From 62c8519c518941a3fdf7731f03e7638698929879 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 4 Aug 2014 16:13:58 +0200
Subject: [PATCH] changed output on getVersion on fail
---
.../sasc/biopet/core/BiopetCommandLineFunctionTrait.scala | 8 +++++---
1 file changed, 5 insertions(+), 3 deletions(-)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
index 8328e5f89..bbceb98e2 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
@@ -85,10 +85,12 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
if (versionCommand == null || versionRegex == null) return "N/A"
val stdout = new StringBuffer()
val stderr = new StringBuffer()
- def outputLog = "\n output log: \n stdout: \n" + stdout.toString + "\n stderr: \n" + stderr.toString
+ def outputLog = "Version command: \n" + versionCommand +
+ "\n output log: \n stdout: \n" + stdout.toString +
+ "\n stderr: \n" + stderr.toString
val process = Process(versionCommand).run(ProcessLogger(stdout append _, stderr append _))
if (!versionExitcode.contains(process.exitValue)) {
- logger.warn("Version command: '" + versionCommand + "' give exit code " + process.exitValue + ", version not found" + outputLog)
+ logger.warn("getVersion give exit code " + process.exitValue + ", version not found \n" + outputLog)
return "N/A"
}
for (line <- stdout.toString.split("\n") ++ stderr.toString.split("\n")) {
@@ -97,7 +99,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
case _ =>
}
}
- logger.warn("Version command: '" + versionCommand + "' give a exit code " + process.exitValue + " but no version was found, executable correct?" + outputLog)
+ logger.warn("getVersion give a exit code " + process.exitValue + " but no version was found, executable correct? \n" + outputLog)
return "N/A"
}
--
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