Commit 18b8594a authored by Peter van 't Hof's avatar Peter van 't Hof

Fixed compile errors

parent c8ac4699
......@@ -66,8 +66,8 @@ object BammetricsReport extends ReportBuilder {
//val pipelineId: Int = summary.getPipelineId(runId, metricsTag).map(_.get)
val wgsExecuted = summary.getStatsSize(runId, metricsTag.right, Some("wgs".right), sample = sampleId.map(_.left), library = libId.map(_.left)) >= 1
val rnaExecuted = summary.getStatsSize(runId, metricsTag.right, Some("rna".right), sample = sampleId.map(_.left), library = libId.map(_.left)) >= 1
val wgsExecuted = summary.getStatsSize(runId, Some(metricsTag.right), Some(Some("wgs".right)), sample = sampleId.map(x => Some(x.left)), library = libId.map(x => Some(x.left))) >= 1
val rnaExecuted = summary.getStatsSize(runId, Some(metricsTag.right), Some(Some("rna".right)), sample = sampleId.map(x => Some(x.left)), library = libId.map(x => Some(x.left))) >= 1
val insertsizeMetrics = summary.getStatKeys(runId, metricsTag.right, Some("CollectInsertSizeMetrics".right),
sample = sampleId.map(_.left), library = libId.map(_.left), Map("metrics" -> List("metrics")))
......
......@@ -23,6 +23,8 @@ import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
import scala.concurrent.Await
import scala.concurrent.duration.Duration
import scalaz._
import Scalaz._
class FlexiprepReport(val parent: Configurable) extends ReportBuilderExtension {
def builder = FlexiprepReport
......@@ -95,15 +97,15 @@ object FlexiprepReport extends ReportBuilder {
tsvWriter.println("Library\tAfter_QC\tClipping\tTrimming\tSynced")
val seqstatPaths = Map("num_total" -> List("reads", "num_total"))
val seqstatStats = summary.getStatsForLibraries(runId, Right("flexiprep"), Right("seqstat_" + read), keyValues = seqstatPaths)
val seqstatQcStats = summary.getStatsForLibraries(runId, Right("flexiprep"), Right("seqstat_" + read + "_qc"), keyValues = seqstatPaths)
val seqstatStats = summary.getStatsForLibraries(runId, "flexiprep".right, Some(("seqstat_" + read).right), keyValues = seqstatPaths)
val seqstatQcStats = summary.getStatsForLibraries(runId, "flexiprep".right, Some(("seqstat_" + read + "_qc").right), 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.getStatsForLibraries(runId, Right("flexiprep"), Right("clipping_" + read), keyValues = clippingPaths)
val clippingStats = summary.getStatsForLibraries(runId, "flexiprep".right, Some(("clipping_" + read).right), keyValues = clippingPaths)
val trimmingPaths = Map("num_reads_discarded" -> List("num_reads_discarded_" + read))
val trimmingStats = summary.getStatsForLibraries(runId, Right("flexiprep"), Right("trimming"), keyValues = trimmingPaths)
val trimmingStats = summary.getStatsForLibraries(runId, "flexiprep".right, Some("trimming".right), keyValues = trimmingPaths)
val libraries = Await.result(summary.getLibraries(runId = runId, sampleId = sampleId), Duration.Inf)
......@@ -154,8 +156,8 @@ object FlexiprepReport extends ReportBuilder {
tsvWriter.println("Library\tAfter_QC\tDiscarded")
val statsPaths = Map("num_total" -> List("bases", "num_total"))
val seqstatStats = summary.getStatsForLibraries(runId, Right("flexiprep"), Right("seqstat_" + read), keyValues = statsPaths)
val seqstatQcStats = summary.getStatsForLibraries(runId, Right("flexiprep"), Right("seqstat_" + read + "_qc"), keyValues = statsPaths)
val seqstatStats = summary.getStatsForLibraries(runId, "flexiprep".right, Some(("seqstat_" + read).right), keyValues = statsPaths)
val seqstatQcStats = summary.getStatsForLibraries(runId, "flexiprep".right, Some(("seqstat_" + read + "_qc").right), keyValues = statsPaths)
val libraries = Await.result(summary.getLibraries(runId = runId, sampleId = sampleId), Duration.Inf)
......
