" + read + "_qc")
.right
), sample = Some(sample.id
.left
), library = Some(lib.id
.left
), keyValues = statsPaths)
val beforeTotal = seqstatStats("num_total").getOrElse(0).toString.toLong
val afterTotal = seqstatQcStats("num_total").getOrElse(0).toString.toLong
...
...
flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFastQcPlot.ssp
View file @
bb9a3e4e
...
...
@@ -5,6 +5,8 @@
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(org.apache.commons.io.FileUtils)
#import(java.io.File)
#import(scalaz._)
#import(Scalaz._)
<%@ var summary: SummaryDb %>
<%@ var runId: Int %>
<%@ var sampleId: Option[Int] %>
...
...
@@ -12,7 +14,7 @@
<%@ var plot: String %>
<%@ var outputDir: File %>
#{
val settings = summary.getSettingKeys(runId,
Right(
"flexiprep"
)
, None, sampleId.map(
Left(_)
), libId.map(
Left(_)
), keyValues = Map(
val settings = summary.getSettingKeys(runId, "flexiprep"
.right
, None, sampleId.map(
_.left
), libId.map(
_.left
), keyValues = Map(
"skip_trim" -> List("skip_trim"), "skip_clip" -> List("skip_clip"), "paired" -> List("paired")))
val paired: Boolean = settings("paired") == Some(true)
...
...
@@ -20,7 +22,7 @@
val skipTrim: Boolean = settings("skip_trim") == Some(true)
def getPlot(read:String) = {
val file = Await.result(summary.getFile(runId,
Right(
"flexiprep"
)
, Some(
Right(read)
), sampleId.map(
Left(_)
), libId.map(
Left(_)
), plot), Duration.Inf)
val file = Await.result(summary.getFile(runId, "flexiprep"
.right
, Some(
read.right
), sampleId.map(
_.left
), libId.map(
_.left
), plot), Duration.Inf)
file.collect {
case path => {
val file = new File(path.path.toString)
...
...
@@ -32,7 +34,7 @@
}
def plotAvailable(read:String) = {
val file = Await.result(summary.getFile(runId,
Right(
"flexiprep"
)
, Some(
Right(read)
), sampleId.map(
Left(_)
), libId.map(
Left(_)
), plot), Duration.Inf)
val file = Await.result(summary.getFile(runId, "flexiprep"
.right
, Some(
read.right
), sampleId.map(
_.left
), libId.map(
_.left
), plot), Duration.Inf)
file.map(x => new File(x.path).exists()).getOrElse(false)
}
...
...
flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp
View file @
bb9a3e4e
...
...
@@ -4,6 +4,8 @@
#import(scala.concurrent.duration.Duration)
#import(java.io.File)
#import(nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport)
#import(scalaz._)
#import(Scalaz._)
<%@ var summary: SummaryDb %>
<%@ var runId: Int %>
<%@ var sampleId: Option[Int] = None %>
...
...
@@ -17,7 +19,7 @@
#{
val samples = Await.result(summary.getSamples(runId = Some(runId), sampleId = sampleId), Duration.Inf)
val libraries = Await.result(summary.getLibraries(runId = Some(runId), sampleId = sampleId), Duration.Inf)
val settings = summary.getSettingsForLibraries(runId,
Right(
"flexiprep"
)
, keyValues = Map(
val settings = summary.getSettingsForLibraries(runId, "flexiprep"
.right
, keyValues = Map(
"skip_trim" -> List("skip_trim"), "skip_clip" -> List("skip_clip"), "paired" -> List("paired")))
settings.count(_._2.getOrElse("skip_trim", None) == Some(true))
val trimCount = settings.count(_._2.getOrElse("skip_trim", None) == Some(true))
...
...
@@ -25,7 +27,7 @@
val librariesCount = libraries.size
val paired: Boolean = if (sampleId.isDefined && libId.isDefined)
summary.getSettingKeys(runId,
Right(
"flexiprep"
)
, None, sampleId.map(
Left(_)
), libId.map(
Left(_)
), keyValues = Map("paired" -> List("paired"))).getOrElse("paired", None) == Some(true)
summary.getSettingKeys(runId, "flexiprep"
.right
, None, sampleId.map(
_.left
), libId.map(
_.left
), keyValues = Map("paired" -> List("paired"))).getOrElse("paired", None) == Some(true)
else settings.count(_._2.getOrElse("paired", None) == Some(true)) >= 1
}#
...
...
@@ -142,15 +144,15 @@
#if (read == "R2") </tr><tr> #end
#{
val seqstatPaths = Map("num_total" -> List("reads", "num_total"))
val seqstatStats = summary.getStatKeys(runId,
Right(
"flexiprep"
)
, Some(
Right
("seqstat_" + read)), sample = Some(
Left(
sample.id
)
), library = Some(
Left(
lib.id
)
), keyValues = seqstatPaths)
val seqstatQcStats = summary.getStatKeys(runId,
Right(
"flexiprep"
)
, Some(
Right
("seqstat_" + read + "_qc")), sample = Some(
Left(
sample.id
)
), library = Some(
Left(
lib.id
)
), keyValues = seqstatPaths)
val seqstatStats = summary.getStatKeys(runId, "flexiprep"
.right
, Some(("seqstat_" + read)
.right
), sample = Some(sample.id
.left
), library = Some(lib.id
.left
), keyValues = seqstatPaths)
val seqstatQcStats = summary.getStatKeys(runId, "flexiprep"
.right
, Some(("seqstat_" + read + "_qc")
.right
), sample = Some(sample.id
.left
), library = Some(lib.id
.left
), keyValues = seqstatPaths)
val clippingPaths = Map("num_reads_discarded_too_short" -> List("num_reads_discarded_too_short"),
"num_reads_discarded_too_long" -> List("num_reads_discarded_too_long"))
val clippingStats = summary.getStatKeys(runId,
Right(
"flexiprep"
)
, Some(
Right
("clipping_" + read)), sample = Some(
Left(
sample.id
)
), library = Some(
Left(
lib.id
)
), keyValues = clippingPaths)
val clippingStats = summary.getStatKeys(runId, "flexiprep"
.right
, Some(("clipping_" + read)
.right
), sample = Some(sample.id
.left
), library = Some(lib.id
.left
), keyValues = clippingPaths)
val trimmingPaths = Map("num_reads_discarded" -> List("num_reads_discarded_" + read))
val trimmingStats = summary.getStatKeys(runId,
Right(
"flexiprep"
)
, Some(
Right(
"trimming"
)
), sample = Some(
Left(
sample.id
)
), library = Some(
Left(
lib.id
)
), keyValues = trimmingPaths)
val trimmingStats = summary.getStatKeys(runId, "flexiprep"
.right
, Some("trimming"
.right
), sample = Some(sample.id
.left
), library = Some(lib.id
.left
), keyValues = trimmingPaths)
val beforeTotal = seqstatStats("num_total").getOrElse(0).toString.toLong
val afterTotal = seqstatQcStats("num_total").getOrElse(0).toString.toLong
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new 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