From ee5ed3c8f87f708bd4541c8795264d4787ce6791 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 30 Jun 2015 15:47:35 +0200
Subject: [PATCH] Adding more information for each executable to summary
---
.../core/BiopetCommandLineFunctionTrait.scala | 12 +++++++++---
.../biopet/core/BiopetJavaCommandLineFunction.scala | 13 +++++++++++++
.../sasc/biopet/core/summary/WriteSummary.scala | 6 ++++--
3 files changed, 26 insertions(+), 5 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
index f6de8b3e4..614aed759 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
@@ -156,7 +156,13 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
protected val versionExitcode = List(0)
/** Executes the version command */
- private def getVersionInternal: Option[String] = {
+ private[core] def getVersionInternal(): Option[String] = {
+ if (versionCommand == null || versionRegex == null) None
+ else getVersionInternal(versionCommand, versionRegex)
+ }
+
+ /** Executes the version command */
+ private[core] def getVersionInternal(versionCommand: String, versionRegex: Regex): Option[String] = {
if (versionCommand == null || versionRegex == null) return None
val exe = new File(versionCommand.trim.split(" ")(0))
if (!exe.exists()) return None
@@ -221,7 +227,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
/** stores global caches */
object BiopetCommandLineFunctionTrait {
import scala.collection.mutable.Map
- private val versionCache: Map[String, String] = Map()
+ private[core] val versionCache: Map[String, String] = Map()
private[core] val executableMd5Cache: Map[String, String] = Map()
- private val executableCache: Map[String, String] = Map()
+ private[core] val executableCache: Map[String, String] = Map()
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
index cd26c269d..d0d4496e9 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
@@ -37,6 +37,19 @@ trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetC
return cmd
}
+ def javaVersionCommand: String = executable + " -version"
+
+ def getJavaVersion: Option[String] = {
+ if (!BiopetCommandLineFunctionTrait.executableCache.contains(executable))
+ preProcesExecutable
+ if (!BiopetCommandLineFunctionTrait.versionCache.contains(javaVersionCommand))
+ getVersionInternal(javaVersionCommand, """java version "(.*)"""".r) match {
+ case Some(version) => BiopetCommandLineFunctionTrait.versionCache += javaVersionCommand -> version
+ case _ =>
+ }
+ BiopetCommandLineFunctionTrait.versionCache.get(javaVersionCommand)
+ }
+
override def setupRetry(): Unit = {
super.setupRetry()
javaMemoryLimit = memoryLimit
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
index f28b4db04..5498c6139 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
@@ -74,11 +74,13 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
case f: BiopetJavaCommandLineFunction => {
f.configName -> Map("version" -> f.getVersion.getOrElse(None),
"java_md5" -> BiopetCommandLineFunctionTrait.executableMd5Cache.getOrElse(f.executable, None),
- "jar_md5" -> SummaryQScript.md5sumCache.getOrElse(f.jarFile, None))
+ "java_version" -> f.getJavaVersion,
+ "jar_path" -> f.jarFile)
}
case f: BiopetCommandLineFunction => {
f.configName -> Map("version" -> f.getVersion.getOrElse(None),
- "md5" -> BiopetCommandLineFunctionTrait.executableMd5Cache.getOrElse(f.executable, None))
+ "md5" -> BiopetCommandLineFunctionTrait.executableMd5Cache.getOrElse(f.executable, None),
+ "path" -> f.executable)
}
case _ => throw new IllegalStateException("This should not be possible")
}
--
GitLab