......@@ -14,7 +14,6 @@
*/
package nl.lumc.sasc.biopet.pipelines.gears
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
......@@ -22,6 +21,9 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import scala.concurrent.Await
import scala.concurrent.duration.Duration
import scalaz._
import Scalaz._
/**
* Report for Gears
*
......@@ -39,10 +41,10 @@ object GearsReport extends MultisampleReportBuilder {
.map(x => ExtFile("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + x, x))
def indexPage = {
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, Right("gears"), None, None, None, key = "qiime_closed_otu_table")
val qiimeOpenOtuTable = summary.getFile(runId, Right("gears"), None, None, None, key = "qiime_open_otu_table")
val krakenExecuted = summary.getStatsSize(runId = runId, pipeline = Some("gearskraken".right), module = Some(Some("krakenreport".right)), library = Some(None), mustHaveSample = true) >= samples.size
val centrifugeExecuted = summary.getStatsSize(runId, Some("gearscentrifuge".right), Some(Some("centrifuge_report".right)), library = Some(None), mustHaveSample = true) >= samples.size
val qiimeClosesOtuTable = summary.getFile(runId, "gears".right, None, None, None, key = "qiime_closed_otu_table")
val qiimeOpenOtuTable = summary.getFile(runId, "gears".right, 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",
......@@ -80,10 +82,10 @@ object GearsReport extends MultisampleReportBuilder {
/** Single sample page */
def samplePage(sampleId: Int, args: Map[String, Any]): ReportPage = {
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, Right("gears"), None, Some(Left(sampleId)), None, "qiime_closed_otu_table"), Duration.Inf)
val qiimeOpenOtuTable = Await.result(summary.getFile(runId, Right("gears"), None, Some(Left(sampleId)), None, "qiime_open_otu_table"), Duration.Inf)
val krakenExecuted = Await.result(summary.getStatsSize(runId, Some("gearskraken".right), Some(Some("krakenreport".right)), sample = Some(Some(sampleId.left)), library = Some(None)), Duration.Inf) == 1
val centrifugeExecuted = Await.result(summary.getStatsSize(runId, Some("gearscentrifuge".right), Some(Some("centrifuge_report".right)), sample = Some(Some(sampleId.left)), library = None), Duration.Inf) == 1
val qiimeClosesOtuTable = Await.result(summary.getFile(runId, "gears".right, None, Some(sampleId.left), None, "qiime_closed_otu_table"), Duration.Inf)
val qiimeOpenOtuTable = Await.result(summary.getFile(runId, "gears".right, None, Some(sampleId.left), None, "qiime_open_otu_table"), Duration.Inf)
ReportPage((if (centrifugeExecuted) List("Centriguge analysis" -> ReportPage(List("Non-unique" -> ReportPage(List(), List("All mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
Map("summaryStatsTag" -> "centrifuge_report")
......@@ -112,12 +114,12 @@ 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(runId, Some(Right("flexiprep")), sample = Some(Left(sampleId)), library = Some(Left(libId))), Duration.Inf) >= 1
val flexiprepExecuted = Await.result(summary.getStatsSize(runId, Some("flexiprep".right), sample = Some(Some(sampleId.left)), library = Some(Some(libId.left))), 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, Right("gears"), None, Some(Left(sampleId)), Some(Left(libId)), "qiime_closed_otu_table"), Duration.Inf)
val qiimeOpenOtuTable = Await.result(summary.getFile(runId, Right("gears"), None, Some(Left(sampleId)), Some(Left(libId)), "qiime_open_otu_table"), Duration.Inf)
val krakenExecuted = Await.result(summary.getStatsSize(runId, Some("gearskraken".right), Some(Some("krakenreport".right)), sample = Some(Some(sampleId.left)), library = Some(Some(libId.left))), Duration.Inf) == 1
val centrifugeExecuted = Await.result(summary.getStatsSize(runId, Some("gearscentrifuge".right), Some(Some("centrifuge_report".right)), sample = Some(Some(sampleId.left)), library = Some(Some(libId.left))), Duration.Inf) == 1
val qiimeClosesOtuTable = Await.result(summary.getFile(runId, "gears".right, None, Some(sampleId.left), Some(libId.left), "qiime_closed_otu_table"), Duration.Inf)
val qiimeOpenOtuTable = Await.result(summary.getFile(runId, "gears".right, None, Some(sampleId.left), Some(libId.left), "qiime_open_otu_table"), Duration.Inf)
ReportPage(
(if (flexiprepExecuted) List("QC" -> FlexiprepReport.flexiprepPage) else Nil
......
