X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.xml;h=04f80a4a2fdfcf93204f752be427bb07fd14a7af;hb=14c406769ac5cd4acfbc4819bb3dc967a51e4bb6;hp=412a049c14aa6ef0561b07c6862b08ef4b2d32ab;hpb=1c8cbe10ed2f25b3b36620a13d16e8cb96f6523f;p=jabaws.git

diff --git a/build.xml b/build.xml
index 412a049..04f80a4 100644
--- a/build.xml
+++ b/build.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
-<project default="minimal-jaba-client-jar" name="Build minimal client for Java Bioinformatics Analysis Web Services" basedir=".">
+<project default="jabaws" name="Build Java Bioinformatics Analysis Web Services" basedir=".">
 
 	<property name="basedir" location="${basedir}/log" />
 	<property name="LD_LIBRARY_PATH" value="/gridware/sge/lib/lx24-amd64"/>
@@ -8,28 +8,39 @@
 	<!-- Distributive file names-->
 	<property name="distdir" value="website/archive"/>
 	<mkdir dir="${distdir}" />
-	<property name="datamodel" value="${distdir}/datamodel-1.2.jar"/>
-	<property name="datamodel-src" value="${distdir}/datamodel-src-1.2.jar"/>
-	<property name="min-jaba-client" value="${distdir}/min-jaba-client.jar"/>
+	
+	<!-- projects details -->
+	<property name="project.url" value="http://www.compbio.dundee.ac.uk/jabaws"/>
+	<property name="product" value="Java Bioinformatics Analyses Web Services"/>
+	<property name="author" value="Peter Troshin"/>
+	
+	<!-- dependencies on other compbio projects  -->
+	<property name="compbio-annotation" value="compbio-annotations-1.0.jar"/>
+	<property name="compbio-util" value="compbio-util-1.4.jar"/>
+	<property name="compbio-ga" value="compbio-ga-1.0.jar"/>
+	
+	<!-- products -->
+	<property name="jaba_version" value="2.1"/>
+	<property name="datamodel" value="${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-${jaba_version}.jar"/>
+	<property name="jaba-client-src" value="${distdir}/jaba-client-src-${jaba_version}.jar"/>
+	
 	<property name="aacon-ws-client" value="${distdir}/aacon-ws-client.jar"/>
-	<property name="full-jaba-client" value="${distdir}/full-jaba-client.jar"/>
-	<property name="jaba-source-jar" value="${distdir}/jaba-source.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="${distdir}/full-jaba-client-pack.zip"/>
-	<property name="jaba-no-jaxws" value="${distdir}/jaba-no-jaxws.war"/>
-	<property name="jaba-no-jaxws-windows" value="${distdir}/jaba-no-jaxws-windows.war"/>
-	<property name="jaba" value="${distdir}/jaba.war"/>
+	<property name="jaba" value="${distdir}/jabaws.war"/>
+	<!-- TODO  
 	<property name="jaba-dundee" value="${distdir}/jaba-dundee.war"/>
-	<property name="jaba-no-jaxws-no-binaries" value="${distdir}/jaba-no-jaxws-no-binaries.war"/>
+	 -->
 	<property name="jaba-no-binaries" value="${distdir}/jaba-no-binaries.war"/>
-	<property name="jaba-windows" value="${distdir}/jaba-windows.war"/>
 	<property name="binaries" value="${distdir}/binaries.zip"/>
-	<property name="win-binaries" value="${distdir}/win-binaries.zip"/>
 	<property name="jaba-devel-web" value="${distdir}/jaba-devel-website.zip"/>
-	<property name="jaxws-lib" value="${distdir}/jaxws-lib.zip"/>
+
 	<!--Whole project archive -->
 	<property name="jaba-project" value="${distdir}/jaba-project.zip"/>
 
-
 	<!-- java -->
 	<property name="test.src" location="${basedir}/testsrc" />
 	<property name="classes" location="${basedir}/WEB-INF/classes" />
@@ -48,7 +59,6 @@
 		</fileset>
 	</path>
 
-
 	<!-- add test classes -->
 	<path id="test.classpath">
 		<fileset dir="${test.lib.path}">
@@ -57,7 +67,47 @@
 		<pathelement location="${classes}" />
 	</path>
 
