From 0848eb1092bfb938ec7703abe6cecc19e978aa6e Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 2 Nov 2015 12:14:27 +0100
Subject: [PATCH] Added a default for the retry arg
---
.../nl/lumc/sasc/biopet/core/PipelineCommand.scala | 10 +++++++++-
.../nl/lumc/sasc/biopet/utils/config/Config.scala | 12 ++++++------
2 files changed, 15 insertions(+), 7 deletions(-)
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
index dcede5257..928bee57a 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
@@ -18,13 +18,14 @@ package nl.lumc.sasc.biopet.core
import java.io.{ File, PrintWriter }
import nl.lumc.sasc.biopet.utils.config.Config
+import nl.lumc.sasc.biopet.utils.ConfigUtils.ImplicitConversions
import nl.lumc.sasc.biopet.core.workaround.BiopetQCommandLine
import nl.lumc.sasc.biopet.utils.{ MainCommand, Logging }
import org.apache.log4j.{ PatternLayout, WriterAppender }
import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
/** Wrapper around executable from Queue */
-trait PipelineCommand extends MainCommand with GatkLogging {
+trait PipelineCommand extends MainCommand with GatkLogging with ImplicitConversions {
/**
* Gets location of compiled class of pipeline
@@ -32,6 +33,8 @@ trait PipelineCommand extends MainCommand with GatkLogging {
*/
def pipeline = "/" + getClass.getName.stripSuffix("$").replaceAll("\\.", "/") + ".class"
+ def pipelineName = getClass.getSimpleName.takeWhile(_ != '$').toLowerCase
+
/** Class can be used directly from java with -cp option */
def main(args: Array[String]): Unit = {
val argsSize = args.length
@@ -87,6 +90,11 @@ trait PipelineCommand extends MainCommand with GatkLogging {
if (!args.contains("--log_to_file") && !args.contains("-log")) {
argv ++= List("--log_to_file", new File(logFile.getParentFile, "queue." + BiopetQCommandLine.timestamp + ".log").getAbsolutePath)
}
+ if (!args.contains("-retry") && !args.contains("--retry_failed")) {
+ val retry: Int = Config.global(pipelineName, Nil, "retry", default = 5)
+ logger.info("No retry flag found, ")
+ argv ++= List("-retry", retry.toString)
+ }
BiopetQCommandLine.main(argv)
}
}
\ No newline at end of file
diff --git a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Config.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Config.scala
index 4c69bf57c..a3b8a8ab0 100644
--- a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Config.scala
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Config.scala
@@ -168,12 +168,12 @@ class Config(protected var _map: Map[String, Any],
* @param freeVar Default true, if set false value must exist in module
* @return Config value
*/
- protected[config] def apply(module: String,
- path: List[String],
- key: String,
- default: Any = null,
- freeVar: Boolean = true,
- fixedValues: Map[String, Any] = Map()): ConfigValue = {
+ def apply(module: String,
+ path: List[String],
+ key: String,
+ default: Any = null,
+ freeVar: Boolean = true,
+ fixedValues: Map[String, Any] = Map()): ConfigValue = {
val requestedIndex = ConfigValueIndex(module, path, key, freeVar)
if (contains(requestedIndex, fixedValues)) {
val fixedValue = fixedCache.get(requestedIndex)
--
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