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Some lost files
authorSasha Sherstnev <a.sherstnev@dundee.ac.uk>
Wed, 23 Oct 2013 16:38:26 +0000 (17:38 +0100)
committerSasha Sherstnev <a.sherstnev@dundee.ac.uk>
Wed, 23 Oct 2013 16:38:26 +0000 (17:38 +0100)
.classpath [new file with mode: 0644] patch | blob
log/log4j.properties [new file with mode: 0644] patch | blob
log/log4j.properties.dundee [new file with mode: 0644] patch | blob
log/log4j.properties.full [new file with mode: 0644] patch | blob
log/log4j.properties.statdb [new file with mode: 0644] patch | blob

diff --git a/.classpath b/.classpath
new file mode 100644 (file)
index 0000000..f6b5f4a
--- /dev/null
+++ b/.classpath
@@ -0,0 +1,29 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+       <classpathentry kind="src" path="datamodel"/>
+       <classpathentry kind="src" path="log"/>
+       <classpathentry kind="src" path="engine"/>
+       <classpathentry kind="src" path="cassdb"/>
+       <classpathentry kind="src" path="webservices"/>
+       <classpathentry excluding="testdata/" kind="src" path="testsrc"/>
+       <classpathentry kind="lib" path="WEB-INF/lib/drmaa.jar"/>
+       <classpathentry kind="lib" path="WEB-INF/lib/log4j-1.2.15.jar"/>
+       <classpathentry kind="lib" path="WEB-INF/lib/compbio-annotations-1.0.jar"/>
+       <classpathentry kind="lib" path="WEB-INF/lib/compbio-util-1.4.jar"/>
+       <classpathentry kind="lib" path="WEB-INF/lib/derby-10.8.2.2.jar"/>
+       <classpathentry kind="lib" path="WEB-INF/lib/compbio-ga-1.1.jar"/>
+       <classpathentry kind="con" path="org.eclipse.jst.server.core.container/org.eclipse.jst.server.tomcat.runtimeTarget/Apache Tomcat v7.0 (v.41)">
+               <attributes>
+                       <attribute name="owner.project.facets" value="jst.web"/>
+               </attributes>
+       </classpathentry>
+       <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/jdk1.6.0_45">
+               <attributes>
+                       <attribute name="owner.project.facets" value="java"/>
+               </attributes>
+       </classpathentry>
+       <classpathentry kind="lib" path="testsrc/lib/testng-5.10-jdk15.jar"/>
+       <classpathentry kind="lib" path="WEB-INF/lib/jstl-1.1.2.jar"/>
+       <classpathentry kind="lib" path="WEB-INF/lib/standard-1.1.2.jar"/>
+       <classpathentry kind="output" path="WEB-INF/classes"/>
+</classpath>
diff --git a/log/log4j.properties b/log/log4j.properties
new file mode 100644 (file)
index 0000000..cd2a406
--- /dev/null
+++ b/log/log4j.properties
@@ -0,0 +1,77 @@
+\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
+# To see debug messages in TldLocationsCache, uncomment the following line:\r
+#org.apache.jasper.compiler.TldLocationsCache.level = FINE\r
+org.apache.catalina.core.ContainerBase.[Catalina].[localhost].level = FINE\r
+\r
+## Uncomment this if you would like the system to log messages into stdout\r
+#log4j.rootLogger=TRACE, rootfile\r
+#log4j.appender.rootfile=org.apache.log4j.RollingFileAppender\r
+#log4j.appender.rootfile.File=JABAWSLogFilename.log\r
+#log4j.appender.rootfile.Target=System.out\r
+#log4j.appender.rootfile.layout=org.apache.log4j.PatternLayout\r
+#log4j.appender.rootfile.layout.ConversionPattern=%t %d %m%n\r
+\r
+## Uncomment to enable JWS2 activity logging to the file\r
+#log4j.logger.compbio=TRACE, ACTIVITY\r
+#log4j.appender.ACTIVITY=org.apache.log4j.RollingFileAppender\r
+################log4j.appender.ACTIVITY.File=${logDir}/activity.log\r
+#log4j.appender.ACTIVITY.File=${catalina.base}/logs/JABAWSLogFilename.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 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
+##################################################################################################################################\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
+#log4j.appender.stdout.layout.ConversionPattern=%m%n\r
+#log4j.rootLogger=info, stdout\r
+\r
+log4j.rootLogger=ERROR, R\r
+log4j.appender.R=org.apache.log4j.FileAppender\r
+log4j.appender.R.File=${catalina.base}/logs/JABAWSErrorFile.log\r
+log4j.appender.R.layout=org.apache.log4j.PatternLayout\r
+log4j.appender.R.layout.ConversionPattern=%m%n %d{MM-dd@HH:mm:ss} %-5p (%13F:%L) %3x - \r
+\r
+# %d{ABSOLUTE} %5p %c{1}:%L -\r
+log4j.logger.compbio=WARN, B\r
+log4j.appender.B=org.apache.log4j.FileAppender\r
+log4j.appender.B.File=${catalina.base}/logs/engine.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
+# %d{ABSOLUTE} %5p %c{1}:%L -\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
+# %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
new file mode 100644 (file)
index 0000000..08af0be
--- /dev/null
+++ b/log/log4j.properties.dundee
@@ -0,0 +1,51 @@
+\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
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
diff --git a/log/log4j.properties.statdb b/log/log4j.properties.statdb
new file mode 100644 (file)
index 0000000..f9541b0
--- /dev/null
+++ b/log/log4j.properties.statdb
@@ -0,0 +1,27 @@
+\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