From 5c1124bf38f007bbcb3646042c3ee8de93ecc978 Mon Sep 17 00:00:00 2001
From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Tue, 30 Jul 2013 11:00:46 +0100
Subject: [PATCH] 1. git rid of jaba (now jabaws is everywhere) 2. fix problem
 with the clearStatDB target

---
 build.xml                   |  103 ++++++++++++++++++++++---------------------
 log/log4j.properties.statdb |   27 ++++++++++++
 2 files changed, 79 insertions(+), 51 deletions(-)
 create mode 100644 log/log4j.properties.statdb

diff --git a/build.xml b/build.xml
index e3ce16a..e0ad3a4 100644
--- a/build.xml
+++ b/build.xml
@@ -2,7 +2,6 @@
 
 <project default="jabaws" name="Build Java Bioinformatics Analysis Web Services" basedir=".">
 
-	<property name="basedir" location="${basedir}/log" />
 	<property name="LD_LIBRARY_PATH" value="/gridware/sge/lib/lx24-amd64"/>
 
 	<!-- Distributive file names-->
@@ -20,26 +19,26 @@
 	<property name="compbio-ga" value="compbio-ga-1.0.jar"/>
 
 	<!-- products -->
-	<property name="jaba_version" value="2.0.1"/>
-	<property name="datamodel" value="${distdir}/datamodel-${jaba_version}.jar"/>
-	<property name="datamodel-src" value="${distdir}/datamodel-src-${jaba_version}.jar"/>
-	<property name="min-jaba-client" value="${distdir}/min-jaba-client-${jaba_version}.jar"/>
-	<property name="min-jaba-client-nolog" value="${distdir}/min-jaba-client-nolog-${jaba_version}.jar"/>
-	<property name="jaba-client-src" value="${distdir}/jabaws-client-src-${jaba_version}.jar"/>
+	<property name="jabaws_version" value="3.0.0"/>
+	<property name="datamodel" value="${distdir}/datamodel-${jabaws_version}.jar"/>
+	<property name="datamodel-src" value="${distdir}/datamodel-src-${jabaws_version}.jar"/>
+	<property name="min-jabaws-client" value="${distdir}/min-jabaws-client-${jabaws_version}.jar"/>
+	<property name="min-jabaws-client-nolog" value="${distdir}/min-jabaws-client-nolog-${jabaws_version}.jar"/>
+	<property name="jabaws-client-src" value="${distdir}/jabaws-client-src-${jabaws_version}.jar"/>
 	<property name="aacon-ws-client" value="${distdir}/aacon-ws-client.jar"/>
-	<property name="full-jaba-client" value="${distdir}/full-jaba-client-${jaba_version}.jar"/>
-	<property name="jaba-source-jar" value="${distdir}/jabaws-src-${jaba_version}.jar"/>
-	<property name="full-jaba-client-pack" value="${distdir}/full-jaba-client-${jaba_version}-pack.zip"/>
-	<property name="jaba" value="${distdir}/jabaws.war"/>
-	<!-- TODO  
-	<property name="jaba-dundee" value="${distdir}/jaba-dundee.war"/>
-	 -->
-	<property name="jaba-no-binaries" value="${distdir}/jabaws-no-binaries.war"/>
+	<property name="full-jabaws-client" value="${distdir}/full-jabaws-client-${jabaws_version}.jar"/>
+	<property name="jabaws-source-jar" value="${distdir}/jabaws-src-${jabaws_version}.jar"/>
+	<property name="full-jabaws-client-pack" value="${distdir}/full-jabaws-client-${jabaws_version}-pack.zip"/>
+	<property name="jabaws" value="${distdir}/jabaws.war"/>
+	<!-- TODO 
+	<property name="jabaws-dundee" value="${distdir}/jabaws-dundee.war"/>
+	-->
+	<property name="jabaws-no-binaries" value="${distdir}/jabaws-no-binaries.war"/>
 	<property name="binaries" value="${distdir}/binaries.zip"/>
-	<property name="jaba-devel-web" value="${distdir}/jaba-devel-website.zip"/>
+	<property name="jabaws-devel-web" value="${distdir}/jabaws-devel-website.zip"/>
 
 	<!--Whole project archive -->
-	<property name="jaba-project" value="${distdir}/jaba-project.zip"/>
+	<property name="jabaws-project" value="${distdir}/jabaws-project.zip"/>
 
 	<!-- java -->
 	<property name="test.src" location="${basedir}/testsrc" />
@@ -81,6 +80,7 @@
 	<!-- Clean temp directories -->
 	<target name="clean">
 		<delete dir="${classes}" />
+		<delete dir="${basedir}/tmplog" />
 		<delete file="${distdir}/binaries.zip" />
 		<delete file="${basedir}/activity.log" />
 		<delete file="${basedir}/derby.log" />
@@ -101,8 +101,9 @@
 
