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biopet.biopet
Commit 99c245a2 authored by Peter van 't Hof's avatar Peter van 't Hof
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Fixed report of Carp

parent 346fcbff
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Showing with 39 additions and 41 deletions
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp
View file @ 99c245a2
#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)
#import(scalaz._)
#import(Scalaz._)
<%@ var summary: SummaryDb %>
<%@ var sampleId: Option[Int] = None %>
<%@ var libId: Option[Int] = None %>
......@@ -89,7 +89,7 @@
"Duplicates" -> List("flagstats", "Duplicates"),
"NotPrimaryAlignment" -> List("flagstats", "NotPrimaryAlignment")
)
val results = summary.getStatKeys(runId, "bammetrics".right, Some("bamstats".right), sample = Some(sample.id.left), library = libId.map(_.left), keyValues = statsPaths)
val results = summary.getStatKeys(runId, "bammetrics", "bamstats", sample = sample.id, library = libId.map(LibraryId).getOrElse(NoLibrary), 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 @ 99c245a2
#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)
#import(scalaz._)
#import(Scalaz._)
<%@ var summary: SummaryDb %>
<%@ var sampleId: Option[Int] = None %>
<%@ var libId: Option[Int] = None %>
......@@ -84,7 +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, "bammetrics".right, Some("bamstats".right), sample = Some(sample.id.left), library = libId.map(_.left), keyValues = statsPaths)
val results = summary.getStatKeys(runId, "bammetrics", "bamstats", sample = sample.id, library = libId.map(LibraryId).getOrElse(NoLibrary), keyValues = statsPaths)
}#
#for (field <- fields)
<td>${results(field)}</td>
......
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp
View file @ 99c245a2
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
#import(scalaz._)
#import(Scalaz._)
<%@ var summary: SummaryDb %>
<%@ var sampleId: Option[Int] = None %>
<%@ var libId: Option[Int] = None %>
......@@ -86,7 +86,7 @@
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
#{
val statsPaths = fields.map(x => x -> List("metrics", x.toUpperCase)).toMap
val results = summary.getStatKeys(runId, "bammetrics".right, Some("CollectInsertSizeMetrics".right), sample = Some(sample.id.left), library = libId.map(_.left), keyValues = statsPaths)
val results = summary.getStatKeys(runId, "bammetrics", "CollectInsertSizeMetrics", sample = sample.id, library = libId.map(LibraryId).getOrElse(NoLibrary), keyValues = statsPaths)
}#
#for (field <- fields)
<td>${results(field)}</td>
......
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp
View file @ 99c245a2
#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)
#import(scalaz._)
#import(Scalaz._)
<%@ var summary: SummaryDb %>
<%@ var sampleId: Option[Int] = None %>
<%@ var libId: Option[Int] = None %>
......@@ -85,7 +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, "bammetrics".right, Some("bamstats".right), sample = Some(sample.id.left), library = libId.map(_.left), keyValues = statsPaths)
val results = summary.getStatKeys(runId, "bammetrics", "bamstats", sample = sample.id, library = libId.map(LibraryId).getOrElse(NoLibrary), keyValues = statsPaths)
}#
#for (field <- fields)
<td>${results(field)}</td>
......
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp
View file @ 99c245a2
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
#import(scalaz._)
#import(Scalaz._)
<%@ var summary: SummaryDb %>
<%@ var sampleId: Option[Int] = None %>
<%@ var libId: Option[Int] = None %>
......@@ -75,7 +75,7 @@
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
#{
val statsPaths = fields.map(x => x -> List("metrics", x)).toMap
val results = summary.getStatKeys(runId, "bammetrics".right, Some("wgs".right), sample = Some(sample.id.left), library = libId.map(_.left), keyValues = statsPaths)
val results = summary.getStatKeys(runId, "bammetrics", "wgs", sample = sample.id, library = libId.map(LibraryId).getOrElse(NoLibrary), keyValues = statsPaths)
}#
#for (field <- fields)
<td>${results(field)}</td>
......
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/reference.ssp
View file @ 99c245a2
#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(scalaz._)
#import(Scalaz._)
<%@ var summary: SummaryDb %>
<%@ var rootPath: String %>
<%@ var pipeline: String %>
<%@ var runId: Int %>
#{
val settings = summary.getSettingKeys(runId, pipeline.right,
val settings = summary.getSettingKeys(runId, pipeline,
keyValues = Map(
"contigs" -> List("reference", "contigs"),
"species" -> List("reference", "species"),
......@@ -19,7 +17,7 @@
))
val contigs = settings.getOrElse("contigs", Some(Map())).getOrElse(Map()).asInstanceOf[Map[String, Map[String, Any]]]
val referenceFile = Await.result(summary.getFile(runId, pipeline.right, None, None, None, key = "referenceFasta"), Duration.Inf)
val referenceFile = Await.result(summary.getFile(runId, pipeline, key = "referenceFasta"), Duration.Inf)
}#
<table class="table">
......
