re-configure log4j location in order to allow log4j using both in Eclipse and ant

diff --git a/.settings/org.eclipse.wst.common.component b/.settings/org.eclipse.wst.common.component
index d25fa4e..f33c768 100644 (file)
--- a/.settings/org.eclipse.wst.common.component
+++ b/.settings/org.eclipse.wst.common.component
@@ -2,13 +2,14 @@
 <project-modules id="moduleCoreId" project-version="1.5.0">
     <wb-module deploy-name="jaba">
         <wb-resource deploy-path="/" source-path="/website" tag="defaultRootSource"/>
-       <wb-resource deploy-path="/binaries" source-path="binaries"/>
-       <wb-resource deploy-path="/jobsout" source-path="jobsout"/>
-       <wb-resource deploy-path="/ExecutionStatistic" source-path="ExecutionStatistic"/>
-       <wb-resource deploy-path="/conf" source-path="conf"/>
-       <wb-resource deploy-path="/statpages" source-path="statpages"/>
+        <wb-resource deploy-path="/binaries" source-path="binaries"/>
+        <wb-resource deploy-path="/jobsout" source-path="jobsout"/>
+        <wb-resource deploy-path="/ExecutionStatistic" source-path="ExecutionStatistic"/>
+        <wb-resource deploy-path="/conf" source-path="conf"/>
+        <wb-resource deploy-path="/statpages" source-path="statpages"/>
         <wb-resource deploy-path="/WEB-INF" source-path="WEB-INF"/>
         <wb-resource deploy-path="/META-INF" source-path="META-INF"/>
+        <wb-resource deploy-path="/WEB-INF/classes" source-path="/log"/>
 <!--        <dependent-module archiveName="jaba-client.jar" deploy-path="/WEB-INF/lib/" handle="module:/resource/jaba-client/jaba-client">
             <dependency-type>uses</dependency-type>
         </dependent-module> -->

diff --git a/conf/log4j.properties.full b/conf/log4j.properties.full
deleted file mode 100644 (file)
index 9c2d2fe..0000000
--- a/conf/log4j.properties.full
+++ /dev/null
@@ -1,62 +0,0 @@
-\r
-## CHANGE THIS (The root directory where to store all the log files)  \r
-#logDir = .\r
-\r
-## Uncomment to enable JWS2 activity logging to standard out (to the console if available)\r
-## for possible log levels please refer to Log4j documentation http://logging.apache.org/log4j/1.2/manual.html \r
-## Valid log levels are:\r
-## TRACE - log everything from below including very detailed messages (useful for debugging only)\r
-## DEBUG - log everything from below including some minor events (useful for debugging only)\r
-## INFO - log everything from below including some information messages\r
-## WARN - log error and warnings\r
-## ERROR - log errors and fatal events only \r
-## FATAL - log fatal events only\r
-\r
-#log4j.rootLogger=ERROR, stdout\r
-#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
-\r
-## Uncomment to enable JWS2 activity logging to the file\r
-#log4j.logger.compbio=ERROR, ACTIVITY\r
-#log4j.appender.ACTIVITY=org.apache.log4j.RollingFileAppender\r
-#log4j.appender.ACTIVITY.File=${logDir}/activity.log\r
-#log4j.appender.ACTIVITY.MaxFileSize=10MB\r
-#log4j.appender.ACTIVITY.MaxBackupIndex=10000\r
-#log4j.appender.ACTIVITY.layout=org.apache.log4j.PatternLayout\r
-#log4j.appender.ACTIVITY.layout.ConversionPattern=%d{MM-dd@HH:mm:ss} %-5p %3x - %m%n\r
-\r
-## Uncomment for web access logging. Please do not change the log level!\r
-#log4j.logger.ClustalWS-stats=INFO, STAT\r
-#log4j.logger.MuscleWS-stats=INFO, STAT\r
-#log4j.logger.TcoffeeWS-stats=INFO, STAT\r
-#log4j.logger.MafftWS-stats=INFO, STAT\r
-#log4j.logger.ProbconsWS-stats=INFO, STAT\r
-#log4j.appender.STAT=org.apache.log4j.RollingFileAppender\r
-#log4j.appender.STAT.File=${logDir}/wsaccess.log\r
-#log4j.appender.STAT.MaxFileSize=10MB\r
-#log4j.appender.STAT.MaxBackupIndex=10000\r
-#log4j.appender.STAT.layout=org.apache.log4j.PatternLayout\r
-#log4j.appender.STAT.layout.ConversionPattern=%t %d %m%n\r
-\r
-## Uncomment for separate local engine execution log (debugging only)\r
-#log4j.logger.compbio.engine.local.LocalExecutorService=INFO, C\r
-#log4j.appender.C=org.apache.log4j.FileAppender\r
-#log4j.appender.C.File=LocalExecutorService.log\r
-#log4j.appender.C.layout=org.apache.log4j.PatternLayout\r
-#log4j.appender.C.layout.ConversionPattern=%m%n\r
-\r
-## Parameter combinator logger (testing only)\r
-#log4j.logger.RunnerLogger=ERROR, RUNNER\r
-#log4j.appender.RUNNER=org.apache.log4j.FileAppender\r
-#log4j.appender.RUNNER.File=RunnerParam.log \r
-#log4j.appender.RUNNER.layout=org.apache.log4j.PatternLayout\r
-#log4j.appender.RUNNER.layout.ConversionPattern=%r [%t] %p %c %x - %m%n\r
-\r
-\r
-## NOT IN USE - collection of patterns choose the one that suits you\r
-# %d{ABSOLUTE} %5p %c{1}:%L -\r
-#log4j.appender.C.layout.ConversionPattern=%-4r [%t] %-5p %c %x - %m%n\r
-# %d{MM-dd@HH:mm:ss} %-5p (%13F:%L) %3x - \r
-#log4j.appender.ClustalWS-stats.layout.ConversionPattern=%p %d %t %C{4} %m%n\r