......@@ -19,6 +19,8 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import scala.concurrent.Await
import scala.concurrent.duration.Duration
import scalaz._
import Scalaz._
class GearsSingleReport(val parent: Configurable) extends ReportBuilderExtension {
def builder = GearsSingleReport
......@@ -33,8 +35,8 @@ object GearsSingleReport extends ReportBuilder {
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
val krakenExecuted = Await.result(summary.getStatsSize(runId, Some("gearskraken".right), Some(Some("krakenreport".right)), sample = Some(sampleId.map(_.left)), library = Some(libId.map(_.left))), Duration.Inf) == 1
val centrifugeExecuted = Await.result(summary.getStatsSize(runId, Some("gearscentrifuge".right), Some(Some("centrifuge_report".right)), sample = Some(sampleId.map(_.left)), library = Some(libId.map(_.left))), Duration.Inf) == 1
ReportPage(
List(
......
......@@ -57,8 +57,8 @@ class KopisuTest extends TestNGSuite with Matchers {
@Test(dataProvider = "shivaSvCallingOptions")
def testKopisu(bams: Int,
freec: Boolean,
conifer: Boolean) = {
freec: Boolean,
conifer: Boolean) = {
val outputDir = Files.createTempDir()
dirs :+= outputDir
......
......@@ -21,6 +21,8 @@ import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
import scala.concurrent.Await
import scala.concurrent.duration.Duration
import scalaz._
import Scalaz._
class MappingReport(val parent: Configurable) extends ReportBuilderExtension {
def builder = MappingReport
......@@ -38,12 +40,12 @@ object MappingReport extends ReportBuilder {
override def extFiles = super.extFiles ++ List("js/gears.js", "js/krona-2.0.js", "img/krona/loading.gif", "img/krona/hidden.png", "img/krona/favicon.ico")
.map(x => ExtFile("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + x, x))
def krakenExecuted: Boolean = Await.result(summary.getStatsSize(runId, Right("gears"), Some(Right("krakenreport")),
sample = sampleId.map(Left(_)), library = libId.map(Left(_))), Duration.Inf) >= 1
def krakenExecuted: Boolean = Await.result(summary.getStatsSize(runId, Some("gears".right), Some(Some("krakenreport".right)),
sample = Some(sampleId.map(_.left)), library = Some(libId.map(_.left))), Duration.Inf) >= 1
/** Root page for single BamMetrcis report */
def indexPage = {
val mappingSettings = summary.getSettingKeys(runId, Right("mapping"), None, sample = sampleId.map(Left(_)), library = libId.map(Left(_)),
val mappingSettings = summary.getSettingKeys(runId, "mapping".right, None, sample = sampleId.map(_.left), library = libId.map(_.left),
keyValues = Map("skip_flexiprep" -> List("skip_flexiprep"), "skip_metrics" -> List("skip_metrics")))
val skipFlexiprep = mappingSettings.get("skip_flexiprep").flatten.getOrElse(false) == true
val bamMetricsPage = if (mappingSettings.get("skip_metrics").flatten.getOrElse(false) == true) {
......
......@@ -21,6 +21,8 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import scala.concurrent.Await
import scala.concurrent.duration.Duration
import scalaz._
import Scalaz._
/**
* Created by pjvanthof on 11/01/16.
