From fd78b5c873320ed46a8f4139d9d98cc4c7987b08 Mon Sep 17 00:00:00 2001
From: pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Date: Thu, 23 Jun 2011 14:15:51 +0000
Subject: [PATCH] update to compbio.utils and a few small changes

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4327 e3abac25-378b-4346-85de-24260fe3988d
---
 .classpath                                          |    4 ++--
 WEB-INF/lib/compbio-util-1.4.jar                    |  Bin 14240 -> 14264 bytes
 conf/log4j.properties                               |    4 ++--
 .../compbio/engine/conf/PropertyHelperManager.java  |   19 ++++++++++---------
 4 files changed, 14 insertions(+), 13 deletions(-)

diff --git a/.classpath b/.classpath
index b83e40e..c9e34d0 100644
--- a/.classpath
+++ b/.classpath
@@ -9,9 +9,9 @@
 	<classpathentry kind="lib" path="testsrc/lib/testng-5.10-jdk15.jar"/>
 	<classpathentry kind="lib" path="lib/servlet-api.jar"/>
 	<classpathentry kind="lib" path="WEB-INF/lib/drmaa.jar"/>
-	<classpathentry kind="lib" path="WEB-INF/lib/compbio-annotations-1.0.jar"/>
 	<classpathentry kind="lib" path="WEB-INF/lib/derby.jar"/>
-	<classpathentry kind="lib" path="WEB-INF/lib/compbio-util-1.4.jar"/>
 	<classpathentry kind="lib" path="WEB-INF/lib/log4j-1.2.15.jar"/>
+	<classpathentry kind="lib" path="WEB-INF/lib/compbio-util-1.4.jar"/>
+	<classpathentry kind="lib" path="WEB-INF/lib/compbio-annotations-1.0.jar"/>
 	<classpathentry kind="output" path="WEB-INF/classes"/>
 </classpath>
diff --git a/WEB-INF/lib/compbio-util-1.4.jar b/WEB-INF/lib/compbio-util-1.4.jar
index 7abd95e8680839672ec0b84801f6066672c458d3..a7d9249e14eedadecc7435fa4cf675f1c67d410d 100644
GIT binary patch
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diff --git a/conf/log4j.properties b/conf/log4j.properties
index 2ce2bf5..94dd72d 100644
--- a/conf/log4j.properties
+++ b/conf/log4j.properties
@@ -17,10 +17,10 @@ log4j.rootLogger=ERROR, stdout
 log4j.appender.stdout=org.apache.log4j.ConsoleAppender
 log4j.appender.stdout.Target=System.out
 log4j.appender.stdout.layout=org.apache.log4j.PatternLayout
-log4j.appender.stdout.layout.ConversionPattern=%m%n
+log4j.appender.stdout.layout.ConversionPattern=%t %d %m%n
 
 ## Uncomment to enable JWS2 activity logging to the file
-log4j.logger.compbio=TRACE, ACTIVITY
+log4j.logger.compbio=INFO, ACTIVITY
 log4j.appender.ACTIVITY=org.apache.log4j.RollingFileAppender
 log4j.appender.ACTIVITY.File=${logDir}/activity.log
 log4j.appender.ACTIVITY.MaxFileSize=10MB
diff --git a/engine/compbio/engine/conf/PropertyHelperManager.java b/engine/compbio/engine/conf/PropertyHelperManager.java
index e8aa9a7..939e5fe 100644
--- a/engine/compbio/engine/conf/PropertyHelperManager.java
+++ b/engine/compbio/engine/conf/PropertyHelperManager.java
@@ -66,8 +66,9 @@ public final class PropertyHelperManager {
 				ph = new PropertyHelper(locEngineProp, clustEngineProp,
 						execProp);
 			} catch (IOException e) {
-				log.warn("Cannot read property files! Reason: "
-						+ e.getLocalizedMessage(), e.getCause());
+				log.warn(
+						"Cannot read property files! Reason: "
+								+ e.getLocalizedMessage(), e.getCause());
 			}
 		}
 		return ph;
@@ -111,11 +112,10 @@ public final class PropertyHelperManager {
 		} catch (IllegalArgumentException e) {
 			// Classes are in the jar file, using different method to determine
 			// the path new File(INCORRECT URL) throws it
-			log
-					.warn(
-							"It looks like classes are in the jar file. "
-									+ "Attempting a different method to determinine the path to the resources "
-									+ e.getLocalizedMessage(), e.getCause());
+			log.debug(
+					"It looks like classes are in the jar file. "
+							+ "Attempting a different method to determinine the path to the resources "
+							+ e.getLocalizedMessage(), e.getCause());
 			try {
 				f = new File(PropertyHelperManager.class.getProtectionDomain()
 						.getCodeSource().getLocation().toURI().getPath());
@@ -128,8 +128,9 @@ public final class PropertyHelperManager {
 					f = f.getParentFile();
 				}
 			} catch (URISyntaxException e1) {
-				log.error("Could not find resources path! "
-						+ e1.getLocalizedMessage(), e1.getCause());
+				log.error(
+						"Could not find resources path! "
+								+ e1.getLocalizedMessage(), e1.getCause());
 				throw new RuntimeException("Could not find resources path! ",
 						e1.getCause());
 			}
-- 
1.7.10.2