-	<!-- The compilation order is 
+	<fileset dir="${basedir}/WEB-INF/classes/" id="fullclient">
+		<!-- Datamodel -->
+		<include name="compbio/data/**"/>
+		<include name="compbio/metadata/**"/>
+		<!-- Engines -->
+		<include name="compbio/engine/**"/>
+		<!-- Runners -->
+		<include name="compbio/runner/**"/>
+		<!-- Logging configuration -->
+	</fileset>
+
+	<!-- Clean temp directories -->
+	<target name="clean">
+		<delete dir="${classes}" />
+		<delete file="${distdir}/binaries.zip" />
+		<delete file="${basedir}/activity.log" />
+		<delete file="${basedir}/derby.log" />
+		<mkdir dir="${classes}" />
+		<copy file="${basedir}/conf/log4j.properties" tofile="${classes}/log4j.properties" />
+	</target>
+
+	<!-- Clean up temp directories and dist directory (all jar, zip, and war files deleted) -->
+	<target name="full-clean" depends="clean">
+		<delete>
+			<fileset dir="${distdir}">
+				<include name="*.jar"/>
+				<include name="*.zip"/>
+				<include name="*.war"/>
+			</fileset>
+		</delete>
+	</target>
+
+	<target name="clearStatDB" description="Remove all records from statistics database">
+		<echo>Cleaning Statistics database</echo>
+		<java classname="compbio.stat.collector.StatDB" fork="false" failonerror="true" classpath="${classes}">
+		<classpath refid="project.classpath" />
+		</java>
+	</target>
+
+	<!--
+	The compilation order is 
 	1. datamodel 
 	2. engine
 	3. runner
@@ -65,7 +115,7 @@
 	5. webservices
 	Packages of the lower order could not have dependencies on the packages on the next layer. 
 	So runners (layer 3) depends on the engines and the datamodel but engines does not depend on 
-	anything in runners or any other layers above. Testscr is not allowed to test webservices. 
+	anything in runners or any other layers above. Testsrc is not allowed to test webservices. 
 	-->
 	<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-->
@@ -103,22 +153,16 @@
 		</javac>
 	</target>
 
-	<!-- Clean temp directories -->
-	<target name="clean">
-		<delete dir="${classes}" />
-		<mkdir dir="${classes}" />
-	</target>
-
 	<!--
-	Compile with optimisation. Do not compile testsrc 
+	Compile with optimisation. Do not compile testsrc
 	The compilation order is 
 	1. datamodel 
 	2. engine
 	3. runner
 	4. webservices
 	Packages of the lower order could not have dependencies on the packages on the next layer. 
-	So runners (layer 3) depends on the engines and the datamodel but engines does not depend on 
-	anything in runners or any other layers above.  
+	So runners (layer 3) depends on the engines and the datamodel but engines does not depend 
+	on anything in runners or any other layers above.
 	-->
 	<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-->
@@ -144,34 +188,54 @@
 			<compilerarg value="-Xlint:-unchecked" />
 			<classpath refid="project.classpath" />
 		</javac>
-
 	</target>
 
-
-	<target name="datamodel-jar" description="Pack data model classes" depends="compile">
+	<target name="datamodel-jar" depends="compile" description="Pack data model classes">
 		<echo>Jar file: Minimal WS client jar</echo>
 		<delete file="${basedir}/${datamodel}">
 		</delete>
 		<jar jarfile="${basedir}/${datamodel}">
 			<zipgroupfileset excludes="META-INF/*.SF" dir="${web.lib.path}" >
-				<include name="compbio-util-1.4.jar"/>
+				<include name="${compbio-util}"/>
+				<include name="${compbio-annotation}"/>
 			</zipgroupfileset>
 			<fileset dir="${basedir}/WEB-INF/classes/">
 				<include name="compbio/data/sequence/*.class"/>
 				<include name="compbio/metadata/*.class"/>
 			</fileset>
 			<manifest>
-				<attribute name="Built-By" value="Peter Troshin" />
+				<attribute name="Built-By" value="${author}" />
 				<attribute name="Class-Path" value="." />
-				<attribute name="Implementation-Title" value="Datamodel for Java Bioinformatics Analyses Web Services " />
-				<attribute name="Implementation-Vendor" value="Peter Troshin" />
-				<attribute name="Implementation-URL" value="http://www.compbio.dundee.ac.uk" />
+				<attribute name="Implementation-Title" value="Datamodel for ${product} " />
+				<attribute name="Implementation-Vendor" value="${author}" />
+				<attribute name="Implementation-URL" value="${project.url}" />
 			</manifest>
 		</jar>
 	</target>
 
