From e10ce872d66998630e1718596de4facc03816ae3 Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Fri, 17 Dec 2021 17:25:06 +0000
Subject: [PATCH] Minimal log4j->log4j2 config properties - some of these are
 not used in JABAWS 2

---
 build.xml                                   |    8 +--
 log/log4j.properties.dundee                 |   51 --------------
 log/log4j2.dundee.properties                |   98 +++++++++++++++++++++++++++
 log/{log4j.properties => log4j2.properties} |   29 +++++---
 4 files changed, 121 insertions(+), 65 deletions(-)
 delete mode 100644 log/log4j.properties.dundee
 create mode 100644 log/log4j2.dundee.properties
 rename log/{log4j.properties => log4j2.properties} (82%)

diff --git a/build.xml b/build.xml
index 256cb45..00dfb50 100644
--- a/build.xml
+++ b/build.xml
@@ -84,7 +84,7 @@
 		<delete file="${basedir}/activity.log" />
 		<delete file="${basedir}/derby.log" />
 		<mkdir dir="${classes}" />
-		<copy file="${basedir}/log/log4j.properties" tofile="${classes}/log4j.properties" />
+		<copy file="${basedir}/log/log4j2.properties" tofile="${classes}/log4j2.properties" />
 	</target>
 
 	<!-- Clean up temp directories and dist directory (all jar, zip, and war files deleted) -->
@@ -119,7 +119,7 @@
 	-->
 	<target name="compile_with_debug" depends="clean" description="Perform a multiple step compilation to ensure layered structure is preserved. Debug enabled.">
 		<!-- copy files to class path-->
-		<copy file="${basedir}/log/log4j.properties" tofile="${classes}/log4j.properties" />
+		<copy file="${basedir}/log/log4j2.properties" tofile="${classes}/log4j2.properties" />
 		<!-- Complile the datamodel first -->
 		<javac srcdir="${basedir}/datamodel" destdir="${classes}" target="${JAVA_TARGET}" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >
 			<compilerarg value="-Xlint:unchecked"/>
@@ -161,7 +161,7 @@
 	-->
 	<target name="compile" depends="clean" description="Perform a multiple step compilation to ensure layered structure is preserved. Debug disabled, optimisation enabled. Tests are not compiled.">
 		<!-- copy files to class path-->
-		<copy file="${basedir}/log/log4j.properties" tofile="${classes}/log4j.properties" />
+		<copy file="${basedir}/log/log4j2.properties" tofile="${classes}/log4j2.properties" />
 		<!-- Complile the datamodel first -->
 		<javac srcdir="${basedir}/datamodel" destdir="${classes}" target="${JAVA_TARGET}" debug="off" optimize="on" encoding="UTF-8" verbose="false" nowarn="true">
 			<compilerarg value="-Xlint:-unchecked" />
@@ -450,7 +450,7 @@
 			<zipfileset dir="${basedir}/docs" excludes="_build/**"/>
 			<zipfileset dir="." includes="${full-jabaws-client}" fullpath="WEB-INF/lib/jabaws-client.jar"/>
 			<!-- Put a copy of log4j configuration file where it can be used  -->
-			<zipfileset dir="log" includes="log4j.properties" prefix="WEB-INF/classes"/>
+			<zipfileset dir="log" includes="log4j2.properties" prefix="WEB-INF/classes"/>
 		</zip>
 	</target>
 
