improve logging system

diff --git a/log/log4j.properties.dundee b/log/log4j.properties.dundee
new file mode 100644 (file)
index 0000000..afcc70b
--- /dev/null
+++ b/log/log4j.properties.dundee
@@ -0,0 +1,51 @@
+\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/log/log4j.properties.full b/log/log4j.properties.full
new file mode 100644 (file)
index 0000000..9c2d2fe
--- /dev/null
+++ b/log/log4j.properties.full
@@ -0,0 +1,62 @@
+\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