From 21fba762da33de78d012f08810137233dd06583b Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 12 Feb 2015 16:10:22 +0100
Subject: [PATCH] Fix some small bugs
---
.../biopet/core/BiopetCommandLineFunctionTrait.scala | 10 ++++++++--
.../scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala | 6 ++++--
.../scala/nl/lumc/sasc/biopet/core/config/Config.scala | 6 +++---
3 files changed, 15 insertions(+), 7 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 498b71c68..905b3a715 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
@@ -48,7 +48,8 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
protected[core] def beforeCmd {}
/**
- * Can override this method. This is executed after the script is done en queue starts to generate the graph
+ * Can overr
+ * ide this method. This is executed after the script is done en queue starts to generate the graph
*/
protected[core] def afterGraph {}
//TODO: function need rename to beforeGraph
@@ -123,7 +124,10 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
beforeCmd
- addJobReportBinding("cores", if (nCoresRequest.get.toInt > 0) nCoresRequest.get.toInt else 1)
+ addJobReportBinding("cores", nCoresRequest match {
+ case Some(n) if n > 0 => n
+ case _ => 1
+ })
addJobReportBinding("version", getVersion)
}
@@ -166,6 +170,8 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
/** Get version from cache otherwise execute the version command */
def getVersion: String = {
+ if (!BiopetCommandLineFunctionTrait.executableCache.contains(executable))
+ checkExecutable
if (!BiopetCommandLineFunctionTrait.versionCache.contains(executable))
BiopetCommandLineFunctionTrait.versionCache += executable -> getVersionInternal
return BiopetCommandLineFunctionTrait.versionCache(executable)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
index db8a9eb49..8b6b0a6f5 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
@@ -73,12 +73,14 @@ trait BiopetQScript extends Configurable with GatkLogging {
case f: BiopetCommandLineFunctionTrait => {
f.checkExecutable
f.afterGraph
+ f.commandLine
}
case _ =>
}
- if (outputDir.canWrite) globalConfig.writeReport(qSettings.runName, outputDir + ".log/" + qSettings.runName)
- else BiopetQScript.addError("Output dir: '" + outputDir + "' is not writeable")
+ if (outputDir.getParentFile.canWrite || (outputDir.exists && outputDir.canWrite))
+ globalConfig.writeReport(qSettings.runName, new File(outputDir, ".log/" + qSettings.runName))
+ else BiopetQScript.addError("Parent of output dir: '" + outputDir.getParent + "' is not writeable, outputdir can not be created")
BiopetQScript.checkErrors
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
index e25e8ef50..faae1634a 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
@@ -140,7 +140,8 @@ class Config(var map: Map[String, Any]) extends Logging {
} else ConfigValue(requestedIndex, null, null, freeVar)
}
- def writeReport(id: String, directory: String): Unit = {
+ def writeReport(id: String, directory: File): Unit = {
+ directory.mkdirs()
def convertIndexValuesToMap(input: List[(ConfigValueIndex, Any)], forceFreeVar: Option[Boolean] = None): Map[String, Any] = {
input.foldLeft(Map[String, Any]())(
@@ -155,8 +156,7 @@ class Config(var map: Map[String, Any]) extends Logging {
}
def writeMapToJsonFile(map: Map[String, Any], name: String): Unit = {
- val file = new File(directory + "/" + id + "." + name + ".json")
- file.getParentFile.mkdirs()
+ val file = new File(directory, id + "." + name + ".json")
val writer = new PrintWriter(file)
writer.write(ConfigUtils.mapToJson(map).spaces2)
writer.close()
--
GitLab