diff --git a/log/log4j.properties.dundee b/log/log4j.properties.dundee
deleted file mode 100644
index afcc70b..0000000
--- a/log/log4j.properties.dundee
+++ /dev/null
@@ -1,51 +0,0 @@
-
-# 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/log4j2.dundee.properties b/log/log4j2.dundee.properties
new file mode 100644
index 0000000..f7caed0
--- /dev/null
+++ b/log/log4j2.dundee.properties
@@ -0,0 +1,98 @@
+status = error
+dest = err
+name = PropertiesConfig
+
+#dest = err
+#name = dundee
+
+# change this 
+property.logDir = www-jws2-logs
+
+
+appender.stdout.type = Console
+appender.stdout.name = stdout
+appender.stdout.layout.type = PatternLayout
+appender.stdout.layout.pattern = %m%n
+appender.stdout.filter.threshold.type = ThresholdFilter
+appender.stdout.filter.threshold.level = ERROR
+
+rootLogger.level = ERROR
+rootLogger.appenderRef.stdout.ref = stdout
+
+appender.ACTIVITY.type = RollingFile
+appender.ACTIVITY.name = ACTIVITY
+appender.ACTIVITY.fileName = ${logDir}/activity.log
+appender.ACTIVITY.filePattern = ${logDir}/activity-%d{MM-dd-yy-HH-mm-ss}-%i.log.gz
+appender.ACTIVITY.policies.type = Policies
+appender.ACTIVITY.policies.size.type = SizeBasedTriggeringPolicy
+appender.ACTIVITY.policies.size.size = 10MB
+appender.ACTIVITY.strategy.type = DefaultRolloverStrategy
+appender.ACTIVITY.strategy.max = 10000
+appender.ACTIVITY.layout.type = PatternLayout
+appender.ACTIVITY.layout.pattern = %d{MM-dd@HH:mm:ss} %-5p %3x - %m%n
+
+
+logger.compbio.level = INFO
+logger.compbio.name = compbio
+logger.compbio.appenderRef.ACTIVITY.ref = ACTIVITY
+
+
+appender.STAT.type = RollingFile
+appender.STAT.name = STAT
+appender.STAT.fileName = ${logDir}/wsaccess.log
+appender.STAT.filePattern = ${logDir}/wsaccess-%d{MM-dd-yy-HH-mm-ss}-%i.log.gz 
+appender.STAT.policies.type = Policies
+appender.STAT.policies.size.type = SizeBasedTriggeringPolicy
+appender.STAT.policies.size.size = 10MB
+appender.STAT.strategy.type = DefaultRolloverStrategy
+appender.STAT.strategy.max = 10000
+appender.STAT.layout.type = PatternLayout
+appender.STAT.layout.pattern = %d{MM-dd@HH:mm:ss} %-5p %3x - %m%n
+
+logger.ClustalWS-stats.name = ClustalWS-stats
+logger.ClustalWS-stats.appenderRef.STAT.ref = STAT
+logger.ClustalWS-stats.level = INFO
+
+logger.MuscleWS-stats.name = MuscleWS-stats
+logger.MuscleWS-stats.appenderRef.STAT.ref = STAT
+logger.MuscleWS-stats.level = INFO
+
+logger.TcoffeeWS-stats.name = TcoffeeWS-stats
+logger.TcoffeeWS-stats.appenderRef.STAT.ref = STAT
+logger.TcoffeeWS-stats.level = INFO
+
+
+logger.MafftWS-stats.name = MafftWS-stats
+logger.MafftWS-stats.appenderRef.STAT.ref = STAT
+logger.MafftWS-stats.level = INFO
+
+logger.ProbconsWSstats.name = ProbconsWSstats
+logger.ProbconsWSstats.appenderRef.STAT.ref = STAT
+logger.ProbconsWSstats.level = INFO
+
+
+
+
+# Uncomment for separate local engine execution log
+# TODO - STILL LOG4J 1.2.x
+#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)
+# TODO - STILL LOG4J 1.2.x
+#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
+# TODO - STILL LOG4J 1.2.x
+# %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 b/log/log4j2.properties
similarity index 82%
rename from log/log4j.properties
rename to log/log4j2.properties
index cd2a406..ff3dc5d 100644
--- a/log/log4j.properties
+++ b/log/log4j2.properties
@@ -50,18 +50,27 @@ org.apache.catalina.core.ContainerBase.[Catalina].[localhost].level = FINE
 #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 - 
+
+appender.R.name = R
+appender.R.type = File
+appender.R.fileName = ${catalina.base}/logs/JABAWSErrorFile.log
+appender.R.layout.type = PatternLayout
+appender.R.layout.pattern=%m%n %d{MM-dd@HH:mm:ss} %-5p (%13F:%L) %3x - 
+
+appender.B.name = B
+appender.B.type = File
+appender.B.fileName=${catalina.base}/logs/engine.log
+appender.B.layout.type = PatternLayout
+appender.B.layout.pattern=%m%n %d{MM-dd@HH:mm:ss} %-5p (%13F:%L) %3x - 
+
+rootLogger.Level = ERROR
+rootLogger.appenderRef = R
 
 # %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 - 
+logger.compbio.level = TRACE
+logger.compbio.appenderRef = B
+logger.compbio.name = compbio
+
 
 # %d{ABSOLUTE} %5p %c{1}:%L -
 #log4j.logger.compbio.engine.local.LocalExecutorService=INFO, C
-- 
1.7.10.2