 	<target name="clearStatDB" description="Remove all records from statistics database">
 		<echo>Cleaning Statistics database</echo>
-		<java classname="compbio.stat.collector.StatDB" fork="false" failonerror="true" classpath="${classes}">
-		<classpath refid="project.classpath" />
+		<java classname="compbio.stat.collector.StatDB" fork="true" failonerror="true" classpath="${classes}">
+			<jvmarg value="-Dlog4j.configuration=file:log/log4j.properties.statdb" />
+			<classpath refid="project.classpath" />
 		</java>
 	</target>
 
@@ -213,11 +214,11 @@
 		</jar>
 	</target>
 
-	<target name="jaba-client-src-jar" depends="datamodel-source-jar" description="Pack metadata, data model, WS interfaces, a simple ws client class">
+	<target name="jabaws-client-src-jar" depends="datamodel-source-jar" description="Pack metadata, data model, WS interfaces, a simple ws client class">
 		<echo>Jar file: JABAWS client source</echo>
-		<delete file="${jaba-client-src}">
+		<delete file="${jabaws-client-src}">
 		</delete>
-		<jar jarfile="${jaba-client-src}">
+		<jar jarfile="${jabaws-client-src}">
 			<zipgroupfileset  excludes="META-INF/*.MF" file="${datamodel-src}"/>
 			<fileset dir="${basedir}/webservices">
 				<!-- This will include JAXWS artifacts. Alternatively they can be generated on the fly. -->
@@ -235,10 +236,10 @@
 		</jar>
 	</target>
 
-	<target name="minimal-jaba-client-jar" depends="compile, datamodel-jar" description="Pack metadata, data model, WS interfaces, a simple ws client class">
+	<target name="minimal-jabaws-client-jar" depends="compile, datamodel-jar" description="Pack metadata, data model, WS interfaces, a simple ws client class">
 		<echo>Jar file: Minimal WS client jar</echo>
-		<delete file="${basedir}/${min-jaba-client}"></delete>
-		<jar jarfile="${basedir}/${min-jaba-client}">
+		<delete file="${basedir}/${min-jabaws-client}"></delete>
+		<jar jarfile="${basedir}/${min-jabaws-client}">
 			<zipgroupfileset excludes="META-INF/*.SF" dir="" includes="${datamodel}" />
 			<fileset dir="${basedir}/WEB-INF/classes/">
 				<!-- This will include JAXWS artifacts. Alternatively they can be generated on the fly. -->
@@ -255,8 +256,8 @@
 				<attribute name="Implementation-URL" value="${project.url}" />
 			</manifest>
 		</jar>
-		<delete file="${basedir}/${min-jaba-client-nolog}"></delete>
-		<jar jarfile="${basedir}/${min-jaba-client-nolog}">
+		<delete file="${basedir}/${min-jabaws-client-nolog}"></delete>
+		<jar jarfile="${basedir}/${min-jabaws-client-nolog}">
 			<zipgroupfileset excludes="META-INF/*.SF" dir="" includes="${datamodel}" />
 			<fileset dir="${basedir}/WEB-INF/classes/">
 				<!-- This will include JAXWS artifacts. Alternatively they can be generated on the fly. -->
@@ -274,11 +275,11 @@
 		</jar>
 	</target>
 
-	<target name="full-jaba-client-jar" depends="compile" description="Pack datamodel, engine and runners">
+	<target name="full-jabaws-client-jar" depends="compile" description="Pack datamodel, engine and runners">
 		<echo>Jar file: Full WS client jar</echo>
-		<delete file="${full-jaba-client}">
+		<delete file="${full-jabaws-client}">
 		</delete>
-		<jar jarfile="${full-jaba-client}">
+		<jar jarfile="${full-jabaws-client}">
 			<zipgroupfileset excludes="META-INF/*.SF" dir="${web.lib.path}" >
 				<include name="${compbio-util}"/>
 				<include name="${compbio-annotation}"/>
@@ -317,22 +318,22 @@
 		</jar>
 	</target>
 
-	<target name="full-jaba-client" depends="full-jaba-client-jar, pack-binaries" description="Pack binaries with sources and configuration files">
+	<target name="full-jabaws-client" depends="full-jabaws-client-jar, pack-binaries" description="Pack binaries with sources and configuration files">
 		<echo>Packing binaries, and configuration files</echo>
-		<zip destfile="${full-jaba-client-pack}" >
+		<zip destfile="${full-jabaws-client-pack}" >
 			<zipgroupfileset file="${binaries}" />
 			<zipfileset dir="conf" prefix="conf" >
 				<exclude name="**/temp/**"/>
 			</zipfileset>
-			<fileset file="${full-jaba-client}" />
+			<fileset file="${full-jabaws-client}" />
 		</zip>
 	</target>
 
 
 	<target name="source-jar" depends="datamodel-source-jar" description="Pack java sources">
-		<delete file="${basedir}/${jaba-source-jar}">
+		<delete file="${basedir}/${jabaws-source-jar}">
 		</delete>
-		<jar jarfile="${basedir}/${jaba-source-jar}">
+		<jar jarfile="${basedir}/${jabaws-source-jar}">
 			<zipgroupfileset  excludes="META-INF/*.MF" file="${datamodel-src}"/>
 			<fileset dir="${basedir}/runner">
 				<include name="**"/>
@@ -372,11 +373,11 @@
 		</jar>
 	</target>
 