+	<target name="jaba-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="${jaba-client-src}">
+		</delete>
+		<jar jarfile="${jaba-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. -->
+				<include name="compbio/data/msa/**"/>
+				<exclude name="compbio/ws/client/ServicesUtil**"/>
+				<exclude name="compbio/ws/client/AAConClient**"/>
+				<include name="compbio/ws/client/**"/>
+			</fileset>
+			<manifest>
+				<attribute name="Built-By" value="${author}" />
+				<attribute name="Implementation-Title" value="${product} Client Source Code" />
+				<attribute name="Implementation-Vendor" value="${author}" />
+				<attribute name="Implementation-URL" value="${project.url}" />
+			</manifest>
+		</jar>
+	</target>
 
-	<target name="minimal-jaba-client-jar" description="Pack metadata, data model, WS interfaces, a simple ws client class" depends="compile, datamodel-jar">
+	<target name="minimal-jaba-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>
@@ -182,18 +246,40 @@
 				<include name="compbio/data/msa/**"/>
 				<include name="compbio/ws/client/**"/>
 			</fileset>
+			<zipgroupfileset excludes="META-INF/*" dir="" includes="WEB-INF/lib/log4j-1.2.15.jar" />
 			<manifest>
-				<attribute name="Built-By" value="Peter Troshin" />
+				<attribute name="Built-By" value="${author}" />
 				<attribute name="Main-Class" value="compbio.ws.client.Jws2Client" />
 				<attribute name="Class-Path" value="." />
-				<attribute name="Implementation-Title" value="Minimal Java Bioinformatics Analyses Web Services Client" />
-				<attribute name="Implementation-Vendor" value="Peter Troshin" />
-				<attribute name="Implementation-URL" value="http://www.compbio.dundee.ac.uk" />
+				<attribute name="Implementation-Title" value="Minimal ${product} Client" />
+				<attribute name="Implementation-Vendor" value="${author}" />
+				<attribute name="Implementation-URL" value="${project.url}" />
+			</manifest>
+		</jar>
+	</target>
+
+	<target name="full-jaba-client-jar" depends="compile" description="Pack datamodel, engine and runners">
+		<echo>Jar file: Full WS client jar</echo>
+		<delete file="${full-jaba-client}">
+		</delete>
+		<jar jarfile="${full-jaba-client}">
+			<zipgroupfileset excludes="META-INF/*.SF" dir="${web.lib.path}" >
+				<include name="${compbio-util}"/>
+				<include name="${compbio-annotation}"/>
+				<include name="drmaa.jar"/>
+			</zipgroupfileset>
+			<fileset refid="fullclient"/>
+			<manifest>
+				<attribute name="Built-By" value="${author}" />
+				<attribute name="Class-Path" value="." />
+				<attribute name="Implementation-Title" value="Full ${product} Client" />
+				<attribute name="Implementation-Vendor" value="${author}" />
+				<attribute name="Implementation-URL" value="${project.url}" />
 			</manifest>
 		</jar>
 	</target>
 
-	<target name="aacon-ws-client-jar" description="Pack metadata, data model, WS interfaces, a simple ws client class" depends="compile, datamodel-jar">
+	<target name="aacon-ws-client-jar" depends="compile, datamodel-jar" description="Pack metadata, data model, WS interfaces, a simple ws client class">
 		<echo>Jar file: AAConWS client jar</echo>
 		<delete file="${basedir}/${aacon-ws-client}">
 		</delete>
@@ -205,23 +291,33 @@
 				<include name="compbio/ws/client/**"/>
 			</fileset>
 			<manifest>
-				<attribute name="Built-By" value="Peter Troshin" />
+				<attribute name="Built-By" value="${author}" />
 				<attribute name="Main-Class" value="compbio.ws.client.AAConClient" />
 				<attribute name="Class-Path" value="." />
 				<attribute name="Implementation-Title" value="AACon Client" />
-				<attribute name="Implementation-Vendor" value="Peter Troshin" />
+				<attribute name="Implementation-Vendor" value="${author}" />
 				<attribute name="Implementation-URL" value="http://www.compbio.dundee.ac.uk/aacon" />
 			</manifest>
 		</jar>
 	</target>
 
