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

diff --git a/.classpath b/.classpath
index b83e40e..c9e34d0 100644 (file)
--- a/.classpath
+++ b/.classpath
@@ -9,9 +9,9 @@
        <classpathentry kind="lib" path="testsrc/lib/testng-5.10-jdk15.jar"/>\r
        <classpathentry kind="lib" path="lib/servlet-api.jar"/>\r
        <classpathentry kind="lib" path="WEB-INF/lib/drmaa.jar"/>\r
-       <classpathentry kind="lib" path="WEB-INF/lib/compbio-annotations-1.0.jar"/>\r
        <classpathentry kind="lib" path="WEB-INF/lib/derby.jar"/>\r
-       <classpathentry kind="lib" path="WEB-INF/lib/compbio-util-1.4.jar"/>\r
        <classpathentry kind="lib" path="WEB-INF/lib/log4j-1.2.15.jar"/>\r
+       <classpathentry kind="lib" path="WEB-INF/lib/compbio-util-1.4.jar"/>\r
+       <classpathentry kind="lib" path="WEB-INF/lib/compbio-annotations-1.0.jar"/>\r
        <classpathentry kind="output" path="WEB-INF/classes"/>\r
 </classpath>\r

diff --git a/WEB-INF/lib/compbio-util-1.4.jar b/WEB-INF/lib/compbio-util-1.4.jar
index 7abd95e..a7d9249 100644 (file)
Binary files a/WEB-INF/lib/compbio-util-1.4.jar and b/WEB-INF/lib/compbio-util-1.4.jar differ

diff --git a/conf/log4j.properties b/conf/log4j.properties
index 2ce2bf5..94dd72d 100644 (file)
--- a/conf/log4j.properties
+++ b/conf/log4j.properties
@@ -17,10 +17,10 @@ log4j.rootLogger=ERROR, stdout
 log4j.appender.stdout=org.apache.log4j.ConsoleAppender\r
 log4j.appender.stdout.Target=System.out\r
 log4j.appender.stdout.layout=org.apache.log4j.PatternLayout\r
-log4j.appender.stdout.layout.ConversionPattern=%m%n\r
+log4j.appender.stdout.layout.ConversionPattern=%t %d %m%n\r
 \r
 ## Uncomment to enable JWS2 activity logging to the file\r
-log4j.logger.compbio=TRACE, ACTIVITY\r
+log4j.logger.compbio=INFO, ACTIVITY\r
 log4j.appender.ACTIVITY=org.apache.log4j.RollingFileAppender\r
 log4j.appender.ACTIVITY.File=${logDir}/activity.log\r
 log4j.appender.ACTIVITY.MaxFileSize=10MB\r

diff --git a/engine/compbio/engine/conf/PropertyHelperManager.java b/engine/compbio/engine/conf/PropertyHelperManager.java
index e8aa9a7..939e5fe 100644 (file)
--- 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,\r
                                                execProp);\r
                        } catch (IOException e) {\r
-                               log.warn("Cannot read property files! Reason: "\r
-                                               + e.getLocalizedMessage(), e.getCause());\r
+                               log.warn(\r
+                                               "Cannot read property files! Reason: "\r
+                                                               + e.getLocalizedMessage(), e.getCause());\r
                        }\r
                }\r
                return ph;\r
@@ -111,11 +112,10 @@ public final class PropertyHelperManager {
                } catch (IllegalArgumentException e) {\r
                        // Classes are in the jar file, using different method to determine\r
                        // the path new File(INCORRECT URL) throws it\r
-                       log\r
-                                       .warn(\r
-                                                       "It looks like classes are in the jar file. "\r
-                                                                       + "Attempting a different method to determinine the path to the resources "\r
-                                                                       + e.getLocalizedMessage(), e.getCause());\r
+                       log.debug(\r
+                                       "It looks like classes are in the jar file. "\r
+                                                       + "Attempting a different method to determinine the path to the resources "\r
+                                                       + e.getLocalizedMessage(), e.getCause());\r
                        try {\r
                                f = new File(PropertyHelperManager.class.getProtectionDomain()\r
                                                .getCodeSource().getLocation().toURI().getPath());\r
@@ -128,8 +128,9 @@ public final class PropertyHelperManager {
                                        f = f.getParentFile();\r
                                }\r
                        } catch (URISyntaxException e1) {\r
-                               log.error("Could not find resources path! "\r
-                                               + e1.getLocalizedMessage(), e1.getCause());\r
+                               log.error(\r
+                                               "Could not find resources path! "\r
+                                                               + e1.getLocalizedMessage(), e1.getCause());\r
                                throw new RuntimeException("Could not find resources path! ",\r
                                                e1.getCause());\r
                        }\r