From d9752f68f5235d71a196ad13181fab827409186b Mon Sep 17 00:00:00 2001
From: Sasha <Main-laptop2>
Date: Mon, 29 Jul 2013 12:55:54 +0100
Subject: [PATCH] improve logging system

---
 log/log4j.properties.dundee |   51 +++++++++++++++++++++++++++++++++++
 log/log4j.properties.full   |   62 +++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 113 insertions(+)
 create mode 100644 log/log4j.properties.dundee
 create mode 100644 log/log4j.properties.full

diff --git a/log/log4j.properties.dundee b/log/log4j.properties.dundee
new file mode 100644
index 0000000..afcc70b
--- /dev/null
+++ b/log/log4j.properties.dundee
@@ -0,0 +1,51 @@
+
+# change this 
+logDir =/homes/www-jws2/logs
+
+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.logger.compbio=TRACE, ACTIVITY
+log4j.appender.ACTIVITY=org.apache.log4j.RollingFileAppender
+log4j.appender.ACTIVITY.File=${logDir}/activity.log
+log4j.appender.ACTIVITY.MaxFileSize=10MB
+log4j.appender.ACTIVITY.MaxBackupIndex=10000
+log4j.appender.ACTIVITY.layout=org.apache.log4j.PatternLayout
+log4j.appender.ACTIVITY.layout.ConversionPattern=%d{MM-dd@HH:mm:ss} %-5p %3x - %m%n
+
+log4j.logger.ClustalWS-stats=INFO, STAT
+log4j.logger.MuscleWS-stats=INFO, STAT
+log4j.logger.TcoffeeWS-stats=INFO, STAT
+log4j.logger.MafftWS-stats=INFO, STAT
+log4j.logger.ProbconsWS-stats=INFO, STAT
+log4j.appender.STAT=org.apache.log4j.RollingFileAppender
+log4j.appender.STAT.File=${logDir}/wsaccess.log
+log4j.appender.STAT.MaxFileSize=10MB
+log4j.appender.STAT.MaxBackupIndex=10000
+log4j.appender.STAT.layout=org.apache.log4j.PatternLayout
+log4j.appender.STAT.layout.ConversionPattern=%t %d %m%n
+
+
+# Uncomment for separate local engine execution log
+#log4j.logger.compbio.engine.local.LocalExecutorService=INFO, C
+#log4j.appender.C=org.apache.log4j.FileAppender
+#log4j.appender.C.File=LocalExecutorService.log
+#log4j.appender.C.layout=org.apache.log4j.PatternLayout
+#log4j.appender.C.layout.ConversionPattern=%m%n
+
+#Parameter combinator logger (testing only)
+#log4j.logger.RunnerLogger=ERROR, RUNNER
+#log4j.appender.RUNNER=org.apache.log4j.FileAppender
+#log4j.appender.RUNNER.File=RunnerParam.log 
+#log4j.appender.RUNNER.layout=org.apache.log4j.PatternLayout
+#log4j.appender.RUNNER.layout.ConversionPattern=%r [%t] %p %c %x - %m%n
+
+
+#Not used - collection of patterns
+# %d{ABSOLUTE} %5p %c{1}:%L -
+#log4j.appender.C.layout.ConversionPattern=%-4r [%t] %-5p %c %x - %m%n
+# %d{MM-dd@HH:mm:ss} %-5p (%13F:%L) %3x - 
+#log4j.appender.ClustalWS-stats.layout.ConversionPattern=%p %d %t %C{4} %m%n
diff --git a/log/log4j.properties.full b/log/log4j.properties.full
new file mode 100644
index 0000000..9c2d2fe
--- /dev/null
+++ b/log/log4j.properties.full
@@ -0,0 +1,62 @@
+
+## CHANGE THIS (The root directory where to store all the log files)  
+#logDir = .
+
+## Uncomment to enable JWS2 activity logging to standard out (to the console if available)
+## for possible log levels please refer to Log4j documentation http://logging.apache.org/log4j/1.2/manual.html 
+## Valid log levels are:
+## TRACE - log everything from below including very detailed messages (useful for debugging only)
+## DEBUG - log everything from below including some minor events (useful for debugging only)
+## INFO - log everything from below including some information messages
+## WARN - log error and warnings
+## ERROR - log errors and fatal events only 
+## FATAL - log fatal events only
+
+#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
+
+## Uncomment to enable JWS2 activity logging to the file
+#log4j.logger.compbio=ERROR, ACTIVITY
+#log4j.appender.ACTIVITY=org.apache.log4j.RollingFileAppender
+#log4j.appender.ACTIVITY.File=${logDir}/activity.log
+#log4j.appender.ACTIVITY.MaxFileSize=10MB
+#log4j.appender.ACTIVITY.MaxBackupIndex=10000
+#log4j.appender.ACTIVITY.layout=org.apache.log4j.PatternLayout
+#log4j.appender.ACTIVITY.layout.ConversionPattern=%d{MM-dd@HH:mm:ss} %-5p %3x - %m%n
+
+## Uncomment for web access logging. Please do not change the log level!
+#log4j.logger.ClustalWS-stats=INFO, STAT
+#log4j.logger.MuscleWS-stats=INFO, STAT
+#log4j.logger.TcoffeeWS-stats=INFO, STAT
+#log4j.logger.MafftWS-stats=INFO, STAT
+#log4j.logger.ProbconsWS-stats=INFO, STAT
+#log4j.appender.STAT=org.apache.log4j.RollingFileAppender
+#log4j.appender.STAT.File=${logDir}/wsaccess.log
+#log4j.appender.STAT.MaxFileSize=10MB
+#log4j.appender.STAT.MaxBackupIndex=10000
+#log4j.appender.STAT.layout=org.apache.log4j.PatternLayout
+#log4j.appender.STAT.layout.ConversionPattern=%t %d %m%n
+
+## Uncomment for separate local engine execution log (debugging only)
+#log4j.logger.compbio.engine.local.LocalExecutorService=INFO, C
+#log4j.appender.C=org.apache.log4j.FileAppender
+#log4j.appender.C.File=LocalExecutorService.log
+#log4j.appender.C.layout=org.apache.log4j.PatternLayout
+#log4j.appender.C.layout.ConversionPattern=%m%n
+
+## Parameter combinator logger (testing only)
+#log4j.logger.RunnerLogger=ERROR, RUNNER
+#log4j.appender.RUNNER=org.apache.log4j.FileAppender
+#log4j.appender.RUNNER.File=RunnerParam.log 
+#log4j.appender.RUNNER.layout=org.apache.log4j.PatternLayout
+#log4j.appender.RUNNER.layout.ConversionPattern=%r [%t] %p %c %x - %m%n
+
+
+## NOT IN USE - collection of patterns choose the one that suits you
+# %d{ABSOLUTE} %5p %c{1}:%L -
+#log4j.appender.C.layout.ConversionPattern=%-4r [%t] %-5p %c %x - %m%n
+# %d{MM-dd@HH:mm:ss} %-5p (%13F:%L) %3x - 
+#log4j.appender.ClustalWS-stats.layout.ConversionPattern=%p %d %t %C{4} %m%n
-- 
1.7.10.2