......@@ -48,20 +50,20 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
/** Root page for the carp report */
def indexPage = {
val krakenExecuted = Await.result(summary.getStatsSize(runId, Right("gearskraken"), Some(Right("krakenreport")),
val krakenExecuted = Await.result(summary.getStatsSize(runId, Some("gearskraken".right), Some(Some("krakenreport".right)),
library = Some(None), mustHaveSample = true), Duration.Inf) >= 1
val centrifugeExecuted = Await.result(summary.getStatsSize(runId, Right("gearscentrifuge"), Some(Right("centrifuge_report")),
val centrifugeExecuted = Await.result(summary.getStatsSize(runId, Some("gearscentrifuge".right), Some(Some("centrifuge_report".right)),
library = Some(None), mustHaveSample = true), Duration.Inf) >= 1
val wgsExecuted = Await.result(summary.getStatsSize(runId, Right("bammetrics"), Some(Right("wgs")),
val wgsExecuted = Await.result(summary.getStatsSize(runId, Some("bammetrics".right), Some(Some("wgs".right)),
library = Some(None), mustHaveSample = true), Duration.Inf) >= 1
val rnaExecuted = Await.result(summary.getStatsSize(runId, Right("bammetrics"), Some(Right("rna")),
val rnaExecuted = Await.result(summary.getStatsSize(runId, Some("bammetrics".right), Some(Some("rna".right)),
library = Some(None), mustHaveSample = true), Duration.Inf) >= 1
val insertsizeExecuted = Await.result(summary.getStatsSize(runId, Right("bammetrics"), Some(Right("CollectInsertSizeMetrics")),
val insertsizeExecuted = Await.result(summary.getStatsSize(runId, Some("bammetrics".right), Some(Some("CollectInsertSizeMetrics".right)),
library = Some(None), mustHaveSample = true), Duration.Inf) >= 1
val mappingExecuted = Await.result(summary.getStatsSize(runId, Right("mapping"), Some(None), mustHaveLibrary = true), Duration.Inf) >= 1
val mappingSettings = summary.getSettingsForLibraries(runId, Right("mapping"), None, keyValues = Map("paired" -> List("paired")))
val mappingExecuted = Await.result(summary.getStatsSize(runId, Some("mapping".right), Some(None), mustHaveLibrary = true), Duration.Inf) >= 1
val mappingSettings = summary.getSettingsForLibraries(runId, "mapping".right, None, keyValues = Map("paired" -> List("paired")))
val pairedFound = !mappingExecuted || mappingSettings.exists(_._2.exists(_._2 == Option(true)))
val flexiprepExecuted = Await.result(summary.getStatsSize(runId, Right("flexiprep"), mustHaveLibrary = true), Duration.Inf) >= 1
val flexiprepExecuted = Await.result(summary.getStatsSize(runId, Some("flexiprep".right), mustHaveLibrary = true), Duration.Inf) >= 1
ReportPage(
List("Samples" -> generateSamplesPage(pageArgs)) ++
......@@ -113,19 +115,19 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
/** Files page, can be used general or at sample level */
def filesPage(sampleId: Option[Int] = None, libraryId: Option[Int] = None): ReportPage = {
val flexiprepExecuted = Await.result(summary.getStatsSize(runId, Right("flexiprep"), Some(None), mustHaveLibrary = true), Duration.Inf) >= 1
val flexiprepExecuted = Await.result(summary.getStatsSize(runId, Some("flexiprep".right), Some(None), mustHaveLibrary = true), Duration.Inf) >= 1
ReportPage(List(), Nil, Map())
}
/** Single sample page */
def samplePage(sampleId: Int, args: Map[String, Any]): ReportPage = {
val krakenExecuted = Await.result(summary.getStatsSize(runId, Right("gearskraken"), Some(Right("krakenreport")),
library = Some(None), sample = Some(Left(sampleId))), Duration.Inf) >= 1
val centrifugeExecuted = Await.result(summary.getStatsSize(runId, Right("gearscentrifuge"), Some(Right("centrifuge_report")),
library = Some(None), sample = Some(Left(sampleId)), mustHaveSample = true), Duration.Inf) >= 1
val flexiprepExecuted = Await.result(summary.getStatsSize(runId, Right("flexiprep"),
sample = Some(Left(sampleId)), mustHaveLibrary = true), Duration.Inf) >= 1
val krakenExecuted = Await.result(summary.getStatsSize(runId, Some("gearskraken".right), Some(Some("krakenreport".right)),
library = Some(None), sample = Some(Some(sampleId.left))), Duration.Inf) >= 1
val centrifugeExecuted = Await.result(summary.getStatsSize(runId, Some("gearscentrifuge".right), Some(Some("centrifuge_report".right)),
