From 2858c357fe831fda3f1114671732540dd55ad43a Mon Sep 17 00:00:00 2001 From: Sasha Sherstnev Date: Wed, 23 Oct 2013 17:38:26 +0100 Subject: [PATCH] Some lost files --- .classpath | 29 ++++++++++++++++ log/log4j.properties | 77 +++++++++++++++++++++++++++++++++++++++++++ log/log4j.properties.dundee | 51 ++++++++++++++++++++++++++++ log/log4j.properties.full | 62 ++++++++++++++++++++++++++++++++++ log/log4j.properties.statdb | 27 +++++++++++++++ 5 files changed, 246 insertions(+) create mode 100644 .classpath create mode 100644 log/log4j.properties create mode 100644 log/log4j.properties.dundee create mode 100644 log/log4j.properties.full create mode 100644 log/log4j.properties.statdb diff --git a/.classpath b/.classpath new file mode 100644 index 0000000..f6b5f4a --- /dev/null +++ b/.classpath @@ -0,0 +1,29 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/log/log4j.properties b/log/log4j.properties new file mode 100644 index 0000000..cd2a406 --- /dev/null +++ b/log/log4j.properties @@ -0,0 +1,77 @@ + +## 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 + +# To see debug messages in TldLocationsCache, uncomment the following line: +#org.apache.jasper.compiler.TldLocationsCache.level = FINE +org.apache.catalina.core.ContainerBase.[Catalina].[localhost].level = FINE + +## Uncomment this if you would like the system to log messages into stdout +#log4j.rootLogger=TRACE, rootfile +#log4j.appender.rootfile=org.apache.log4j.RollingFileAppender +#log4j.appender.rootfile.File=JABAWSLogFilename.log +#log4j.appender.rootfile.Target=System.out +#log4j.appender.rootfile.layout=org.apache.log4j.PatternLayout +#log4j.appender.rootfile.layout.ConversionPattern=%t %d %m%n + +## Uncomment to enable JWS2 activity logging to the file +#log4j.logger.compbio=TRACE, ACTIVITY +#log4j.appender.ACTIVITY=org.apache.log4j.RollingFileAppender +################log4j.appender.ACTIVITY.File=${logDir}/activity.log +#log4j.appender.ACTIVITY.File=${catalina.base}/logs/JABAWSLogFilename.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 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 + +################################################################################################################################## +# log4j.properties from runner/ + +#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.rootLogger=info, stdout + +log4j.rootLogger=ERROR, R +log4j.appender.R=org.apache.log4j.FileAppender +log4j.appender.R.File=${catalina.base}/logs/JABAWSErrorFile.log +log4j.appender.R.layout=org.apache.log4j.PatternLayout +log4j.appender.R.layout.ConversionPattern=%m%n %d{MM-dd@HH:mm:ss} %-5p (%13F:%L) %3x - + +# %d{ABSOLUTE} %5p %c{1}:%L - +log4j.logger.compbio=WARN, B +log4j.appender.B=org.apache.log4j.FileAppender +log4j.appender.B.File=${catalina.base}/logs/engine.log +log4j.appender.B.layout=org.apache.log4j.PatternLayout +log4j.appender.B.layout.ConversionPattern=%m%n %d{MM-dd@HH:mm:ss} %-5p (%13F:%L) %3x - + +# %d{ABSOLUTE} %5p %c{1}:%L - +#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 +# %d{MM-dd@HH:mm:ss} %-5p (%13F:%L) %3x - + +#log4j.logger.RunnerLogger=ERROR, D +#log4j.appender.D=org.apache.log4j.ConsoleAppender +#log4j.appender.D.layout=org.apache.log4j.PatternLayout +#log4j.appender.D.layout.ConversionPattern=%r [%t] %p %c %x - %m%n diff --git a/log/log4j.properties.dundee b/log/log4j.properties.dundee new file mode 100644 index 0000000..08af0be --- /dev/null +++ b/log/log4j.properties.dundee @@ -0,0 +1,51 @@ + +# change this +logDir =/homes/www-protcache/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 diff --git a/log/log4j.properties.statdb b/log/log4j.properties.statdb new file mode 100644 index 0000000..f9541b0 --- /dev/null +++ b/log/log4j.properties.statdb @@ -0,0 +1,27 @@ + +## 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, R +log4j.appender.R=org.apache.log4j.FileAppender +log4j.appender.R.File=logs/StatDBcleaningErrorFile.log +log4j.appender.R.layout=org.apache.log4j.PatternLayout +log4j.appender.R.layout.ConversionPattern=%m%n %d{MM-dd@HH:mm:ss} %-5p (%13F:%L) %3x - + +# %d{ABSOLUTE} %5p %c{1}:%L - +log4j.logger.compbio=WARN, B +log4j.appender.B=org.apache.log4j.FileAppender +log4j.appender.B.File=logs/StatDBcleaningWarningFile.log +log4j.appender.B.layout=org.apache.log4j.PatternLayout +log4j.appender.B.layout.ConversionPattern=%m%n %d{MM-dd@HH:mm:ss} %-5p (%13F:%L) %3x - -- 1.7.10.2