-	<target name="source-jar" description="Pack java sources" depends="compile">
+	<target name="full-jaba-client" depends="full-jaba-client-jar, pack-binaries" description="Pack binaries with sources and configuration files">
+		<echo>Packing binaries, and configuration files</echo>
+		<zip destfile="${full-jaba-client-pack}" >
+			<zipgroupfileset file="${binaries}" />
+			<zipfileset dir="conf" prefix="conf" >
+				<exclude name="**/temp/**"/>
+			</zipfileset>
+			<fileset file="${full-jaba-client}" />
+		</zip>
+	</target>
+
+
+	<target name="source-jar" depends="datamodel-source-jar" description="Pack java sources">
 		<delete file="${basedir}/${jaba-source-jar}">
 		</delete>
 		<jar jarfile="${basedir}/${jaba-source-jar}">
-			<fileset dir="${basedir}/datamodel">
-				<include name="**"/>
-			</fileset>
+			<zipgroupfileset  excludes="META-INF/*.MF" file="${datamodel-src}"/>
 			<fileset dir="${basedir}/runner">
 				<include name="**"/>
 			</fileset>
@@ -232,110 +328,65 @@
 				<include name="**"/>
 			</fileset>
 			<manifest>
-				<attribute name="Built-By" value="Peter Troshin" />
+				<attribute name="Built-By" value="${author}" />
 				<attribute name="Class-Path" value="." />
-				<attribute name="Implementation-Title" value="Java Bioinformatics Analyses Web Services Source Code Archive" />
-				<attribute name="Implementation-Vendor" value="Peter Troshin" />
-				<attribute name="Implementation-URL" value="http://www.compbio.dundee.ac.uk" />
+				<attribute name="Implementation-Title" value="${product} Source Code Archive" />
+				<attribute name="Implementation-Vendor" value="${author}" />
+				<attribute name="Implementation-URL" value="${project.url}" />
 			</manifest>
 		</jar>
-
 	</target>
-	
-	<target name="datamodel-source-jar" description="Pack java sources" depends="compile">
-			<delete file="${datamodel-src}">
-			</delete>
-			<jar jarfile="${datamodel-src}">
-				<fileset dir="${basedir}/datamodel">
-					<include name="**"/>
-				</fileset>
-				<manifest>
-					<attribute name="Built-By" value="Peter Troshin" />
-					<attribute name="Implementation-Title" value="Java Bioinformatics Analyses Web Services Datamodel Source Code Archive" />
-					<attribute name="Implementation-Vendor" value="Peter Troshin" />
-					<attribute name="Implementation-URL" value="http://www.compbio.dundee.ac.uk/jabaws" />
-				</manifest>
-			</jar>
-		</target>
-
-	<fileset dir="${basedir}/WEB-INF/classes/" id="fullclient">
-		<!-- Datamodel -->
-		<include name="compbio/data/**"/>
-		<include name="compbio/metadata/**"/>
-		<!-- Engines -->
-		<include name="compbio/engine/**"/>
-		<!-- Runners -->
-		<include name="compbio/runner/**"/>
-	</fileset>
 
