Skip to content

GitLab

Commit b27102c7 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files
Options

Try with Either class

parent d4d307a2
Expand all Hide whitespace changes
Inline Side-by-side
Showing with 309 additions and 174 deletions
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @ b27102c7
......@@ -14,12 +14,17 @@
*/
package nl.lumc.sasc.biopet.pipelines.bammetrics
import java.io.{ File, PrintWriter }
import java.io.{File, PrintWriter}
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.report.{ ReportBuilderExtension, ReportBuilder, ReportPage, ReportSection }
import nl.lumc.sasc.biopet.utils.summary.{ Summary, SummaryValue }
import nl.lumc.sasc.biopet.utils.rscript.{ StackedBarPlot, LinePlot }
import nl.lumc.sasc.biopet.core.report.{ReportBuilder, ReportBuilderExtension, ReportPage, ReportSection}
import nl.lumc.sasc.biopet.utils.ConfigUtils
import nl.lumc.sasc.biopet.utils.rscript.{LinePlot, StackedBarPlot}
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
import scala.concurrent.ExecutionContext.Implicits.global
import scala.concurrent.Await
import scala.concurrent.duration.Duration
class BammetricsReport(val parent: Configurable) extends ReportBuilderExtension {
def builder = BammetricsReport
......@@ -52,23 +57,26 @@ object BammetricsReport extends ReportBuilder {
}
/** Generates a page with alignment stats */
def bamMetricsPage(summary: Summary,
sampleId: Option[String],
libId: Option[String],
def bamMetricsPage(summary: SummaryDb,
sampleId: Option[Int],
libId: Option[Int],
metricsTag: String = "bammetrics") = {
val wgsExecuted = summary.getValue(sampleId, libId, metricsTag, "stats", "wgs").isDefined
val rnaExecuted = summary.getValue(sampleId, libId, metricsTag, "stats", "rna").isDefined
//val pipelineId: Int = summary.getPipelineId(runId, metricsTag).map(_.get)
val insertsizeMetrics = summary.getValue(sampleId, libId, metricsTag, "stats", "CollectInsertSizeMetrics", "metrics") match {
case Some(None) => false
case Some(_) => true
case _ => false
}
val wgsExecuted = summary.getStatsSize(runId, Right(metricsTag), Some(Right("wgs")), sample = sampleId.map(Left(_)), library = libId.map(Left(_))) >= 1
val rnaExecuted = summary.getStatsSize(runId, Right(metricsTag), Some(Right("rna")), sample = sampleId.map(Left(_)), library = libId.map(Left(_))) >= 1
val insertsizeMetrics = summary.getStatKeys(runId, Right(metricsTag), Some(Right("CollectInsertSizeMetrics")),
sample = sampleId.map(Left(_)), library = libId.map(Left(_)), Map("metrics" -> List("metrics")))
.exists(_._2.isDefined)
val targetSettings = summary.getSettingKeys(runId, Right(metricsTag),None, sample = sampleId.map(Left(_)), library = libId.map(Left(_)),
Map("amplicon_name" -> List("amplicon_name"), "roi_name" -> List("roi_name")))
val targets = (
summary.getValue(sampleId, libId, metricsTag, "settings", "amplicon_name"),
summary.getValue(sampleId, libId, metricsTag, "settings", "roi_name")
targetSettings("amplicon_name"),
targetSettings("roi_name")
) match {
case (Some(amplicon: String), Some(roi: List[_])) => amplicon :: roi.map(_.toString)
case (_, Some(roi: List[_])) => roi.map(_.toString)
......@@ -108,44 +116,43 @@ object BammetricsReport extends ReportBuilder {
*/
def alignmentSummaryPlot(outputDir: File,
prefix: String,
summary: Summary,
summary: SummaryDb,
libraryLevel: Boolean = false,
sampleId: Option[String] = None): Unit = {
sampleId: Option[Int] = None): Unit = {