diff --git a/dundee-conf/log4j.properties b/dundee-conf/log4j.properties
deleted file mode 100644 (file)
index afcc70b..0000000
--- a/dundee-conf/log4j.properties
+++ /dev/null
@@ -1,51 +0,0 @@
-\r
-# change this \r
-logDir =/homes/www-jws2/logs\r
-\r
-log4j.rootLogger=ERROR, stdout\r
-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
-\r
-log4j.logger.compbio=TRACE, ACTIVITY\r
-log4j.appender.ACTIVITY=org.apache.log4j.RollingFileAppender\r
-log4j.appender.ACTIVITY.File=${logDir}/activity.log\r
-log4j.appender.ACTIVITY.MaxFileSize=10MB\r
-log4j.appender.ACTIVITY.MaxBackupIndex=10000\r
-log4j.appender.ACTIVITY.layout=org.apache.log4j.PatternLayout\r
-log4j.appender.ACTIVITY.layout.ConversionPattern=%d{MM-dd@HH:mm:ss} %-5p %3x - %m%n\r
-\r
-log4j.logger.ClustalWS-stats=INFO, STAT\r
-log4j.logger.MuscleWS-stats=INFO, STAT\r
-log4j.logger.TcoffeeWS-stats=INFO, STAT\r
-log4j.logger.MafftWS-stats=INFO, STAT\r
-log4j.logger.ProbconsWS-stats=INFO, STAT\r
-log4j.appender.STAT=org.apache.log4j.RollingFileAppender\r
-log4j.appender.STAT.File=${logDir}/wsaccess.log\r
-log4j.appender.STAT.MaxFileSize=10MB\r
-log4j.appender.STAT.MaxBackupIndex=10000\r
-log4j.appender.STAT.layout=org.apache.log4j.PatternLayout\r
-log4j.appender.STAT.layout.ConversionPattern=%t %d %m%n\r
-\r
-\r
-# Uncomment for separate local engine execution log\r
-#log4j.logger.compbio.engine.local.LocalExecutorService=INFO, C\r
-#log4j.appender.C=org.apache.log4j.FileAppender\r
-#log4j.appender.C.File=LocalExecutorService.log\r
-#log4j.appender.C.layout=org.apache.log4j.PatternLayout\r
-#log4j.appender.C.layout.ConversionPattern=%m%n\r
-\r
-#Parameter combinator logger (testing only)\r
-#log4j.logger.RunnerLogger=ERROR, RUNNER\r
-#log4j.appender.RUNNER=org.apache.log4j.FileAppender\r
-#log4j.appender.RUNNER.File=RunnerParam.log \r
-#log4j.appender.RUNNER.layout=org.apache.log4j.PatternLayout\r
-#log4j.appender.RUNNER.layout.ConversionPattern=%r [%t] %p %c %x - %m%n\r
-\r
-\r
-#Not used - collection of patterns\r
-# %d{ABSOLUTE} %5p %c{1}:%L -\r
-#log4j.appender.C.layout.ConversionPattern=%-4r [%t] %-5p %c %x - %m%n\r
-# %d{MM-dd@HH:mm:ss} %-5p (%13F:%L) %3x - \r
-#log4j.appender.ClustalWS-stats.layout.ConversionPattern=%p %d %t %C{4} %m%n\r

diff --git a/conf/log4j.properties b/log/log4j.properties
similarity index 88%
rename from conf/log4j.properties
rename to log/log4j.properties
index f1567cc..fc6e3a9 100644 (file)
--- a/conf/log4j.properties
+++ b/log/log4j.properties
@@ -46,17 +46,16 @@
 #log4j.appender.stdout.layout.ConversionPattern=%m%n\r
 #log4j.rootLogger=info, stdout\r
 \r
-log4j.rootLogger=TRACE, rootfile\r
-log4j.appender.rootfile=org.apache.log4j.FileAppender\r
-log4j.appender.rootfile.File=${catalina.base}/logs/JABAWSLogFilename.log1\r
-log4j.appender.rootfile.Target=System.out\r
-log4j.appender.rootfile.layout=org.apache.log4j.PatternLayout\r
-log4j.appender.rootfile.layout.ConversionPattern=%t %d %m%n\r
+log4j.rootLogger=ERROR, errorfile\r
+log4j.appender.errorfile=org.apache.log4j.FileAppender\r
+log4j.appender.errorfile.File=${catalina.base}/logs/JABAWSErrorFile.log\r
+log4j.appender.errorfile.Target=System.out\r
+log4j.appender.errorfile.layout=org.apache.log4j.PatternLayout\r
+log4j.appender.errorfile.layout.ConversionPattern=%t %d %m%n\r
 \r
 # %d{ABSOLUTE} %5p %c{1}:%L -\r
 log4j.logger.compbio=TRACE, B\r
 log4j.appender.B=org.apache.log4j.FileAppender\r
-#log4j.appender.B.File=engine.log\r
 log4j.appender.B.File=${catalina.base}/logs/engine.log\r
 log4j.appender.B.layout=org.apache.log4j.PatternLayout\r
 log4j.appender.B.layout.ConversionPattern=%m%n %d{MM-dd@HH:mm:ss} %-5p (%13F:%L) %3x - \r