-	<target name="full-jaba-client-jar" description="Pack datamodel, engine and runners" depends="compile">
-		<echo>Jar file: Full WS client jar</echo>
-		<delete file="${full-jaba-client}">
+	<target name="datamodel-source-jar" depends="compile" description="Pack java sources">
+		<delete file="${datamodel-src}">
 		</delete>
-		<jar jarfile="${full-jaba-client}">
-			<zipgroupfileset excludes="META-INF/*.SF" dir="${web.lib.path}" >
-				<include name="log4j-1.2.15.jar"/>
-				<include name="compbio-util-1.3.jar"/>
-				<include name="compbio-annotations-1.0.jar"/>
-				<include name="drmaa.jar"/>
+		<jar jarfile="${datamodel-src}">
+			<fileset dir="${basedir}/datamodel">
+				<include name="**"/>
+			</fileset>
+			<zipgroupfileset excludes="META-INF/*.MF" dir="${lib.path}/src">
+				<include name="**"/>
 			</zipgroupfileset>
-			<fileset refid="fullclient"/>
 			<manifest>
-				<attribute name="Built-By" value="Peter Troshin" />
-				<attribute name="Class-Path" value="." />
-				<attribute name="Implementation-Title" value="Full Java Bioinformatics Analyses Web Services Client" />
-				<attribute name="Implementation-Vendor" value="Peter Troshin" />
-				<attribute name="Implementation-URL" value="http://www.compbio.dundee.ac.uk" />
+				<attribute name="Built-By" value="${author}" />
+				<attribute name="Implementation-Title" value="${product} Datamodel Source Code Archive" />
+				<attribute name="Implementation-Vendor" value="${author}" />
+				<attribute name="Implementation-URL" value="${project.url}" />
 			</manifest>
 		</jar>
 	</target>
 
-	<target name="full-jaba-client" description="Pack binaries with sources and configuration files" 
-			depends="full-jaba-client-jar, pack-binaries">
-		<echo>Packing binaries, and configuration files</echo>
-		<zip destfile="${full-jaba-client-pack}" >
-			<zipgroupfileset file="${binaries}" />
-			<zipfileset dir="${basedir}/conf" prefix="conf"/>
-			<fileset dir="." includes="${full-jaba-client}" />
-		</zip>
-	</target>
-
-
-	<target name="full-jaba-jar" description="Pack datamodel, engine, runners, configuration, binaries and webservices" depends="compile">
+	<target name="full-jaba-jar" depends="compile" description="Pack datamodel, engine, runners, configuration, binaries and webservices">
 		<echo>Jar file: Full WS client jar</echo>
 		<delete file="${full-jaba-client}">
 		</delete>
 		<jar jarfile="${full-jaba-client}">
 			<zipgroupfileset excludes="META-INF/*.SF" dir="${web.lib.path}" >
 				<include name="log4j-1.2.15.jar"/>
-				<include name="compbio-util-1.3.jar"/>
-				<include name="compbio-annotations-1.0.jar"/>
+				<include name="${compbio-util}"/>
+				<include name="${compbio-annotation}"/>
 				<include name="drmaa.jar"/>
 			</zipgroupfileset>
 			<fileset refid="fullclient">
 			</fileset>
 			<fileset dir="${basedir}/WEB-INF/classes/">
+				<!-- Statistics web application -->
+				<include name="compbio/stat/**"/>
 				<!-- Web services-->
 				<include name="compbio/ws/**"/>
 			</fileset>
 			<!-- Set WSTester as main to help user to test their deployments -->
 			<manifest>
-				<attribute name="Built-By" value="Peter Troshin" />
+				<attribute name="Built-By" value="${author}" />
 				<attribute name="Class-Path" value="." />
 				<attribute name="Main-Class" value="compbio.ws.client.WSTester" />
-				<attribute name="Implementation-Title" value="Java Bioinformatics Analyses Web Services" />
-				<attribute name="Implementation-Vendor" value="Peter Troshin" />
-				<attribute name="Implementation-URL" value="http://www.compbio.dundee.ac.uk" />
+				<attribute name="Implementation-Title" value="${product}" />
+				<attribute name="Implementation-Vendor" value="${author}" />
+				<attribute name="Implementation-URL" value="${project.url}" />
 			</manifest>
 		</jar>
 	</target>
 
-	<target name="clearStatDB" description="Remove all records from statistics database">
-		 <java classname="compbio.stat.collector.StatDB" fork="true" failonerror="true" classpath="${classes}">
-	            <classpath refid="project.classpath" />
-	     </java>
-	</target>
-	
 	<target name="pack-binaries" description="Zip all binary files">
 		<delete file="${binaries}" failonerror="false"/>
 		<zip destfile="${binaries}" >
@@ -343,49 +394,35 @@
 		</zip>
 	</target>
 