val tsvFile = new File(outputDir, prefix + ".tsv")
val pngFile = new File(outputDir, prefix + ".png")
val tsvWriter = new PrintWriter(tsvFile)
if (libraryLevel) tsvWriter.print("Library") else tsvWriter.print("Sample")
tsvWriter.println("\tMapped\tDuplicates\tUnmapped\tSecondary")
def getLine(summary: Summary, sample: String, lib: Option[String] = None): String = {
val mapped = new SummaryValue(List("bammetrics", "stats", "bamstats", "flagstats", "Mapped"),
summary, Some(sample), lib).value.getOrElse(0).toString.toLong
val duplicates = new SummaryValue(List("bammetrics", "stats", "bamstats", "flagstats", "Duplicates"),
summary, Some(sample), lib).value.getOrElse(0).toString.toLong
val total = new SummaryValue(List("bammetrics", "stats", "bamstats", "flagstats", "All"),
summary, Some(sample), lib).value.getOrElse(0).toString.toLong
val secondary = new SummaryValue(List("bammetrics", "stats", "bamstats", "flagstats", "NotPrimaryAlignment"),
summary, Some(sample), lib).value.getOrElse(0).toString.toLong
val statsPaths = Map(
"Mapped" -> List("flagstats", "Mapped"),
"Duplicates" -> List("flagstats", "Duplicates"),
"All" -> List("flagstats", "All"),
"NotPrimaryAlignment" -> List("flagstats", "NotPrimaryAlignment")
)
val pipelineId: Int = summary.getPipelineId(runId, "bammetrics").map(_.get)
val moduleId: Option[Int] = summary.getmoduleId(runId, "bamstats", pipelineId)
val results: Map[(Int, Option[Int]), Map[String, Option[Any]]] = if (libraryLevel) {
summary.getStatsForLibraries(runId = runId, pipelineName = "bammetrics", moduleName = Some("bamstats"), sampleId = sampleId, keyValues = statsPaths).map(x => (x._1._1, Some(x._1._2)) -> x._2)
} else summary.getStatsForSamples(runId, pipelineId, moduleId, sample = sampleId, keyValues = statsPaths).map(x => (x._1, None) -> x._2)
for (((s,l),result) <- results) {
val sampleName: String = summary.getSampleName(s).map(_.get)
val libName: Option[String] = l.flatMap(x => Await.result(summary.getLibraryName(x), Duration.Inf))
val sb = new StringBuffer()
if (lib.isDefined) sb.append(sample + "-" + lib.get + "\t") else sb.append(sample + "\t")
if (libName.isDefined) sb.append(sampleName + "-" + libName.get + "\t") else sb.append(sampleName + "\t")
val mapped = ConfigUtils.any2long(result("Mapped"))
val duplicates = ConfigUtils.any2long(result("Duplicates"))
val total = ConfigUtils.any2long(result("All"))
val secondary = ConfigUtils.any2long(result("NotPrimaryAlignment"))
sb.append((mapped - duplicates - secondary) + "\t")
sb.append(duplicates + "\t")
sb.append((total - mapped) + "\t")
sb.append(secondary)
sb.toString
}
if (libraryLevel) {
for (
sample <- summary.samples if sampleId.isEmpty || sample == sampleId.get;
lib <- summary.libraries(sample)
) {
tsvWriter.println(getLine(summary, sample, Some(lib)))
}
} else {
for (sample <- summary.samples if sampleId.isEmpty || sample == sampleId.get) {
tsvWriter.println(getLine(summary, sample))
}
tsvWriter.println(sb.toString)
}
tsvWriter.close()
......@@ -155,8 +162,8 @@ object BammetricsReport extends ReportBuilder {
plot.output = pngFile
plot.ylabel = Some("Reads")
if (libraryLevel) {
plot.width = Some(200 + (summary.libraries.filter(s => sampleId.getOrElse(s._1) == s._1).foldLeft(0)(_ + _._2.size) * 10))
} else plot.width = Some(200 + (summary.samples.count(s => sampleId.getOrElse(s) == s) * 10))
plot.width = Some(200 + (libraries.filter(s => sampleId.getOrElse(s.id) == s.id).size) * 10)
