Fix logging system and add jabaws libs into the system

diff --git a/.classpath b/.classpath
index 1e750dd..394889c 100644 (file)
--- a/.classpath
+++ b/.classpath
@@ -1,6 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
        <classpathentry kind="src" path="datadb"/>
+       <classpathentry kind="src" path="engine"/>
        <classpathentry kind="src" path="server"/>
        <classpathentry excluding="testdata/" kind="src" path="testsrc"/>
        <classpathentry kind="lib" path="testsrc/lib/testng-5.10-jdk15.jar"/>
@@ -14,6 +15,7 @@
        <classpathentry kind="lib" path="WEB-INF/lib/jackson-core-asl-1.9.13.jar"/>
        <classpathentry kind="lib" path="WEB-INF/lib/jackson-mapper-asl-1.9.13.jar"/>
        <classpathentry kind="lib" path="WEB-INF/lib/displaytag-1.2.jar"/>
+       <classpathentry kind="lib" path="WEB-INF/lib/jabaws-core-2.1.0.jar" sourcepath="WEB-INF/lib/jabaws-core-src-2.1.0.jar"/>
        <classpathentry kind="con" path="org.eclipse.jst.server.core.container/org.eclipse.jst.server.tomcat.runtimeTarget/Apache Tomcat v7.0">
                <attributes>
                        <attribute name="owner.project.facets" value="jst.web"/>

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 (file)
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 (file)
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 (file)
--- a/log/log4j.properties
+++ b/log/log4j.properties
@@ -1,9 +1,4 @@
-\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
+## Uncomment to enable ProteoCache activity logging\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
@@ -25,6 +20,7 @@ org.apache.catalina.core.ContainerBase.[Catalina].[localhost].level = FINE
 #log4j.appender.rootfile.layout.ConversionPattern=%t %d %m%n\r
 \r
 ## Uncomment to enable JWS2 activity logging to the file\r
+#logDir = .\r
 #log4j.logger.compbio=TRACE, ACTIVITY\r
 #log4j.appender.ACTIVITY=org.apache.log4j.RollingFileAppender\r
 ################log4j.appender.ACTIVITY.File=${logDir}/activity.log\r
@@ -42,8 +38,6 @@ org.apache.catalina.core.ContainerBase.[Catalina].[localhost].level = FINE
 #log4j.appender.C.layout.ConversionPattern=%m%n\r
 \r
 ##################################################################################################################################\r
-# log4j.properties from runner/\r
-\r
 #log4j.appender.stdout=org.apache.log4j.ConsoleAppender\r
 #log4j.appender.stdout.Target=System.out\r
 #log4j.appender.stdout.layout=org.apache.log4j.PatternLayout\r
@@ -52,14 +46,14 @@ org.apache.catalina.core.ContainerBase.[Catalina].[localhost].level = FINE
 \r
 log4j.rootLogger=ERROR, R\r
 log4j.appender.R=org.apache.log4j.FileAppender\r
-log4j.appender.R.File=${catalina.base}/logs/JABAWSErrorFile.log\r
+log4j.appender.R.File=${catalina.base}/logs/errors.log\r
 log4j.appender.R.layout=org.apache.log4j.PatternLayout\r
 log4j.appender.R.layout.ConversionPattern=%m%n %d{MM-dd@HH:mm:ss} %-5p (%13F:%L) %3x - \r
 \r
 # %d{ABSOLUTE} %5p %c{1}:%L -\r
-log4j.logger.compbio=WARN, B\r
+log4j.logger.compbio=DEBIG, B\r
 log4j.appender.B=org.apache.log4j.FileAppender\r
-log4j.appender.B.File=${catalina.base}/logs/engine.log\r
+log4j.appender.B.File=${catalina.base}/logs/debugging.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
 \r
@@ -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\r
 #log4j.appender.C.layout.ConversionPattern=%m%n\r
 # %d{MM-dd@HH:mm:ss} %-5p (%13F:%L) %3x - \r
-\r
-#log4j.logger.RunnerLogger=ERROR, D\r
-#log4j.appender.D=org.apache.log4j.ConsoleAppender \r
-#log4j.appender.D.layout=org.apache.log4j.PatternLayout\r
-#log4j.appender.D.layout.ConversionPattern=%r [%t] %p %c %x - %m%n\r

diff --git a/log/log4j.properties.dundee b/log/log4j.properties.dundee
deleted file mode 100644 (file)
index 08af0be..0000000
--- a/log/log4j.properties.dundee
+++ /dev/null
@@ -1,51 +0,0 @@
-\r
-# change this \r
-logDir =/homes/www-protcache/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
deleted file mode 100644 (file)
index 9c2d2fe..0000000
--- a/log/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/log/log4j.properties.statdb b/log/log4j.properties.statdb
deleted file mode 100644 (file)
index f9541b0..0000000
--- a/log/log4j.properties.statdb
+++ /dev/null
@@ -1,27 +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
-##################################################################################################################################\r
-log4j.rootLogger=ERROR, R\r
-log4j.appender.R=org.apache.log4j.FileAppender\r
-log4j.appender.R.File=logs/StatDBcleaningErrorFile.log\r
-log4j.appender.R.layout=org.apache.log4j.PatternLayout\r
-log4j.appender.R.layout.ConversionPattern=%m%n %d{MM-dd@HH:mm:ss} %-5p (%13F:%L) %3x - \r
-\r
-# %d{ABSOLUTE} %5p %c{1}:%L -\r
-log4j.logger.compbio=WARN, B\r
-log4j.appender.B=org.apache.log4j.FileAppender\r
-log4j.appender.B.File=logs/StatDBcleaningWarningFile.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