From: Sasha Sherstnev Date: Fri, 8 Nov 2013 10:20:24 +0000 (+0000) Subject: Fix logging system and add jabaws libs into the system X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=cc4bc0878cb61dd358a8661070db715e1cae5702;p=proteocache.git Fix logging system and add jabaws libs into the system --- diff --git a/.classpath b/.classpath index 1e750dd..394889c 100644 --- a/.classpath +++ b/.classpath @@ -1,6 +1,7 @@ + @@ -14,6 +15,7 @@ + diff --git a/WEB-INF/lib/jabaws-core-2.1.0.jar b/WEB-INF/lib/jabaws-core-2.1.0.jar new file mode 100644 index 0000000..ad5d733 Binary files /dev/null and b/WEB-INF/lib/jabaws-core-2.1.0.jar differ diff --git a/WEB-INF/lib/jabaws-core-src-2.1.0.jar b/WEB-INF/lib/jabaws-core-src-2.1.0.jar new file mode 100644 index 0000000..7c6cdb2 Binary files /dev/null and b/WEB-INF/lib/jabaws-core-src-2.1.0.jar differ diff --git a/log/log4j.properties b/log/log4j.properties index cd2a406..d186883 100644 --- a/log/log4j.properties +++ b/log/log4j.properties @@ -1,9 +1,4 @@ - -## 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 +## Uncomment to enable ProteoCache activity logging ## 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) @@ -25,6 +20,7 @@ org.apache.catalina.core.ContainerBase.[Catalina].[localhost].level = FINE #log4j.appender.rootfile.layout.ConversionPattern=%t %d %m%n ## Uncomment to enable JWS2 activity logging to the file +#logDir = . #log4j.logger.compbio=TRACE, ACTIVITY #log4j.appender.ACTIVITY=org.apache.log4j.RollingFileAppender ################log4j.appender.ACTIVITY.File=${logDir}/activity.log @@ -42,8 +38,6 @@ org.apache.catalina.core.ContainerBase.[Catalina].[localhost].level = FINE #log4j.appender.C.layout.ConversionPattern=%m%n ################################################################################################################################## -# log4j.properties from runner/ - #log4j.appender.stdout=org.apache.log4j.ConsoleAppender #log4j.appender.stdout.Target=System.out #log4j.appender.stdout.layout=org.apache.log4j.PatternLayout @@ -52,14 +46,14 @@ org.apache.catalina.core.ContainerBase.[Catalina].[localhost].level = FINE log4j.rootLogger=ERROR, R log4j.appender.R=org.apache.log4j.FileAppender -log4j.appender.R.File=${catalina.base}/logs/JABAWSErrorFile.log +log4j.appender.R.File=${catalina.base}/logs/errors.log log4j.appender.R.layout=org.apache.log4j.PatternLayout log4j.appender.R.layout.ConversionPattern=%m%n %d{MM-dd@HH:mm:ss} %-5p (%13F:%L) %3x - # %d{ABSOLUTE} %5p %c{1}:%L - -log4j.logger.compbio=WARN, B +log4j.logger.compbio=DEBIG, B log4j.appender.B=org.apache.log4j.FileAppender -log4j.appender.B.File=${catalina.base}/logs/engine.log +log4j.appender.B.File=${catalina.base}/logs/debugging.log log4j.appender.B.layout=org.apache.log4j.PatternLayout log4j.appender.B.layout.ConversionPattern=%m%n %d{MM-dd@HH:mm:ss} %-5p (%13F:%L) %3x - @@ -70,8 +64,3 @@ log4j.appender.B.layout.ConversionPattern=%m%n %d{MM-dd@HH:mm:ss} %-5p (%13F:%L) #log4j.appender.C.layout=org.apache.log4j.PatternLayout #log4j.appender.C.layout.ConversionPattern=%m%n # %d{MM-dd@HH:mm:ss} %-5p (%13F:%L) %3x - - -#log4j.logger.RunnerLogger=ERROR, D -#log4j.appender.D=org.apache.log4j.ConsoleAppender -#log4j.appender.D.layout=org.apache.log4j.PatternLayout -#log4j.appender.D.layout.ConversionPattern=%r [%t] %p %c %x - %m%n diff --git a/log/log4j.properties.dundee b/log/log4j.properties.dundee deleted file mode 100644 index 08af0be..0000000 --- a/log/log4j.properties.dundee +++ /dev/null @@ -1,51 +0,0 @@ - -# change this -logDir =/homes/www-protcache/logs - -log4j.rootLogger=ERROR, stdout -log4j.appender.stdout=org.apache.log4j.ConsoleAppender -log4j.appender.stdout.Target=System.out -log4j.appender.stdout.layout=org.apache.log4j.PatternLayout -log4j.appender.stdout.layout.ConversionPattern=%m%n - -log4j.logger.compbio=TRACE, ACTIVITY -log4j.appender.ACTIVITY=org.apache.log4j.RollingFileAppender -log4j.appender.ACTIVITY.File=${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 deleted file mode 100644 index 9c2d2fe..0000000 --- a/log/log4j.properties.full +++ /dev/null @@ -1,62 +0,0 @@ - -## 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 deleted file mode 100644 index f9541b0..0000000 --- a/log/log4j.properties.statdb +++ /dev/null @@ -1,27 +0,0 @@ - -## 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 -