} else plot.width = Some(200 + (samples.count(s => sampleId.getOrElse(s) == s) * 10))
plot.title = Some("Aligned reads")
plot.runLocal()
}
......@@ -172,18 +179,27 @@ object BammetricsReport extends ReportBuilder {
*/
def insertSizePlot(outputDir: File,
prefix: String,
summary: Summary,
summary: SummaryDb,
libraryLevel: Boolean = false,
sampleId: Option[String] = None,
libId: Option[String] = None): Unit = {
sampleId: Option[Int] = None,
libId: Option[Int] = None): Unit = {
val tsvFile = new File(outputDir, prefix + ".tsv")
val pngFile = new File(outputDir, prefix + ".png")
def paths(name: String) = Map(
"insert_size" -> List("bammetrics", "stats", "CollectInsertSizeMetrics", "histogram", "insert_size"),
name -> List("bammetrics", "stats", "CollectInsertSizeMetrics", "histogram", "All_Reads.fr_count")
val statsPaths = Map(
"insert_size" -> List("histogram", "insert_size"),
"All_Reads.fr_count" -> List("histogram", "All_Reads.fr_count")
)
val pipelineId: Int = summary.getPipelineId(runId, "bammetrics").map(_.get)
val moduleId: Option[Int] = summary.getmoduleId(runId, "CollectInsertSizeMetrics", pipelineId)
val results: Map[(Int, Option[Int]), Map[String, Option[Array[Any]]]] = if (libraryLevel) {
summary.getStatsForLibraries(runId, pipelineId, moduleId, sampleId = sampleId, keyValues = statsPaths)
.map(x => (x._1._1, Some(x._1._2)) -> x._2.map(x => x._1 -> x._2.map(ConfigUtils.any2list(_).toArray)))
} else summary.getStatsForSamples(runId, pipelineId, moduleId, sample = sampleId, keyValues = statsPaths)
.map(x => (x._1, None) -> x._2.map(x => x._1 -> x._2.map(ConfigUtils.any2list(_).toArray)))
val tables = getSampleLibraries(summary, sampleId, libId, libraryLevel)
.map {
case (sample, lib) =>
......@@ -200,10 +216,10 @@ object BammetricsReport extends ReportBuilder {
def mappingQualityPlot(outputDir: File,
prefix: String,
summary: Summary,
summary: SummaryDb,
libraryLevel: Boolean = false,
sampleId: Option[String] = None,
libId: Option[String] = None): Unit = {
sampleId: Option[Int] = None,
libId: Option[Int] = None): Unit = {
val tsvFile = new File(outputDir, prefix + ".tsv")
val pngFile = new File(outputDir, prefix + ".png")
......@@ -228,10 +244,10 @@ object BammetricsReport extends ReportBuilder {
def clippingPlot(outputDir: File,
prefix: String,
summary: Summary,
summary: SummaryDb,
libraryLevel: Boolean = false,
sampleId: Option[String] = None,
libId: Option[String] = None): Unit = {
sampleId: Option[Int] = None,
libId: Option[Int] = None): Unit = {
val tsvFile = new File(outputDir, prefix + ".tsv")
val pngFile = new File(outputDir, prefix + ".png")
......@@ -265,10 +281,10 @@ object BammetricsReport extends ReportBuilder {
*/
def wgsHistogramPlot(outputDir: File,
prefix: String,
summary: Summary,
summary: SummaryDb,
libraryLevel: Boolean = false,
sampleId: Option[String] = None,
libId: Option[String] = None): Unit = {
sampleId: Option[Int] = None,
libId: Option[Int] = None): Unit = {
val tsvFile = new File(outputDir, prefix + ".tsv")
val pngFile = new File(outputDir, prefix + ".png")
......@@ -302,7 +318,7 @@ object BammetricsReport extends ReportBuilder {
*/
def rnaHistogramPlot(outputDir: File,
prefix: String,
summary: Summary,
summary: SummaryDb,
libraryLevel: Boolean = false,
sampleId: Option[String] = None,
libId: Option[String] = None): Unit = {
......@@ -328,20 +344,20 @@ object BammetricsReport extends ReportBuilder {