-	<target name="full-jaba-jar" depends="compile" description="Pack datamodel, engine, runners, configuration, binaries and webservices">
+	<target name="full-jabaws-jar" depends="compile" description="Pack datamodel, engine, runners, configuration, binaries and webservices">
 		<echo>Jar file: Full WS client jar</echo>
-		<delete file="${full-jaba-client}">
+		<delete file="${full-jabaws-client}">
 		</delete>
-		<jar jarfile="${full-jaba-client}">
+		<jar jarfile="${full-jabaws-client}">
 			<zipgroupfileset excludes="META-INF/*.SF" dir="${web.lib.path}" >
 				<include name="log4j-1.2.15.jar"/>
 				<include name="${compbio-util}"/>
@@ -410,11 +411,11 @@
 		</zip>
 	</target>
 
-	<target name="jaba-no-binaries" depends="full-jaba-jar, clearStatDB" description="Prepare JABAWS war file without native binaries">
+	<target name="jabaws-no-binaries" depends="full-jabaws-jar, clearStatDB" description="Prepare JABAWS war file without native binaries">
 		<echo>Preparing a war file without binaries</echo>
-		<delete file="${jaba-no-binaries}">
+		<delete file="${jabaws-no-binaries}">
 		</delete>
-		<zip destfile="${jaba-no-binaries}" whenempty="create">
+		<zip destfile="${jabaws-no-binaries}" whenempty="create">
 			<zipfileset dir="${basedir}/WEB-INF" prefix="WEB-INF">
 				<exclude name="classes"/>
 				<!-- These are included into JABA client so exclude the jars -->
@@ -435,7 +436,7 @@
 			</zipfileset>
 			<!-- Add JABAWS web site apart from the binary archive -->
 			<zipfileset dir="${basedir}/website" excludes="archive/**, devel*.html, tests/**, template.html"/>
-			<zipfileset dir="." includes="${full-jaba-client}" fullpath="WEB-INF/lib/jaba-client.jar"/>
+			<zipfileset dir="." includes="${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"/>
 		</zip>
@@ -443,31 +444,31 @@
 
 	<target name="build-devel-website" description="Pack developement related pages, tests, javadoc" >
 		<echo>Packing data for internal web site</echo>
-		<delete file="${jaba-devel-web}">
+		<delete file="${jabaws-devel-web}">
 		</delete>
-		<zip destfile="${jaba-devel-web}" whenempty="create">
+		<zip destfile="${jabaws-devel-web}" whenempty="create">
 			<!-- Add JABAWS web site apart from the binary archive -->
 			<zipfileset dir="${basedir}/website" excludes="template.html, download.html, index.html, manual.html, howto.html, archive/**, prog_docs/**"/>
 		</zip>
 	</target>
 
-	<target name="jaba-complete" depends="jaba-no-binaries, pack-binaries" description="Prepare JABAWS war file without runtime dependency - JAXWS jars">
+	<target name="jabaws-complete" depends="jabaws-no-binaries, pack-binaries" description="Prepare JABAWS war file without runtime dependency - JAXWS jars">
 		<echo>Preparing a complete war file</echo>
-		<delete file="${jaba}">
+		<delete file="${jabaws}">
 		</delete>
-		<copy tofile="${jaba}" file="${jaba-no-binaries}"/>
-		<zip destfile="${jaba}" update="true" >
+		<copy tofile="${jabaws}" file="${jabaws-no-binaries}"/>
+		<zip destfile="${jabaws}" update="true" >
 			<zipgroupfileset file="${binaries}" />
 		</zip>
 	</target>
 
-	<target name="build-all" depends="full-jaba-client, minimal-jaba-client-jar, jaba-no-binaries, jaba-complete, datamodel-jar, datamodel-source-jar, source-jar, jaba-client-src-jar" description="Build-all the distributives"/>
+	<target name="build-all" depends="full-jabaws-client, minimal-jabaws-client-jar, jabaws-no-binaries, jabaws-complete, datamodel-jar, datamodel-source-jar, source-jar, jabaws-client-src-jar" description="Build-all the distributives"/>
 
 	<!-- This task does not really depends on compile, but it is better to make sure that the code is sound -->
 	<target name="archive-project" description="Pack everything in the project for those who do not have access to SVN" depends="compile">
-		<delete file="${jaba-project}">
+		<delete file="${jabaws-project}">
 		</delete>
-		<zip destfile="${jaba-project}" whenempty="create" >
+		<zip destfile="${jabaws-project}" whenempty="create" >
 			<fileset dir="." excludes="${distdir}/**, jobsout/**, test-output/**, **.svn, dundee-conf/**, TODO.txt, IDEAS.txt, ${activity.log}, **/*.zip, **/*.war"/>
 			<!-- Add jobsout directory but no content -->
 			<zipfileset dir="${basedir}/jobsout" prefix="jobsout" excludes="*/**"/>
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