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Commit 6a024afb authored by Peter van 't Hof's avatar Peter van 't Hof
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Added status to nodes

parent 6d87ea53
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Showing with 47 additions and 24 deletions
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/PipelineStatus.scala
View file @ 6a024afb
......@@ -155,7 +155,7 @@ object PipelineStatus extends ToolCommand {
}
def compressedName(jobName: String) = jobName match {
case numberRegex(name, number) => (name, number.toInt)
case numberRegex(name, number) => (name, number.toInt)
}
def writeGraphvizFile(jobsDeps: Map[String, List[String]],
......@@ -169,25 +169,48 @@ object PipelineStatus extends ToolCommand {
val writer = new PrintWriter(outputFile)
writer.println("digraph graphname {")
graph.foreach { case (job, jobDeps) =>
// Writing color of node
val compressTotal = if (compress) Some(deps.jobs.keys.count(compressedName(_)._1 == job)) else None
val compressDone = if (compress) Some(jobDone.count(compressedName(_)._1 == job)) else None
val compressFailed = if (compress) Some(jobFailed.count(compressedName(_)._1 == job)) else None
val compressStart = if (compress) Some(jobsStart.count(compressedName(_)._1 == job)) else None
val compressIntermediate = if (compress) Some(deps.jobs.filter(x => x._2.intermediate)
.count(x => compressedName(x._1)._1 == job)) else None
if (jobDone.contains(job) || compress && compressTotal == compressDone) writer.println(s" $job [color = green]")
else if (jobFailed.contains(job) || compress && compressTotal == compressFailed) writer.println(s" $job [color = red]")
else if (jobsStart.contains(job) || compress && compressTotal == compressStart) writer.println(s" $job [color = orange]")
// Dashed lined for intermediate jobs
if ((deps.jobs.contains(job) && deps.jobs(job).intermediate) || (compress && compressTotal == compressIntermediate))
writer.println(s" $job [style = dashed]")
// Writing Node deps
jobDeps.foreach(c => writer.println(s" $c -> $job;"))
graph.foreach {
case (job, jobDeps) =>
// Writing color of node
val compressTotal = if (compress) Some(deps.jobs.keys.filter(compressedName(_)._1 == job)) else None
val compressDone = if (compress) Some(jobDone.filter(compressedName(_)._1 == job)) else None
val compressFailed = if (compress) Some(jobFailed.filter(compressedName(_)._1 == job)) else None
val compressStart = if (compress) Some(jobsStart.filter(compressedName(_)._1 == job)) else None
val compressIntermediate = if (compress) Some(deps.jobs.filter(x => compressedName(x._1)._1 == job).forall(_._2.intermediate)) else None
if (compress) {
val pend = compressTotal.get.size - compressFailed.get.filterNot(compressStart.get.contains(_)).size - compressStart.get.size - compressDone.get.size
writer.println(s""" $job [label = "$job
|Total: ${compressTotal.get.size}
|Fail: ${compressFailed.get.size}
|Pend:${pend}
|Start/run: ${compressStart.get.filterNot(compressFailed.get.contains(_)).size}
|Done: ${compressDone.get.size}"]""".stripMargin)
}
if (jobDone.contains(job) || compress && compressTotal == compressDone) writer.println(s" $job [color = green]")
else if (jobFailed.contains(job) || compress && compressFailed.get.nonEmpty) writer.println(s" $job [color = red]")
else if (jobsStart.contains(job) || compress && compressTotal == compressStart) writer.println(s" $job [color = orange]")
// Dashed lined for intermediate jobs
if ((deps.jobs.contains(job) && deps.jobs(job).intermediate) || (compressIntermediate == Some(true)))
writer.println(s" $job [style = dashed]")
// Writing Node deps
jobDeps.foreach { dep =>
if (compress) {
val depsNames = deps.jobs.filter(x => compressedName(x._1)._1 == dep)
.filter(_._2.outputUsedByJobs.exists(x => compressedName(x)._1 == job))
.map(x => x._1 -> x._2.outputUsedByJobs.filter(x => compressedName(x)._1 == job))
val total = depsNames.size
val done = depsNames.map(x => x._2.exists(y => jobDone.contains(x._1))).count(_ == true).toFloat / total
val fail = depsNames.map(x => x._2.exists(y => jobFailed.contains(x._1))).count(_ == true).toFloat / total
val start = (depsNames.map(x => x._2.exists(y => jobsStart.contains(x._1))).count(_ == true).toFloat / total) - fail
if (total > 0) writer.println(s""" $dep -> $job [color="red;%f:orange;%f:green;%f:black;%f"];"""
.format(fail, start, done, 1.0f - done - fail - start))
else writer.println(s" $dep -> $job;")
} else writer.println(s" $dep -> $job;")
}
}
writer.println("}")
writer.close()
......
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @ 6a024afb
......@@ -19,11 +19,11 @@ import java.util.Date
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.bowtie.{Bowtie, Bowtie2}
import nl.lumc.sasc.biopet.extensions.bwa.{BwaAln, BwaMem, BwaSampe, BwaSamse}
import nl.lumc.sasc.biopet.extensions.bowtie.{ Bowtie, Bowtie2 }
import nl.lumc.sasc.biopet.extensions.bwa.{ BwaAln, BwaMem, BwaSampe, BwaSamse }
import nl.lumc.sasc.biopet.extensions.gmap.Gsnap
import nl.lumc.sasc.biopet.extensions.hisat.Hisat2
import nl.lumc.sasc.biopet.extensions.picard.{AddOrReplaceReadGroups, MarkDuplicates, MergeSamFiles, ReorderSam, SortSam}
import nl.lumc.sasc.biopet.extensions.picard.{ AddOrReplaceReadGroups, MarkDuplicates, MergeSamFiles, ReorderSam, SortSam }
import nl.lumc.sasc.biopet.extensions.tools.FastqSplitter
import nl.lumc.sasc.biopet.extensions._
import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
......@@ -31,7 +31,7 @@ import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
import nl.lumc.sasc.biopet.pipelines.gears.GearsSingle
import nl.lumc.sasc.biopet.pipelines.mapping.scripts.TophatRecondition
import nl.lumc.sasc.biopet.utils.{Logging, textToSize}
import nl.lumc.sasc.biopet.utils.{ Logging, textToSize }
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
......
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