removeZero = true).runLocal()
}
private def getSampleLibraries(summary: Summary,
sampleId: Option[String] = None,
LibId: Option[String] = None,
libraryLevel: Boolean = false): List[(String, Option[String])] = {
private def getSampleLibraries(summary: SummaryDb,
sampleId: Option[Int] = None,
LibId: Option[Int] = None,
libraryLevel: Boolean = false): List[(Int, Option[Int])] = {
if (LibId.isDefined) require(sampleId.isDefined)
if (libraryLevel || LibId.isDefined)
for ((sample, libs) <- summary.libraries.toList; lib <- libs) yield (sample, Some(lib))
else for ((sample, libs) <- summary.libraries.toList) yield (sample, None)
}
def getTableFromSummary(summary: Summary,
def getTableFromSummary(summary: SummaryDb,
paths: Map[String, List[String]],
sampleId: Option[String] = None,
libId: Option[String] = None): Map[String, Array[Any]] = {
sampleId: Option[Int] = None,
libId: Option[Int] = None): Map[String, Array[Any]] = {
val pathValues: Map[String, Array[Any]] = paths.map {
case (key, path) =>
val value = summary.getValueAsArray(sampleId, libId, path: _*)
......
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
View file @ b27102c7
......@@ -17,13 +17,15 @@ package nl.lumc.sasc.biopet.core.report
import java.io._
import nl.lumc.sasc.biopet.core.ToolCommandFunction
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
import scala.concurrent.{Await, Future}
import scala.concurrent.duration.Duration
import scala.language.postfixOps
......@@ -72,6 +74,7 @@ trait ReportBuilderExtension extends ToolCommandFunction {
trait ReportBuilder extends ToolCommand {
implicit def toOption[T](x: T) : Option[T] = Option(x)
implicit def autoWait[T](x: Future[T]) : T = Await.result(x, Duration.Inf)
case class Args(summaryDbFile: File = null,
outputDir: File = null,
......@@ -115,21 +118,10 @@ trait ReportBuilder extends ToolCommand {
final def runId = setRunId
private var setSampleCache: Map[String, Int] = _
final def sampleCache = setSampleCache
private var setLibraryCache: Map[(String, String), Int] = _
final def libraryCache = setSampleCache
private var setPipelineCache: Map[String, Int] = _
final def pipelineCache = setPipelineCache
private var setModuleCache: Map[String, Int] = _
final def moduleCache = setModuleCache
private var _setSamples = Seq[Sample]()
final def samples = _setSamples
private var _setLibraries = Seq[Library]()
final def libraries = _setLibraries
/** default args that are passed to all page withing the report */
def pageArgs: Map[String, Any] = Map()
......@@ -137,9 +129,9 @@ trait ReportBuilder extends ToolCommand {
private var done = 0
private var total = 0
private var _sampleId: Option[String] = None
private var _sampleId: Option[Int] = None
protected[report] def sampleId = _sampleId
private var _libId: Option[String] = None
private var _libId: Option[Int] = None
protected[report] def libId = _libId
case class ExtFile(resourcePath: String, targetPath: String)
......@@ -168,20 +160,26 @@ trait ReportBuilder extends ToolCommand {
require(cmdArgs.outputDir.exists(), "Output dir does not exist")
require(cmdArgs.outputDir.isDirectory, "Output dir is not a directory")
setSummary = SummaryDb.openSqliteSummary(cmdArgs.summaryDbFile)
setRunId = cmdArgs.runId
cmdArgs.pageArgs.get("sampleId") match {
case Some(s: String) =>
cmdArgs.pageArgs += "sampleId" -> Some(s)
_sampleId = Some(s)
_sampleId = Await.result(summary.getSampleId(runId, s), Duration.Inf)