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
View file @ 99c245a2
......@@ -21,13 +21,13 @@ import nl.lumc.sasc.biopet.utils.summary.db.Schema.{ Library, Sample }
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
import nl.lumc.sasc.biopet.utils.{ IoUtils, Logging, ToolCommand }
import org.broadinstitute.gatk.utils.commandline.Input
import nl.lumc.sasc.biopet.utils.tryToParseNumber
import org.fusesource.scalate.{ TemplateEngine, TemplateSource }
import scala.collection.mutable
import scala.concurrent.{ Await, Future }
import scala.concurrent.duration.Duration
import scala.language.postfixOps
import scala.language.implicitConversions
/**
* This trait is meant to make an extension for a report object
......
flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp
View file @ 99c245a2
#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.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 %>
......@@ -20,7 +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, "flexiprep".right, keyValues = Map(
val settings = summary.getSettingsForLibraries(runId, "flexiprep", 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))
......@@ -28,7 +28,7 @@
val librariesCount = libraries.size
val paired: Boolean = if (sampleId.isDefined && libId.isDefined)
summary.getSettingKeys(runId, "flexiprep".right, None, sampleId.map(_.left), libId.map(_.left), keyValues = Map("paired" -> List("paired"))).getOrElse("paired", None) == Some(true)
summary.getSettingKeys(runId, "flexiprep", NoModule, SampleId(sampleId.get), LibraryId(libId.get), keyValues = Map("paired" -> List("paired"))).getOrElse("paired", None) == Some(true)
else settings.count(_._2.getOrElse("paired", None) == Some(true)) >= 1
}#
#if (showIntro)
......@@ -139,8 +139,8 @@
#if (read == "R2") </tr><tr> #end
#{
val statsPaths = Map("num_total" -> List("bases", "num_total"))
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 seqstatStats = summary.getStatKeys(runId, "flexiprep", "seqstat_" + read, sample = sample.id, library = lib.id, keyValues = statsPaths)
val seqstatQcStats = summary.getStatKeys(runId, "flexiprep", "seqstat_" + read + "_qc", sample = sample.id, library = lib.id, 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 @ 99c245a2
#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.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] %>
......@@ -14,7 +14,7 @@
<%@ var plot: String %>
<%@ var outputDir: File %>
#{
val settings = summary.getSettingKeys(runId, "flexiprep".right, None, sampleId.map(_.left), libId.map(_.left), keyValues = Map(
val settings = summary.getSettingKeys(runId, "flexiprep", NoModule, SampleId(sampleId.get), LibraryId(libId.get), keyValues = Map(
"skip_trim" -> List("skip_trim"), "skip_clip" -> List("skip_clip"), "paired" -> List("paired")))
val paired: Boolean = settings("paired") == Some(true)
......@@ -22,7 +22,7 @@
val skipTrim: Boolean = settings("skip_trim") == Some(true)
def getPlot(read:String) = {
val file = Await.result(summary.getFile(runId, "flexiprep".right, Some(read.right), sampleId.map(_.left), libId.map(_.left), plot), Duration.Inf)
val file = Await.result(summary.getFile(runId, "flexiprep", read, SampleId(sampleId.get), LibraryId(libId.get), plot), Duration.Inf)
file.collect {
case path => {
val file = new File(path.path.toString)
......@@ -34,7 +34,7 @@
}
def plotAvailable(read:String) = {
val file = Await.result(summary.getFile(runId, "flexiprep".right, Some(read.right), sampleId.map(_.left), libId.map(_.left), plot), Duration.Inf)
val file = Await.result(summary.getFile(runId, "flexiprep", read, SampleId(sampleId.get), LibraryId(libId.get), 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 @ 99c245a2
#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(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 %>
......@@ -19,7 +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, "flexiprep".right, keyValues = Map(
val settings = summary.getSettingsForLibraries(runId, "flexiprep", 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))
......@@ -27,7 +27,7 @@
val librariesCount = libraries.size
val paired: Boolean = if (sampleId.isDefined && libId.isDefined)
summary.getSettingKeys(runId, "flexiprep".right, None, sampleId.map(_.left), libId.map(_.left), keyValues = Map("paired" -> List("paired"))).getOrElse("paired", None) == Some(true)
summary.getSettingKeys(runId, "flexiprep", NoModule, SampleId(sampleId.get), LibraryId(libId.get), keyValues = Map("paired" -> List("paired"))).getOrElse("paired", None) == Some(true)
else settings.count(_._2.getOrElse("paired", None) == Some(true)) >= 1
}#
......@@ -144,15 +144,15 @@
#if (read == "R2") </tr><tr> #end
#{
val seqstatPaths = Map("num_total" -> List("reads", "num_total"))
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 seqstatStats = summary.getStatKeys(runId, "flexiprep", "seqstat_" + read, sample = sample.id, library = lib.id, keyValues = seqstatPaths)
val seqstatQcStats = summary.getStatKeys(runId, "flexiprep", "seqstat_" + read + "_qc", sample = sample.id, library = lib.id, 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, "flexiprep".right, Some(("clipping_" + read).right), sample = Some(sample.id.left), library = Some(lib.id.left), keyValues = clippingPaths)
val clippingStats = summary.getStatKeys(runId, "flexiprep", "clipping_" + read, sample = sample.id, library = lib.id, keyValues = clippingPaths)
val trimmingPaths = Map("num_reads_discarded" -> List("num_reads_discarded_" + read))
val trimmingStats = summary.getStatKeys(runId, "flexiprep".right, Some("trimming".right), sample = Some(sample.id.left), library = Some(lib.id.left), keyValues = trimmingPaths)
val trimmingStats = summary.getStatKeys(runId, "flexiprep", "trimming", sample = sample.id, library = lib.id, keyValues = trimmingPaths)
val beforeTotal = seqstatStats("num_total").getOrElse(0).toString.toLong
val afterTotal = seqstatQcStats("num_total").getOrElse(0).toString.toLong
......
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