Commit a332996e authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Java jobs now show diffrent version output in summary

parent ddc6e115
...@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.core.summary ...@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.core.summary
import java.io.File import java.io.File
import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunctionTrait, BiopetCommandLineFunction, SampleLibraryTag, BiopetQScript } import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.extensions.Md5sum import nl.lumc.sasc.biopet.extensions.Md5sum
import scala.collection.mutable import scala.collection.mutable
...@@ -104,8 +104,13 @@ trait SummaryQScript extends BiopetQScript { ...@@ -104,8 +104,13 @@ trait SummaryQScript extends BiopetQScript {
} }
//Automatic checksums //Automatic checksums
for ((_, summarizableList) <- summarizables; summarizable <- summarizableList; (_, file) <- summarizable.summaryFiles) for ((_, summarizableList) <- summarizables; summarizable <- summarizableList; (_, file) <- summarizable.summaryFiles) {
addChecksum(file) addChecksum(file)
summarizable match {
case f: BiopetJavaCommandLineFunction => if (f.jarFile != null) addChecksum(f.jarFile)
case _ =>
}
}
for ((_, file) <- this.summaryFiles) for ((_, file) <- this.summaryFiles)
addChecksum(file) addChecksum(file)
......
...@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.core.summary ...@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.core.summary
import java.io.{ FileInputStream, PrintWriter, File } import java.io.{ FileInputStream, PrintWriter, File }
import java.security.MessageDigest import java.security.MessageDigest
import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunctionTrait, SampleLibraryTag } import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, BiopetCommandLineFunction, BiopetCommandLineFunctionTrait, SampleLibraryTag }
import nl.lumc.sasc.biopet.core.config.Configurable import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.utils.ConfigUtils import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.queue.function.{ QFunction, InProcessFunction } import org.broadinstitute.gatk.queue.function.{ QFunction, InProcessFunction }
...@@ -56,7 +56,12 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config ...@@ -56,7 +56,12 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
val executables: Map[String, Any] = { val executables: Map[String, Any] = {
(for (f <- qscript.functions if f.isInstanceOf[BiopetCommandLineFunctionTrait]) yield { (for (f <- qscript.functions if f.isInstanceOf[BiopetCommandLineFunctionTrait]) yield {
f match { f match {
case f: BiopetCommandLineFunctionTrait => { case f: BiopetJavaCommandLineFunction => {
f.configName -> Map("version" -> f.getVersion,
"java_md5" -> BiopetCommandLineFunctionTrait.executableMd5Cache.getOrElse(f.executable, None),
"jar_md5" -> SummaryQScript.md5sumCache.getOrElse(f.jarFile, None))
}
case f: BiopetCommandLineFunction => {
f.configName -> Map("version" -> f.getVersion, f.configName -> Map("version" -> f.getVersion,
"md5" -> BiopetCommandLineFunctionTrait.executableMd5Cache.getOrElse(f.executable, None)) "md5" -> BiopetCommandLineFunctionTrait.executableMd5Cache.getOrElse(f.executable, None))
} }
......
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