cmdArgs.pageArgs += "sampleId" -> sampleId
case _ =>
}
cmdArgs.pageArgs.get("libId") match {
case Some(l: String) =>
cmdArgs.pageArgs += "libId" -> Some(l)
_libId = Some(l)
_libId = Await.result(summary.getLibraryId(runId, sampleId.get, l), Duration.Inf)
cmdArgs.pageArgs += "libId" -> libId
case _ =>
}
_setSamples = Await.result(summary.getSamples(runId = Some(runId), sampleId = sampleId), Duration.Inf)
_setLibraries = Await.result(summary.getLibraries(runId = Some(runId), sampleId = sampleId, libId = libId), Duration.Inf)
logger.info("Copy Base files")
// Static files that will be copied to the output folder, then file is added to [resourceDir] it's need to be added here also
......@@ -196,14 +194,6 @@ trait ReportBuilder extends ToolCommand {
createDirs = true)
)
logger.info("Parsing summary")
setSummary = SummaryDb.openSqliteSummary(cmdArgs.summaryDbFile)
setRunId = cmdArgs.runId
setSampleCache = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf).map(r => r.name -> r.id).toMap
setLibraryCache = Await.result(summary.getLibraries(runId = Some(runId)), Duration.Inf).map(r => (setSampleCache.find(_._2 == r.sampleId).get._1, r.name) -> r.id).toMap
setPipelineCache = Await.result(summary.getPipelines(runId = Some(runId)), Duration.Inf).map(r => r.name -> r.id).toMap
setModuleCache = Await.result(summary.getModules(runId = Some(runId)), Duration.Inf).map(r => r.name -> r.id).toMap
total = ReportBuilder.countPages(indexPage)
logger.info(total + " pages to be generated")
......
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/implicits/Either.scala 0 → 100644
View file @ b27102c7
package nl.lumc.sasc.biopet.utils.implicits
/**
* Created by pjvanthof on 20/02/2017.
*/
object Either {
implicit def optionEitherLeft[T](x: Option[Either[T,_]]): Option[Option[T]] = {
x match {
case Some(i:Either[T, _]) if i.isLeft => Some(i.left.toOption)
case _ => None
}
}
implicit def optionEitherRight[T](x: Option[Either[_,T]]): Option[Option[T]] = {
x match {
case Some(i:Either[_,T]) if i.isRight => Some(i.right.toOption)
case _ => None
}
}
implicit def eitherLeft[T](x: Either[T,_]): Option[T] = {
x match {
case Left(x) => Some(x)
case _ => None
}
}
implicit def eitherRight[T](x: Either[_,T]): Option[T] = {
x match {
case Right(x) => Some(x)
case _ => None
}
}
implicit def left[T](x:T): Left[T, _] = Left(x)
implicit def right[T](x:T): Right[_, T] = Right(x)
implicit def left[T](x:Option[T]): Option[Left[T, _]] = x.map(Left(_))
implicit def right[T](x:Option[T]): Option[Right[_, T]] = x.map(Right(_))
}
biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/summary/db/SummaryDbTest.scala
View file @ b27102c7
......@@ -23,9 +23,9 @@ class SummaryDbTest extends TestNGSuite with Matchers {
Await.result(db.createOrUpdateSetting(0, 0, None, None, None, """{"content": "test" }"""), Duration.Inf)
val bla = Await.result(db.getSettings(Some(0)), Duration.Inf)
Await.result(db.getSetting(0, 0, None, None, None), Duration.Inf) shouldBe Some(Map("content" -> "test"))
Await.result(db.getSetting(0, Left(0), None, None, None), Duration.Inf) shouldBe Some(Map("content" -> "test"))
Await.result(db.createOrUpdateSetting(0, 0, None, None, None, """{"content": "test2" }"""), Duration.Inf)
Await.result(db.getSetting(0, 0, None, None, None), Duration.Inf) shouldBe Some(Map("content" -> "test2"))
Await.result(db.getSetting(0, Left(0), None, None, None), Duration.Inf) shouldBe Some(Map("content" -> "test2"))