-	<target name="pack-jaxws" description="Zip all JAXWS libraries">
-		<delete file="${jaxws-lib}" failonerror="false"/>
-		<zip destfile="${jaxws-lib}" update="false" >
-			<zipfileset dir="${web.lib.path}" includes="webservices-tools.jar"  prefix="WEB-INF/lib"  />
-			<zipfileset dir="${web.lib.path}" includes="webservices-rt.jar"   prefix="WEB-INF/lib" />
-			<zipfileset dir="${web.lib.path}" includes="webservices-api.jar"  prefix="WEB-INF/lib" />
-		</zip>
-	</target>
-
-	<target name="pack-windows-binaries" description="Zip only windows binary files">
-		<delete file="${win-binaries}" failonerror="false" />
-		<zip destfile="${win-binaries}">
-			<zipfileset dir="${basedir}/binaries" prefix="binaries" >
-				<include name="clustalw2.exe"/>
-				<include name="muscle.exe"/>
-				<include name="matrices/*" />
-			</zipfileset>
-		</zip>
-	</target>
-
-	<target name="jaba-no-jaxws-no-binaries" description="Prepare JWS2 war file without runtime dependency - JAXWS jars and native binaries" depends="full-jaba-jar">
-		<echo>Preparing war file without JAXWS and binaries</echo>
-		<delete file="${jaba}">
+	<target name="jaba-no-binaries" depends="full-jaba-jar, clearStatDB" description="Prepare JABAWS war file without native binaries">
+		<echo>Preparing a war file without binaries</echo>
+		<delete file="${jaba-no-binaries}">
 		</delete>
-		<delete file="${jaba-no-jaxws-no-binaries}">
-		</delete>
-		<zip destfile="${jaba-no-jaxws-no-binaries}" whenempty="create">
+		<zip destfile="${jaba-no-binaries}" whenempty="create">
 			<zipfileset dir="${basedir}/WEB-INF" prefix="WEB-INF">
+				<exclude name="classes"/>
+				<!-- These are included into JABA client so exclude the jars -->
+				<exclude name="lib/drmaa.jar"/>
+				<exclude name="lib/log4j-1.2.15.jar"/>
+				<exclude name="lib/${compbio-annotation}"/>
+				<exclude name="lib/${compbio-util}"/>
+				
 				<include name="web.xml"/>
 				<include name="sun-jaxws.xml"/>
-				<exclude name="classes"/>
-				<exclude name="lib"/>
+				<include name="lib/*"/>
 			</zipfileset>
 			<zipfileset dir="${basedir}/ExecutionStatistic" prefix="ExecutionStatistic" />
+			<zipfileset dir="${basedir}/statpages" prefix="statpages" />
 			<zipfileset dir="${basedir}/jobsout" prefix="jobsout" excludes="**/*"/>
-			<zipfileset dir="${basedir}/conf" prefix="conf" excludes="**/log4j.properties*"/>
-			<!-- Add JSW2 web site apart from the binary archive -->
-			<zipfileset dir="${basedir}/website" excludes="archive/**, full_javadoc/**, devel*.html, tests/**, template.html"/>
+			<zipfileset dir="conf" prefix="conf" >
+				<exclude name="**/temp/**"/>
+				<exclude name="**/log4j.properties*"/>
+			</zipfileset>
+			<!-- Add JABAWS web site apart from the binary archive -->
+			<zipfileset dir="${basedir}/website" excludes="archive/**, devel*.html, tests/**, template.html"/>
 			<zipfileset dir="." includes="${full-jaba-client}" fullpath="WEB-INF/lib/jaba-client.jar"/>
 			<!-- Put a copy of log4j configuration file where it can be used  -->
 			<zipfileset dir="conf" includes="log4j.properties" prefix="WEB-INF/classes"/>
-			<!-- This is runtime dependency must be supplied by the container -->
-			<!-- zipfileset dir="${web.lib.path}" includes="servlet-api.jar" prefix="WEB-INF/lib" / -->
 		</zip>
 	</target>
 
@@ -394,74 +431,22 @@
 		<delete file="${jaba-devel-web}">
 		</delete>
 		<zip destfile="${jaba-devel-web}" whenempty="create">
-			<!-- Add JSW2 web site apart from the binary archive -->
+			<!-- 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-without-jaxws" description="Prepare JWS2 war file without runtime dependency - JAXWS jars" depends="jaba-no-jaxws-no-binaries, pack-binaries">
-		<echo>Preparing war file without JAXWS</echo>
-		<delete file="${jaba-no-jaxws}">
-		</delete>
-		<copy tofile="${jaba-no-jaxws}" file="${jaba-no-jaxws-no-binaries}"/>
-		<zip destfile="${jaba-no-jaxws}" update="true" >
-			<zipgroupfileset file="${binaries}" />
-		</zip>
-	</target>
-
-	<target name="jaba-without-jaxws-windows" description="Prepare JWS2 war file without runtime dependency - JAXWS jars" 
-		depends="full-jaba-jar, pack-windows-binaries">
-		<echo>Preparing war file without JAXWS</echo>
-		<delete file="${jaba-windows}">
-		</delete>
-		<delete dir="${basedir}/jobsout/*"/>
-		<delete file="${jaba-no-jaxws-windows}">
-		</delete>
-		<zip destfile="${jaba-no-jaxws-windows}" >
-			<zipfileset dir="${basedir}/WEB-INF" prefix="WEB-INF">
-				<include name="web.xml"/>
-				<include name="sun-jaxws.xml"/>
-				<exclude name="classes"/>
-				<exclude name="lib"/>
-			</zipfileset>
-			<zipgroupfileset file="${win-binaries}" />
-			<zipfileset dir="${basedir}/jobsout" prefix="jobsout" excludes="**/*"/>
-			<zipfileset dir="${basedir}/conf" prefix="conf" excludes="**/log4j.properties*"/>
-			<zipfileset dir="." includes="${full-jaba-client}" fullpath="WEB-INF/lib/jaba-client.jar"/>
-			<zipfileset dir="conf" includes="log4j.properties" prefix="WEB-INF/classes"/>
-			<!-- Add JSW2 web site apart from the binary archive -->
-			<zipfileset dir="${basedir}/website" excludes="archive/**, full_javadoc/**, devel*.html, tests/**, template.html"/>
-		</zip>
-	</target>
-
-
-
-	<target name="jaba-complete" description="Prepare JWS2 war file" depends="jaba-without-jaxws, pack-jaxws">
+	<target name="jaba-complete" depends="jaba-no-binaries, pack-binaries" description="Prepare JABAWS war file without runtime dependency - JAXWS jars">
 		<echo>Preparing a complete war file</echo>
-		<copy tofile="${jaba}" file="${jaba-no-jaxws}"/>
+		<delete file="${jaba}">
+		</delete>
+		<copy tofile="${jaba}" file="${jaba-no-binaries}"/>
 		<zip destfile="${jaba}" update="true" >
-			<zipgroupfileset file="${jaxws-lib}"/>
-		</zip>
-	</target>
-
-	<target name="jaba-no-binaries" description="Prepare JWS2 war file without native binaries" depends="jaba-no-jaxws-no-binaries, pack-jaxws">
-		<echo>Preparing a complete war file</echo>
-		<copy tofile="${jaba-no-binaries}" file="${jaba-no-jaxws-no-binaries}"/>
-		<zip destfile="${jaba-no-binaries}" update="true" >
-			<zipgroupfileset file="${jaxws-lib}"/>
-		</zip>
-	</target>
-
-	<target name="jaba-complete-windows" description="Prepare JWS2 war file for windows" depends="jaba-without-jaxws-windows, pack-jaxws">
-		<echo>Preparing a complete war file</echo>
-		<copy tofile="${jaba-windows}" file="${jaba-no-jaxws-windows}"/>
-		<zip destfile="${jaba-windows}" update="true" >
-			<zipgroupfileset file="${jaxws-lib}"/>
+			<zipgroupfileset file="${binaries}" />
 		</zip>
 	</target>
 
-	<target name="build-all" description="Build-all the distributives"
-		depends="full-jaba-client, minimal-jaba-client-jar, jaba-no-jaxws-no-binaries, jaba-no-binaries, jaba-complete, jaba-complete-windows"/>
+	<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"/>
 
 	<!-- 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">
@@ -474,24 +459,7 @@
 		</zip>
 	</target>
 