library = Some(None), sample = Some(Some(sampleId.left)), mustHaveSample = true), Duration.Inf) >= 1
val flexiprepExecuted = Await.result(summary.getStatsSize(runId, Some("flexiprep".right),
sample = Some(Some(sampleId.left)), mustHaveLibrary = true), Duration.Inf) >= 1
ReportPage(List(
"Libraries" -> generateLibraryPage(args),
......@@ -153,12 +155,12 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
/** Library page */
def libraryPage(sampleId: Int, libId: Int, args: Map[String, Any]): ReportPage = {
val krakenExecuted = Await.result(summary.getStatsSize(runId, Right("gearskraken"), Some(Right("krakenreport")),
library = Some(Left(libId)), sample = Some(Left(sampleId))), Duration.Inf) >= 1
val centrifugeExecuted = Await.result(summary.getStatsSize(runId, Right("gearscentrifuge"), Some(Right("centrifuge_report")),
library = Some(Left(libId)), sample = Some(Left(sampleId)), mustHaveSample = true), Duration.Inf) >= 1
val flexiprepExecuted = Await.result(summary.getStatsSize(runId, Right("flexiprep"), library = Some(Left(libId)),
sample = Some(Left(sampleId)), mustHaveLibrary = true), Duration.Inf) >= 1
val krakenExecuted = Await.result(summary.getStatsSize(runId, Some("gearskraken".right), Some(Some("krakenreport".right)),
library = Some(Some(libId.left)), sample = Some(Some(sampleId.left))), Duration.Inf) >= 1
val centrifugeExecuted = Await.result(summary.getStatsSize(runId, Some("gearscentrifuge".right), Some(Some("centrifuge_report".right)),
library = Some(Some(libId.left)), sample = Some(Some(sampleId.left)), mustHaveSample = true), Duration.Inf) >= 1
val flexiprepExecuted = Await.result(summary.getStatsSize(runId, Some("flexiprep".right), library = Some(Some(libId.left)),
sample = Some(Some(sampleId.left)), mustHaveLibrary = true), Duration.Inf) >= 1
ReportPage(
("Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), Some(libId))) ::
......
......@@ -25,6 +25,8 @@ import nl.lumc.sasc.biopet.utils.summary.{ Summary, SummaryValue }
import scala.concurrent.Await
import scala.concurrent.duration.Duration
import scalaz._
import Scalaz._
/**
* With this extension the report is executed within a pipeline
......@@ -41,7 +43,7 @@ object ShivaReport extends ShivaReportTrait
/** Trait for report generation for Shiva pipeline, this can be extended */
trait ShivaReportTrait extends MultisampleMappingReportTrait {
def variantcallingExecuted = summary.getSettingKeys(runId, Right("shiva"), None, keyValues = Map("multisample_variantcalling" -> List("multisample_variantcalling"))).get("multisample_variantcalling")
def variantcallingExecuted = summary.getSettingKeys(runId, "shiva".right, None, keyValues = Map("multisample_variantcalling" -> List("multisample_variantcalling"))).get("multisample_variantcalling")
.flatten match {
case Some(true) => true
case _ => false
......@@ -65,8 +67,8 @@ trait ShivaReportTrait extends MultisampleMappingReportTrait {
/** Generate a page with all target coverage stats */
def regionsPage: Option[(String, ReportPage)] = {
val roi = summary.getSetting(runId, Right("shiva")).get("regions_of_interest")
val amplicon = summary.getSetting(runId, Right("shiva")).get("amplicon_bed")
val roi = summary.getSetting(runId, "shiva".right).get("regions_of_interest")
val amplicon = summary.getSetting(runId, "shiva".right).get("amplicon_bed")
var regionPages: Map[String, ReportPage] = Map()
......@@ -155,7 +157,7 @@ trait ShivaReportTrait extends MultisampleMappingReportTrait {
case _ => s"multisample-vcfstats-$caller"
}
val results = summary.getStatKeys(runId, Right("shivavariantcalling"), Some(Right(moduleName)), sampleId.map(Left(_)), keyValues = statsPaths)
val results = summary.getStatKeys(runId, "shivavariantcalling".right, Some(moduleName.right), sampleId.map(_.left), keyValues = statsPaths)
for (sample <- samples if sampleId.isEmpty || sample.id == sampleId.get) {
tsvWriter.println(sample.name + "\t" + field.map(f => results(s"${sample.name};$f").getOrElse("")).mkString("\t"))
......
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