db.close()
}
......@@ -37,9 +37,9 @@ class SummaryDbTest extends TestNGSuite with Matchers {
db.createTables()
Await.result(db.createOrUpdateStat(0, 0, None, None, None, """{"content": "test" }"""), Duration.Inf)
Await.result(db.getStat(0, 0, None, None, None), Duration.Inf) shouldBe Some(Map("content" -> "test"))
Await.result(db.getStat(0, Left(0), None, None, None), Duration.Inf) shouldBe Some(Map("content" -> "test"))
Await.result(db.createOrUpdateStat(0, 0, None, None, None, """{"content": "test2" }"""), Duration.Inf)
Await.result(db.getStat(0, 0, None, None, None), Duration.Inf) shouldBe Some(Map("content" -> "test2"))
Await.result(db.getStat(0, Left(0), None, None, None), Duration.Inf) shouldBe Some(Map("content" -> "test2"))
db.close()
}
......
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
View file @ b27102c7
......@@ -14,8 +14,7 @@
*/
package nl.lumc.sasc.biopet.pipelines.gears
import java.io.File
import nl.lumc.sasc.biopet.utils.implicits.Either._
import nl.lumc.sasc.biopet.core.report.{MultisampleReportBuilder, ReportBuilderExtension, ReportPage, ReportSection}
import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
import nl.lumc.sasc.biopet.utils.config.Configurable
......@@ -40,10 +39,10 @@ object GearsReport extends MultisampleReportBuilder {
.map(x => ExtFile("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + x, x))
def indexPage = {
val krakenExecuted = Await.result(summary.getStatsSize(runId, "gearskraken", Some("krakenreport"), libName = None, mustHaveSample = true), Duration.Inf) >= sampleCache.size
val centrifugeExecuted = Await.result(summary.getStatsSize(runId, "gearscentrifuge", Some("centrifuge_report"), libName = None, mustHaveSample = true), Duration.Inf) >= sampleCache.size
val qiimeClosesOtuTable = Await.result(summary.getFile(runId, "gears", None, None, None, key = "qiime_closed_otu_table"), Duration.Inf)
val qiimeOpenOtuTable = Await.result(summary.getFile(runId, "gears", None, None, None, key = "qiime_open_otu_table"), Duration.Inf)
val krakenExecuted = summary.getStatsSize(runId = runId, pipeline = Right("gearskraken"), module = Some(Right("krakenreport")), library = Some(None), mustHaveSample = true) >= samples.size
val centrifugeExecuted = summary.getStatsSize(runId, Right("gearscentrifuge"), Some(Right("centrifuge_report")), library = Some(None), mustHaveSample = true) >= samples.size
val qiimeClosesOtuTable = summary.getFile(runId, "gears", None, None, None, key = "qiime_closed_otu_table")
val qiimeOpenOtuTable = summary.getFile(runId, "gears", None, None, None, key = "qiime_open_otu_table")
ReportPage(
(if (centrifugeExecuted) List("Centriguge analysis" -> ReportPage(List("Non-unique" -> ReportPage(List(), List("All mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
......@@ -82,8 +81,8 @@ object GearsReport extends MultisampleReportBuilder {
/** Single sample page */
def samplePage(sampleId: Int, args: Map[String, Any]): ReportPage = {
val sampleName = Await.result(summary.getSampleName(sampleId), Duration.Inf)
val krakenExecuted = Await.result(summary.getStatsSize(runId, "gearskraken", Some("krakenreport"), sampleName = sampleName, libName = None), Duration.Inf) == 1
val centrifugeExecuted = Await.result(summary.getStatsSize(runId, "gearscentrifuge", Some("centrifuge_report"), sampleName = sampleName, libName = None), Duration.Inf) == 1