-	<!-- This is JUNIT test 
-	<target name="testEngine" depends="compileTest">
-			<delete file="${activity.log}"/> 
-			<junit filtertrace="false" haltonfailure="true" haltonerror="true" fork="true" forkmode="once">
-		        <jvmarg value="-server" />
-		        <jvmarg value="-enableassertions" />
-		        <jvmarg value="-Xms512m" />
-		        <jvmarg value="-Xmx512m" />
-				<env key="LD_LIBRARY_PATH" value="/gridware/sge/lib/lx24-amd64"/>
-		        <classpath refid="test.classpath" />
-		    	<classpath refid="project.classpath" />
-		        <formatter type="plain" usefile="false" />
-		        <test name="compbio.engine.cluster.AllTestSuit" />
-		        <sysproperty key="TestingDataPath" value="${data.src}"/>
-		    </junit>
-		</target>
-	-->
-
+<!-- Test targets -->
 	<taskdef name="testNG" classname="org.testng.TestNGAntTask">
 		<classpath refid="test.classpath">
 		</classpath>
@@ -529,7 +497,7 @@
 
 	<target name="Test" depends="compile_with_debug">
 		<delete file="${activity.log}"/>
-		<testNG haltonfailure="true" enableassert="true" verbose="3" excludedgroups="performance" >
+		<testNG haltonfailure="true" enableassert="true" verbose="3" excludedgroups="performance, webservices" >
 			<jvmarg value="-server" />
 			<jvmarg value="-enableassertions" />
 			<jvmarg value="-Xms1024m" />
@@ -629,61 +597,4 @@
 			<sysproperty key="TestingDataPath" value="${data.src}"/>
 		</testNG>
 	</target>
-
-	<!-- <zipfileset excludes="META-INF/*.SF" src="jarfilename.jar"/> 
-		
-		<target name="build-jar" description="Pack cluster  and runners into a jar" depends="compile">
-			<echo>Jar file: integration</echo>
-			<delete file="${basedir}/.jar"></delete>
-			<copy file="${basedir}/conf/" tofile="${classes}/log4j.properties" />
-			<jar jarfile="${basedir}/.jar">
-				<fileset dir="${basedir}/WEB-INF/classes/" includes="compbio/**" />
-				<manifest>
-					<attribute name="Built-By" value="Peter Troshin" />
-					<attribute name="Main-Class" value="compbio.clust..JobStatus" />
-					<attribute name="Class-Path" value=" . /gridware/sge/lib/drmaa.jar" />
-					<attribute name="Implementation-Title" value="Cluster Submission Engine" />
-					<attribute name="Implementation-Vendor" value="Peter Troshin" />
-					<attribute name="Implementation-URL" value="xxx" />
-				</manifest>
-			</jar>
-		</target>
-		
-		
-		<target name="build-jar-local" description="Pack cluster  and runners with dependencies" depends="compile">
-			<echo>Jar file: integration</echo>
-			<delete file="${basedir}/.jar"></delete>
-			<jar jarfile="${basedir}/.jar">
-				<zipgroupfileset excludes="META-INF/*.SF" dir="${lib.path}"></zipgroupfileset>
-				<fileset dir="${basedir}/WEB-INF/classes/" includes="**" />
-				<manifest>
-					<attribute name="Built-By" value="Peter Troshin" />
-					<attribute name="Main-Class" value="compbio..cluster.JobStatus" />
-					<attribute name="Class-Path" value="." />
-					<attribute name="Implementation-Title" value="Cluster Submission Engine" />
-					<attribute name="Implementation-Vendor" value="Peter Troshin" />
-					<attribute name="Implementation-URL" value="xxx" />
-				</manifest>
-			</jar>
-		</target>
-		
-		-->
-
-	<!--
-		<target name="run-client-jar" description="EXAMPLE TASK ONLY">
-			<java jar="${basedir}/resources/wsclient.jar" fork="true"
-				failonerror="true" maxmemory="256m">
-				<arg
-					value="C:/Documents and Settings/pvt43/Desktop/Leeds Sequencing/Copy of Files to up load" />
-			</java>
-		</target>
-		<target name="run-client-class" description="EXAMPLE TASK ONLY">
-			<java classname="org.pimslims.ws.client.FileUploadClient" fork="true"
-				failonerror="true" maxmemory="256m">
-				<classpath refid="project.classpath" />
-				<classpath refid="instrument.classpath" />
-			</java>
-		</target>
-	-->
-
-</project>
\ No newline at end of file
+</project>