val krakenExecuted = Await.result(summary.getStatsSize(runId, Right("gearskraken"), Some(Right("krakenreport")), sample = Left(sampleId), library = Some(None)), Duration.Inf) == 1
val centrifugeExecuted = Await.result(summary.getStatsSize(runId, Right("gearscentrifuge"), Some(Right("centrifuge_report")), sample = Left(sampleId), library = None), Duration.Inf) == 1
val qiimeClosesOtuTable = Await.result(summary.getFile(runId, "gears", None, sampleName, None, key = "qiime_closed_otu_table"), Duration.Inf)
val qiimeOpenOtuTable = Await.result(summary.getFile(runId, "gears", None, sampleName, None, key = "qiime_open_otu_table"), Duration.Inf)
......@@ -115,10 +114,10 @@ object GearsReport extends MultisampleReportBuilder {
val sName = Await.result(summary.getSampleName(sampleId), Duration.Inf)
val lName = Await.result(summary.getLibraryName(libId), Duration.Inf)
val flexiprepExecuted = Await.result(summary.getStatsSize(Some(runId), Some("flexiprep"), None, Some(sName),Some(lName)), Duration.Inf) >= 1
val flexiprepExecuted = Await.result(summary.getStatsSize(runId, Some(Right("flexiprep")), sample = Some(Left(sampleId)), library = Some(Left(libId))), Duration.Inf) >= 1
val krakenExecuted = Await.result(summary.getStatsSize(runId, "gearskraken", Some("krakenreport"), sampleName = sName, libName = lName), Duration.Inf) == 1
val centrifugeExecuted = Await.result(summary.getStatsSize(runId, "gearscentrifuge", Some("centrifuge_report"), sampleName = sName, libName = lName), Duration.Inf) == 1
val krakenExecuted = Await.result(summary.getStatsSize(runId, Right("gearskraken"), Some(Right("krakenreport")), sample = Some(Left(sampleId)), library = Some(Left(libId))), Duration.Inf) == 1
val centrifugeExecuted = Await.result(summary.getStatsSize(runId, Right("gearscentrifuge"), Some(Right("centrifuge_report")), sample = Some(Left(sampleId)), library = Some(Left(libId))), Duration.Inf) == 1
val qiimeClosesOtuTable = Await.result(summary.getFile(runId, "gears", None, sName, lName, key = "qiime_closed_otu_table"), Duration.Inf)
val qiimeOpenOtuTable = Await.result(summary.getFile(runId, "gears", None, sName, lName, key = "qiime_open_otu_table"), Duration.Inf)
......
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleReport.scala
View file @ b27102c7
......@@ -30,9 +30,11 @@ object GearsSingleReport extends ReportBuilder {
.map(x => ExtFile("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + x, x))
def indexPage = {
Await.result(summary.getStatsSize(runId, "gearscentrifuge", Some("centrifuge_report"), sampleId, libId), Duration.Inf) == 1
val krakenExecuted = Await.result(summary.getStatsSize(runId, "gearskraken", Some("krakenreport"), sampleId, libId), Duration.Inf) == 1
val centrifugeExecuted = Await.result(summary.getStatsSize(runId, "gearscentrifuge", Some("centrifuge_report"), sampleId, libId), Duration.Inf) == 1
val sampleName = sampleId.flatMap(x => Await.result(summary.getSampleName(x), Duration.Inf))
val libraryName = libId.flatMap(x => Await.result(summary.getLibraryName(x), Duration.Inf))
val krakenExecuted = summary.getStatsSize(runId, Right("gearskraken"), Some(Right("krakenreport")), sample = sampleId.map(Left(_)), library = libId.map(Left(_))) == 1
val centrifugeExecuted = summary.getStatsSize(runId, Right("gearscentrifuge"), Some(Right("centrifuge_report")), sample = sampleId.map(Left(_)), library = libId.map(Left(_))) == 1
ReportPage(
List(
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment